Speciation has long been regarded as an irreversible process once the reproductive barriers had been established.However,unlike in natural populations,artificial selection might either accelerate or prevent speciation...Speciation has long been regarded as an irreversible process once the reproductive barriers had been established.However,unlike in natural populations,artificial selection might either accelerate or prevent speciation processes in domesticated species.Asian cultivated rice is a target crop for both domestication and artificial breeding;it contains two subspecies of indica and japonica,which usually produce sterile inter-subspecific hybrids due to reproductive barriers.In this study,we constructed the evolutionary trajectory of a reproductive isolation system S5,which regulates fertility in indica-japonica hybrids via three adjacent genes,based on the data of 606 accessions including two cultivated and 11 wild rice species.Although hybrid sterility haplotypes at S5 lead to establishment of a killer-protector reproductive barrier,origin of wide-compatibility haplotypes by complex hybridization and recombination provides an opposing force to reproductive isolation and thus prevents speciation during domestication.Analysis in a diallel set of 209 crosses involving 21 parents showed that the wide-compatibility genotypes largely rescued fertility of indica-japonica hybrids,indicating that the wide-compatibility gene would enable gene flow to maintain species coherence.This counteracting system indicates that combined effects of natural evolution and artificial selection may result in reversible processes of speciation in rice,which may also have implications for genetic improvement of rice.展开更多
Flowering links vegetative growth and reproductive growth and involves the coordination of local environmental cues and plant genetic information.Appropriate timing of floral initiation and maturation in both wild and...Flowering links vegetative growth and reproductive growth and involves the coordination of local environmental cues and plant genetic information.Appropriate timing of floral initiation and maturation in both wild and cultivated plants is important to their fitness and productivity in a given growth environment.The domestication of plants into crops,and later crop expansion and improvement,has often involved selection for early flowering.In this review,we analyze the basic rules for photoperiodic adaptation in several economically important and/or well-researched crop species.The ancestors of rice(Oryza sativa),maize(Zea mays),soybean(Glycine max),and tomato(Solanum lycopersicum)are short-day plants whose photosensitivity was reduced or lost during domestication and expansion to high-latitude areas.Wheat(Triticum aestivum)and barley(Hordeum vulgare)are long-day crops whose photosensitivity is influenced by both latitude and vernalization type.Here,we summarize recent studies about where these crops were domesticated,how they adapted to photoperiodic conditions as their growing area expanded from domestication locations to modern cultivating regions,and how allelic variants of photoperiodic flowering genes were selected during this process.A deeper understanding of photoperiodic flowering in each crop will enable better molecular design and breeding of high-yielding cultivars suited to particular local environments.展开更多
The preference-performance relationship in plant-insect interactions is a cen- tral theme in evolutionary ecology. Among many insects, eggs are vulnerable and larvae have limited mobility, making the choice of an appr...The preference-performance relationship in plant-insect interactions is a cen- tral theme in evolutionary ecology. Among many insects, eggs are vulnerable and larvae have limited mobility, making the choice of an appropriate oviposition site one of the most important decisions for a female. We investigated the evolution of oviposition preferences in Drosophila melanogaster Meigen and Drosophila simulans Sturtevant by artificially selecting for the preference for 2 natural resources, grape and quince. The main finding of our study is the differential responses of D. melanogaster and D. simulans. Although preferences evolved in the experimental populations of D. melanogaster, responses were not consistent with the selection regimes applied. In contrast, responses in D. simulans were consistent with expectations, demonstrating that this species has selectable genetic variation for the trait. Furthermore, crosses between D. simulans divergent lines showed that the genetic factors involved in grape preference appear to be largely recessive. In summary, our artificial selection study suggests that D. melanogaster and D. simulans possess different genetic architectures for this trait.展开更多
Pacific oyster(Crassostrea gigas)is one of the most important mollusks cultured all around the world.Selective breeding programs of Pacific oysters in China is initiated since 2006 and developed the genetically improv...Pacific oyster(Crassostrea gigas)is one of the most important mollusks cultured all around the world.Selective breeding programs of Pacific oysters in China is initiated since 2006 and developed the genetically improved strain with fast-growing trait.However,little is known about the metabolic signatures of the fast-growing trait.In the present study,the non-targeted metabolomics was performed to analyze the metabolic signatures of adductor muscle tissue in one-year old Pacific oysters from fast-growing strain and the wild population.A total of 7767 and 10174 valid peaks were extracted and quantified in ESI^(+)and ESI^(−)modes,resulting in 399 and 381 annotated metabolites,respectively.PCA and OPLS-DA revealed that considerable separation among samples from fastgrowing strain and wild population,suggesting the differences in metabolic signatures.Meanwhile,81 significantly different metabolites(SDMs)were identified in the comparisons between fast-growing strain and wild population,based on the strict thresholds.It was found that there were highly correlation and conserved coordination among these SDMs.KEGG enrichment analysis indicated that the SDMs were tightly related to pantothenate and CoA biosynthesis,steroid hormone biosynthesis,riboflavin metabolism,and arginine and proline metabolism.Of them,the CoA biosynthesis and metabolism,affected by pantetheine and pantothenic acid,might be important for the growth of Pacific oysters under artificial selective breeding.The study provides the comprehensive views of metabolic signatures in response to artificially selective breeding,and is helpful to better understand the molecular mechanism of fastgrowing traits in Pacific oysters.展开更多
Background:As one of the most utilized commercial composite boar lines,Duroc pigs have been introduced to China and undergone strongly human-induced selection over the past decades.However,the efficiencies and limitat...Background:As one of the most utilized commercial composite boar lines,Duroc pigs have been introduced to China and undergone strongly human-induced selection over the past decades.However,the efficiencies and limitations of previous breeding of Chinese Duroc pigs are largely understudied.The objective of this study was to uncover directional polygenic selection in the Duroc pig genome,and investigate points overlooked in the past breeding process.Results:Here,we utilized the Generation Proxy Selection Mapping(GPSM)on a dataset of 1067 Duroc pigs with 8,766,074 imputed SNPs.GPSM detected a total of 5649 putative SNPs actively under selection in the Chinese Duroc pig population,and the potential functions of the selection regions were mainly related to production,meat and carcass traits.Meanwhile,we observed that the allele frequency of variants related to teat number(NT)relevant traits was also changed,which might be influenced by genes that had pleiotropic effects.First,we identified the direction of selection on NT traits by G,and further pinpointed large-effect genomic regions associated with NT relevant traits by selection signature and GWAS.Combining results of NT relevant traits-specific selection signatures and GWAS,we found three common genome regions,which were overlapped with QTLs related to production,meat and carcass traits besides“teat number”QTLs.This implied that there were some pleiotropic variants underlying NT and economic traits.We further found that rs346331089 has pleiotropic effects on NT and economic traits,e.g.,litter size at weaning(LSW),litter weight at weaning(LWW),days to 100 kg(D100),backfat thickness at 100 kg(B100),and loin muscle area at 100 kg(L100)traits.Conclusions:The selected loci that we identified across methods displayed the past breeding process of Chinese Duroc pigs,and our findings could be used to inform future breeding decision.展开更多
Accordion-shaped traps are widely used in China to catch the Asian paddle crab C harybdis japonica but traps of conventional design often catch juvenile crabs. A new type of accordion-shaped trap with an escape vent(L...Accordion-shaped traps are widely used in China to catch the Asian paddle crab C harybdis japonica but traps of conventional design often catch juvenile crabs. A new type of accordion-shaped trap with an escape vent(L×W=4.3 cm×3.0 cm) was designed and a comparative study between the newly designed and conventional traps was performed in the artifi cial reef area of Zhuwang, Laizhou Bay, China from June to August 2012. The mean catch per unit effort(CPUE) of undersized crabs was signifi cantly lower in the vented traps than in the conventional traps(paired t-test, n =30, P <0.001), while the CPUE of marketable crabs was signifi cantly higher in the vented traps(paired t-test, n =30, P <0.001). The mean size of crabs(carapace length) caught in the vented traps was signifi cantly larger than in conventional traps(paired t-test, n =29, P <0.001). The ratio of undersized crabs was 35.05%±2.57% in conventional traps and 12.53%±0.69% in vented traps(signifi cantly lower, paired t-test, n =29, P <0.001). Therefore, a 4.3 cm×3.0 cm escape vent was considered appropriate for C. japonica fi shing in the artifi cial reef area. This fi nding will assist the development of more sustainable and effi cient crab fi shing methods using accordion-shaped traps.展开更多
Intermuscular bones(IBs)are slender linear bones embedded in muscle,which ossify from tendons through a process of intramembranous ossification,and only exist in basal teleosts.IBs are essential for fish swimming,but ...Intermuscular bones(IBs)are slender linear bones embedded in muscle,which ossify from tendons through a process of intramembranous ossification,and only exist in basal teleosts.IBs are essential for fish swimming,but they present a choking risk during human consumption,especially in children,which can lead to commercial risks that have a negative impact on the aquaculture of these fish.In this review,we discuss the morphogenesis and functions of IBs,including their underlying molecular mechanisms,as well as the advantages and disadvantages of different methods for IB studies and techniques for breeding and generating IB-free fish lines.This review reveals that the many key genes involved in tendon development,osteoblast differentiation,and bone formation,e.g.,scxa,msxC,sost,twist,bmps,and osterix,also play roles in IB development.Thus,this paper provides useful information for the breeding of new fish strains without IBs via genome editing and artificial selection.展开更多
The morphology of the plant and ear is a preliminary selection characteristic in breeding new varieties of maize.As new maize cultivars were developed from the 1950s through the 2010s in China,most had changes in both...The morphology of the plant and ear is a preliminary selection characteristic in breeding new varieties of maize.As new maize cultivars were developed from the 1950s through the 2010s in China,most had changes in both plant and ear morphological characteristics that contributed substantially to maize yield gains.Over the seven decades,plant and ear height fluctuated with a small increase from the 1950s to 2000s,and then a decrease in the 2010s,while the ear ratio and internodes length below the ear decreased significantly.Leaf angles became significantly more upright,especially for the leaves above the ear,and the leaf area per plant improved markedly.Leaf orientation increased from the 1950s to the 2000s then decreased in the 2010s.Tassel size and the anthesis-silking interval were both reduced substantially.Ear diameter,kernel number,and kernel weight increased from the 1950 to the 2000s,then decreased in the 2010s under the same cultivation conditions.We found that modern maize hybrids have a lower plant height,ear height and ear ratio which increased lodging resistance,a more erect leaf which increased high-density planting tolerance,and smaller ears and kernels which facilitated rapid dehydration during late grain filling.These morphological selection criteria,which are suitable for mechanized operations,are proposed as the focus for future maize breeding.展开更多
The insect brain is the central part of the neurosecretory system,which controls morphology,physiology,and behavior during the insect’s lifecycle.Lepidoptera are holometabolous insects,and their brains develop during...The insect brain is the central part of the neurosecretory system,which controls morphology,physiology,and behavior during the insect’s lifecycle.Lepidoptera are holometabolous insects,and their brains develop during the larval period and metamorphosis into the adult form.As the only fully domesticated insect,the Lepidoptera silkworm Bombyx mori experienced changes in larval brain morphology and certain behaviors during the domestication process.Hormonal regulation in insects is a key factor in multiple processes.However,how juvenile hormone(JH)signals regulate brain development in Lepidoptera species,especially in the larval stage,remains elusive.We recently identified the JH receptor Methoprene tolerant 1(Met1)as a putative domestication gene.How artificial selection on Met1 impacts brain and behavioral domestication is another important issue addressing Darwin’s theory on domestication.Here,CRISPR/Cas9-mediated knockout of Bombyx Met1 caused developmental retardation in the brain,unlike precocious pupation of the cuticle.At the whole transcriptomelevel,theecdysteroid(20-hydroxyecdysone,20 E)signaling and downstream pathways were overactivated in the mutant cuticle but not in the brain.Pathways related to cell proliferation and specialization processes,such as extracellular matrix(ECM)-receptor interaction and tyrosine metabolism pathways,were suppressed in the brain.Molecular evolutionary analysis and in vitro assay identified an amino acid replacement located in a novel motif under positive selection in B.mori,which decreased transcriptional binding activity.The B.mori MET1 protein showed a changed structure and dynamic features,as well as a weakened co-expression gene network,compared with B.mandarina.Based on comparative transcriptomic analyses,we proposed a pathway downstream of JH signaling(i.e.,tyrosine metabolism pathway)that likely contributed to silkworm larval brain development and domestication and highlighted the importance of the biogenic amine system in larval evolution during silkworm domestication.展开更多
Common carp are among the oldest domesticated fish in the world.As such,there are many food and ornamental carp strains with abundant phenotypic variations due to natural and artificial selection.Hebao red carp(HB,Cyp...Common carp are among the oldest domesticated fish in the world.As such,there are many food and ornamental carp strains with abundant phenotypic variations due to natural and artificial selection.Hebao red carp(HB,Cyprinus carpio wuyuanensis),an indigenous strain in China,is renowned for its unique body morphology and reddish skin.To reveal the genetic basis underlying the distinct skin color of HB,we constructed an improved highfidelity(HiFi) HB genome with good contiguity,completeness,and correctness.Genome structure comparison was conducted between HB and a representative wild strain,Yellow River carp(YR,C.carpio haematopterus),to identify structural variants and genes under positive selection.Signatures of artificial selection during domestication were identified in HB and YR populations,while phenotype mapping was performed in a segregating population generated by HB×YR crosses.Body color in HB was associated with regions with fixed mutations.The simultaneous mutation and superposition of a pair of homologous genes(mitfa) in chromosomes A06 and B06 conferred the reddish color in domesticated HB.Transcriptome analysis of common carp with different alleles of the mitfa mutation confirmed that gene duplication can buffer the deleterious effects of mutation in allotetraploids.This study provides new insights into genotype-phenotype associations in allotetraploid species and lays a foundation for future breeding of common carp.展开更多
Animal behavior is remarkably variable at all taxonomic levels. Over the last decades, research on animal behavior has focused on understanding ultimate processes. Yet, it has progressively become more evident that to...Animal behavior is remarkably variable at all taxonomic levels. Over the last decades, research on animal behavior has focused on understanding ultimate processes. Yet, it has progressively become more evident that to fully understand beha- vioral variation, ultimate explanations need to be complemented with proximate ones. In particular, the mechanisms generating variation in sexual behavior remain an open question. Variation in aspects of brain morphology has been suggested as a plausible mechanism underlying this variation. However, our knowledge of this potential association is based almost exclusively on com- parative analyses. Experimental studies are needed to establish causality and bridge the gap between micro- and macroevolutio- nary mechanisms concerning the link between brain and sexual behavior. We used male guppies that had been artificially selected for large or small relative brain size to study this association. We paired males with females and scored the full known set of male and female sexual behaviors described in guppies. We found several previously demonstrated associations between male traits, male behavior and female behavior. Females responded more strongly towards males that courted more and males with more orange coloration. Also, larger males and males with less conspicuous coloration attempted more coerced copulations. However, courting, frequency of coerced copulation attempts, total intensity of sexual behavior, and female response did not differ between large- and small-brained males. Our data suggest that relative brain size is an unlikely mechanism underlying variation in sexual behavior of the male guppy. We discuss these findings in the context of the conditions under which relative brain size might affect male sexual behavior .展开更多
Producing sperm is costly and males have been selected to strategically adjust their sperm produc- tion and/or expenditure according to the fitness return associated with a specific mating. For exam- ple, males respon...Producing sperm is costly and males have been selected to strategically adjust their sperm produc- tion and/or expenditure according to the fitness return associated with a specific mating. For exam- ple, males respond to fluctuations in the mating opportunities by adjusting the number of ＂ready＂ sperm. This phenomenon is known as ＂sperm priming＂ and is interpreted as a strategy to econo- mize the investment in sperm. The cost and benefits of the sperm priming response, however, are expected to depend on a male＇s baseline sperm production （BSP） in the absence of females, because of the different risk of sperm depletion and the nonlinearly increasing costs of sperm pro- duction. We tested this prediction in 2 replicated lines of male guppies Poecilia reticulata that were artificially selected for high and low BSP. BSP has a large genetic variance and a high sire heritabil- ity in guppies, and males respond to the perceived mating opportunities by increasing the number of ＂ready＂ sperm. We investigated whether males with a different BSP differed in their sperm pri- ming response. We found that when the perceived mating opportunities increased, males from low-sperm lines had a stronger sperm priming response than those from high-sperm lines. This result suggests that adaptive plasticity in sperm priming has the potential to evolve in response to different levels of BSP. The comparison between guppy populations with different levels of sperm production would allow to test whether the pattern reported here is also observed at the interpopulation level.展开更多
Screening for agronomic traits associated with grain moisture is important for mechanical grainharvesting of maize. Cob color as a visual indicator has received limited attention, though it has been subjected to artif...Screening for agronomic traits associated with grain moisture is important for mechanical grainharvesting of maize. Cob color as a visual indicator has received limited attention, though it has been subjected to artificial selection, and may have some association with threshability. To investigate the relationships between cob color and grain moisture and other agronomic traits, field experiments were conducted during 2016–2017 using 23 commercial hybrids with red or white cobs. Kernels of red-cob hybrids dehydrated faster, showing lower moisture content at harvest than white-cob hybrids. A cob color index(CCI) was established as a quantitative measure of cob color in the hybrid panel. Ranging from0(whitest) to 17.98(reddest), CCI correlated well with grain dehydration and other agronomic traits associated with growth ontogeny, plant morphology, and plant N content. Strong selection of red cob for recently released hybrids suitable for mechanical grain-harvesting indirectly validated the observed link between cob color and grain dehydration. We propose that cob color and CCI could be used in future selection of maize cultivars bred for mechanical grain-harvesting.展开更多
The Great Spotted Woodpecker Dendrocopos major （L.）, one of the natural predators of Anoplophora glabripennis （Motsch.） （Coleoptera： Cerambycidae）, is resident to Wulate Qianqi County of the Inner Mongolia and ...The Great Spotted Woodpecker Dendrocopos major （L.）, one of the natural predators of Anoplophora glabripennis （Motsch.） （Coleoptera： Cerambycidae）, is resident to Wulate Qianqi County of the Inner Mongolia and widely found in shelter plantations. In August 2005 and 2006, 174 and 153 nest-cavities of Great Spotted Woodpeckers were found respectively in Wulate Qianqi County and 22 breeding nest-cavities were investigated in 2007. The results showed that mostly willow species were selected for nesting by the Great Spotted Woodpecker, but mature poplar trees also could be chosen. Nest cavities were often found with a protuberance above the cavity entrance or with a downward sloping gradient, or both. The selection of the height of the nest-cavity height was not significant. The vertical diameter of the nest-cavity entrance （VDE） and the horizontal diameter of the nest-cavity entrance （HDE） ranged from 5.0 to 5.8 cm. The results also indicated that the compass orientation of more than 60% of nest-cavities were towards the north, northeast and east. This study suggests a convergence of some nest-cavity characteristics of the Great Spotted Woodpecker in shelter plantations and will help us to make artificial nest for conserving the woodpecker and, as well, use the bird for controlling pests.展开更多
In the face of accelerating global climate change,developing crops that can withstand extreme environmental conditions,such as cold temperatures at high latitudes,has become a critical challenge for ensuring global fo...In the face of accelerating global climate change,developing crops that can withstand extreme environmental conditions,such as cold temperatures at high latitudes,has become a critical challenge for ensuring global food security.In addition,as the population increases,it is essential to expand planting areas to northern regions with lower accumulated yearly temperatures.Natural variations of crops are artificially selected to adapt to extreme temperature environments during their domestication.For the temperate crops like maize and rice,striking a tradeoff between growth development and cold tolerance is essential for breeding.展开更多
Photoperiod responsiveness is a key factor limiting the geographic distribution of cultivated soybean and its wild ancestor.In particular,the genetic basis of the adaptation in wild soybean remains poorly understood.I...Photoperiod responsiveness is a key factor limiting the geographic distribution of cultivated soybean and its wild ancestor.In particular,the genetic basis of the adaptation in wild soybean remains poorly understood.In this study,by combining whole-genome resequencing and genome-wide association studies we identified a novel locus,Time of Flowering 5(Tof5),which promotes flowering and enhances adaptation to high latitudes in both wild and cultivated soybean.By genomic,genetic and transgenic analyses we showed that Tof5 en-codes a homolog of Arabidopsis thaliana FRUITFULL(FUL).Importantly,further analyses suggested that different alleles of Tof5 have undergone parallel selection.The Tof5H1 allele was strongly selected by humans after the early domestication of cultivated soybean,while Tof5H2 allele was naturally selected in wild soybean,and in each case facilitating adaptation to high latitudes.Moreover,we found that the key flowering repressor E1 suppresses the transcription of Tof5 by binding to its promoter.In turn,Tof5 physically associates with the promoters of two important FLOWERING LOCUS T(FT),FT2a and FT5a,to upregulate their transcription and promote flowering under long photoperiods.Collectively,ourfindings provide insights into how wild soybean adapted to high latitudes through natural selection and indicate that cultivated soybean underwent changes in the same gene but evolved a distinct allele that was artificially selected after domestication.展开更多
Imidacloprid is a neonicotinoid insecticide used for managing the Asian citrus psyllid,Diaphorina citri Kuwayama,which serves as vector of phytopathogens causing citrus greening.However,development of resistance to ne...Imidacloprid is a neonicotinoid insecticide used for managing the Asian citrus psyllid,Diaphorina citri Kuwayama,which serves as vector of phytopathogens causing citrus greening.However,development of resistance to neonicotinoids among populations of D.citri has coincided with occasional control failures in the field.The objectives of this research were to(1)survey current levels of imidacloprid resistance in Florida citrus;(2)compare feeding behavior between imidacloprid-resistant and susceptible D.citri using electrical penetration graph recordings,and(3)investigate the possible amplification of insecticide hormoligosis associated with resistance.Field surveys confirmed that the susceptibility of D.citri populations to imidacloprid has decreased in commercial Florida citrus groves compared with a laboratory-susceptible population.Following 12 generations of selection,resistance to imidacloprid increased by 438 fold compared with the susceptible strain.Imidacloprid-susceptible D.citri feeding on citrus exhibited significantly more bouts associated with intercellular pathway(C),phloem penetration(D),phloem salivation(E1),and nonprobing(Np)activities than imidacloprid-resistant counterparts.However,there were no differences observed in the frequency or duration of phloem ingestion or xylem feeding between susceptible and resistant D.citri.There was no statistical difference in fecundity between resistant and susceptible strains.However,the fecundity of imidacloprid-susceptible female D.citri treated with a sublethal concentration of imidacloprid(LC_(25))increased significantly compared with controls,while such hormoligosis was less pronounced among imidacloprid-resistant psyllids.Our results suggest that imidacloprid-resistant psyllids may cease feeding sooner than susceptible counterparts following sublethal exposure to this insecticide,indicative of a behavioral resistance mechanism.展开更多
Domestication is a selection process that genetically modifies species to meet human needs. A most intriguing feature of domestication is the extreme phenotypic diversification among breeds. What could be the ultimate...Domestication is a selection process that genetically modifies species to meet human needs. A most intriguing feature of domestication is the extreme phenotypic diversification among breeds. What could be the ultimate source of such genetic variations？ Another notable outcome of artificial selection is the reduction In the fitness of domesticated species when they live In the wild without human assistance. The complete sequences of the two subspecies of rice cultlvars provide an opportunity to address these questions. Between the two subspecies, we found much higher rates of non-synonymous （N） than synonymous （S） substitutions and the N/S ratios are higher between cultivars than between wild species. Most interestingly, substitutions of highly dissimilar amino acids that are deleterious and uncommon between natural species are disproportionately common between the two subspecies of rice. We suggest strong selection in the absence of effective recombination may be the driving force, which we called the domestication-associated Hill-Robertson effect. These hitchhiking mutations may contribute to some fitness reduction in cultivars. Comparisons of the two genomes also reveal the existence of highly divergent regions in the genomes. Haplotypes in these regions often form highly polymorphic linkage blocks that are much older than speciation between wild species. Genes from such regions could contribute to the differences between indica and japonica and are likely to be involved in the diversifying selection under domestication. Their existence suggests that the amount of genetic variation within the single progenitor species Oryza rufipogon may be insufficient to account for the variation among rice cultivars, which may come from a more inclusive gene pool comprising most of the A-genome wild species. Genes from the highly polymorphic regions also provide strong support for the Independent domestication of the two subspecies. The genomic variation in rice has revealing implications for studying the genetic basis of indica-japonica differentiation under rice domestication and subsequent improvement.展开更多
Body size is the most important economic trait for animal production and breeding.Several hundreds of loci have been reported to be associated with growth trait and body weight in chickens.The loci are mapped to large...Body size is the most important economic trait for animal production and breeding.Several hundreds of loci have been reported to be associated with growth trait and body weight in chickens.The loci are mapped to large genomic regions due to the low density and limited number of genetic markers in previous studies.Herein,we employed comparative population genomics to identify genetic basis underlying the small body size of Yuanbao chicken(a famous ornamental chicken)based on 89 whole genomes.The most significant signal was mapped to the BMP10 gene,whose expression was upregulated in the Yuanbao chicken.Overexpression of BMP10 induced a significant decrease in body length by inhibiting angiogenic vessel development in zebrafish.In addition,three other loci on chromosomes 1,2,and 24 were also identified to be potentially involved in the development of body size.Our results provide a paradigm shift in identification of novel loci controlling body size variation,availing a fast and efficient strategy.These loci,particularly BMP10,add insights into ongoing research of the evolution of body size under artificial selection and have important implications for future chicken breeding.展开更多
Piao chicken,a rare Chinese native poultry breed,lacks primary tail structures,such as pygostyle,caudal vertebra,uropygial gland,and tail feathers.So far,the molecular mechanisms underlying tail absence in this breed ...Piao chicken,a rare Chinese native poultry breed,lacks primary tail structures,such as pygostyle,caudal vertebra,uropygial gland,and tail feathers.So far,the molecular mechanisms underlying tail absence in this breed remain unclear.In this study,we comprehensively employed comparative transcriptomic and genomic analyses to unravel potential genetic underpinnings of rumplessness in Piao chicken.Our results reveal many biological factors involved in tail development and several genomic regions under strong positive selection in this breed.These regions contain candidate genes associated with rumplessness,including Irx4,Il18,Hspb2,and Cryab.Retrieval of quantitative trait loci(QTL)and gene functions implies that rumplessness might be consciously or unconsciously selected along with the high-yield traits in Piao chicken.We hypothesize that strong selection pressures on regulatory elements might lead to changes in gene activity in mesenchymal stem cells of the tail bud.The ectopic activity could eventually result in tail truncation by impeding differentiation and proliferation of the stem cells.Our study provides fundamental insights into early initiation and genetic basis of the rumpless phenotype in Piao chicken.展开更多
基金This research was supported by grants from the National Natural Science Foundation of China(31991223,30800678,and 31821005)the Hubei Provincial Natural Science Foundation of China(2019CFA061)the National Program for Support of Top-notch Young Professionals.
文摘Speciation has long been regarded as an irreversible process once the reproductive barriers had been established.However,unlike in natural populations,artificial selection might either accelerate or prevent speciation processes in domesticated species.Asian cultivated rice is a target crop for both domestication and artificial breeding;it contains two subspecies of indica and japonica,which usually produce sterile inter-subspecific hybrids due to reproductive barriers.In this study,we constructed the evolutionary trajectory of a reproductive isolation system S5,which regulates fertility in indica-japonica hybrids via three adjacent genes,based on the data of 606 accessions including two cultivated and 11 wild rice species.Although hybrid sterility haplotypes at S5 lead to establishment of a killer-protector reproductive barrier,origin of wide-compatibility haplotypes by complex hybridization and recombination provides an opposing force to reproductive isolation and thus prevents speciation during domestication.Analysis in a diallel set of 209 crosses involving 21 parents showed that the wide-compatibility genotypes largely rescued fertility of indica-japonica hybrids,indicating that the wide-compatibility gene would enable gene flow to maintain species coherence.This counteracting system indicates that combined effects of natural evolution and artificial selection may result in reversible processes of speciation in rice,which may also have implications for genetic improvement of rice.
基金by Grants from the National Natural Science Foundation of China to F.K.(32090064)and to X.L.(32001568)supported by the Major Program of Guangdong Basic and Applied Research to F.K.(2019B030302006).
文摘Flowering links vegetative growth and reproductive growth and involves the coordination of local environmental cues and plant genetic information.Appropriate timing of floral initiation and maturation in both wild and cultivated plants is important to their fitness and productivity in a given growth environment.The domestication of plants into crops,and later crop expansion and improvement,has often involved selection for early flowering.In this review,we analyze the basic rules for photoperiodic adaptation in several economically important and/or well-researched crop species.The ancestors of rice(Oryza sativa),maize(Zea mays),soybean(Glycine max),and tomato(Solanum lycopersicum)are short-day plants whose photosensitivity was reduced or lost during domestication and expansion to high-latitude areas.Wheat(Triticum aestivum)and barley(Hordeum vulgare)are long-day crops whose photosensitivity is influenced by both latitude and vernalization type.Here,we summarize recent studies about where these crops were domesticated,how they adapted to photoperiodic conditions as their growing area expanded from domestication locations to modern cultivating regions,and how allelic variants of photoperiodic flowering genes were selected during this process.A deeper understanding of photoperiodic flowering in each crop will enable better molecular design and breeding of high-yielding cultivars suited to particular local environments.
文摘The preference-performance relationship in plant-insect interactions is a cen- tral theme in evolutionary ecology. Among many insects, eggs are vulnerable and larvae have limited mobility, making the choice of an appropriate oviposition site one of the most important decisions for a female. We investigated the evolution of oviposition preferences in Drosophila melanogaster Meigen and Drosophila simulans Sturtevant by artificially selecting for the preference for 2 natural resources, grape and quince. The main finding of our study is the differential responses of D. melanogaster and D. simulans. Although preferences evolved in the experimental populations of D. melanogaster, responses were not consistent with the selection regimes applied. In contrast, responses in D. simulans were consistent with expectations, demonstrating that this species has selectable genetic variation for the trait. Furthermore, crosses between D. simulans divergent lines showed that the genetic factors involved in grape preference appear to be largely recessive. In summary, our artificial selection study suggests that D. melanogaster and D. simulans possess different genetic architectures for this trait.
基金supported by grants from the Earmarked Fund for Agriculture Seed Improvement Project of Shandong Province(Nos.2021ZLGX03 and 2022LZGCQY010)the China Agriculture Research System Project(No.CARS-49).
文摘Pacific oyster(Crassostrea gigas)is one of the most important mollusks cultured all around the world.Selective breeding programs of Pacific oysters in China is initiated since 2006 and developed the genetically improved strain with fast-growing trait.However,little is known about the metabolic signatures of the fast-growing trait.In the present study,the non-targeted metabolomics was performed to analyze the metabolic signatures of adductor muscle tissue in one-year old Pacific oysters from fast-growing strain and the wild population.A total of 7767 and 10174 valid peaks were extracted and quantified in ESI^(+)and ESI^(−)modes,resulting in 399 and 381 annotated metabolites,respectively.PCA and OPLS-DA revealed that considerable separation among samples from fastgrowing strain and wild population,suggesting the differences in metabolic signatures.Meanwhile,81 significantly different metabolites(SDMs)were identified in the comparisons between fast-growing strain and wild population,based on the strict thresholds.It was found that there were highly correlation and conserved coordination among these SDMs.KEGG enrichment analysis indicated that the SDMs were tightly related to pantothenate and CoA biosynthesis,steroid hormone biosynthesis,riboflavin metabolism,and arginine and proline metabolism.Of them,the CoA biosynthesis and metabolism,affected by pantetheine and pantothenic acid,might be important for the growth of Pacific oysters under artificial selective breeding.The study provides the comprehensive views of metabolic signatures in response to artificially selective breeding,and is helpful to better understand the molecular mechanism of fastgrowing traits in Pacific oysters.
基金financially supported by the National Natural Science Foundation of China (32022078)China Agriculture Research System of MOF and MARA
文摘Background:As one of the most utilized commercial composite boar lines,Duroc pigs have been introduced to China and undergone strongly human-induced selection over the past decades.However,the efficiencies and limitations of previous breeding of Chinese Duroc pigs are largely understudied.The objective of this study was to uncover directional polygenic selection in the Duroc pig genome,and investigate points overlooked in the past breeding process.Results:Here,we utilized the Generation Proxy Selection Mapping(GPSM)on a dataset of 1067 Duroc pigs with 8,766,074 imputed SNPs.GPSM detected a total of 5649 putative SNPs actively under selection in the Chinese Duroc pig population,and the potential functions of the selection regions were mainly related to production,meat and carcass traits.Meanwhile,we observed that the allele frequency of variants related to teat number(NT)relevant traits was also changed,which might be influenced by genes that had pleiotropic effects.First,we identified the direction of selection on NT traits by G,and further pinpointed large-effect genomic regions associated with NT relevant traits by selection signature and GWAS.Combining results of NT relevant traits-specific selection signatures and GWAS,we found three common genome regions,which were overlapped with QTLs related to production,meat and carcass traits besides“teat number”QTLs.This implied that there were some pleiotropic variants underlying NT and economic traits.We further found that rs346331089 has pleiotropic effects on NT and economic traits,e.g.,litter size at weaning(LSW),litter weight at weaning(LWW),days to 100 kg(D100),backfat thickness at 100 kg(B100),and loin muscle area at 100 kg(L100)traits.Conclusions:The selected loci that we identified across methods displayed the past breeding process of Chinese Duroc pigs,and our findings could be used to inform future breeding decision.
基金Supported by the Public Science and Technology Research Funds Projects of Ocean(Nos.201305043,201405010)the National Natural Science Foundation of China(No.41006075)
文摘Accordion-shaped traps are widely used in China to catch the Asian paddle crab C harybdis japonica but traps of conventional design often catch juvenile crabs. A new type of accordion-shaped trap with an escape vent(L×W=4.3 cm×3.0 cm) was designed and a comparative study between the newly designed and conventional traps was performed in the artifi cial reef area of Zhuwang, Laizhou Bay, China from June to August 2012. The mean catch per unit effort(CPUE) of undersized crabs was signifi cantly lower in the vented traps than in the conventional traps(paired t-test, n =30, P <0.001), while the CPUE of marketable crabs was signifi cantly higher in the vented traps(paired t-test, n =30, P <0.001). The mean size of crabs(carapace length) caught in the vented traps was signifi cantly larger than in conventional traps(paired t-test, n =29, P <0.001). The ratio of undersized crabs was 35.05%±2.57% in conventional traps and 12.53%±0.69% in vented traps(signifi cantly lower, paired t-test, n =29, P <0.001). Therefore, a 4.3 cm×3.0 cm escape vent was considered appropriate for C. japonica fi shing in the artifi cial reef area. This fi nding will assist the development of more sustainable and effi cient crab fi shing methods using accordion-shaped traps.
基金This work was supported by the National Natural Science Foundation of China(U1702233 and U1902202)Program of the Chinese Academy of Sciences(XDA24030505 and XDA23080502)Program of Yunnan Provincial Science and Technology Department(202003AD150017 and 2018FY001-007)。
文摘Intermuscular bones(IBs)are slender linear bones embedded in muscle,which ossify from tendons through a process of intramembranous ossification,and only exist in basal teleosts.IBs are essential for fish swimming,but they present a choking risk during human consumption,especially in children,which can lead to commercial risks that have a negative impact on the aquaculture of these fish.In this review,we discuss the morphogenesis and functions of IBs,including their underlying molecular mechanisms,as well as the advantages and disadvantages of different methods for IB studies and techniques for breeding and generating IB-free fish lines.This review reveals that the many key genes involved in tendon development,osteoblast differentiation,and bone formation,e.g.,scxa,msxC,sost,twist,bmps,and osterix,also play roles in IB development.Thus,this paper provides useful information for the breeding of new fish strains without IBs via genome editing and artificial selection.
基金the National Key Research and Development Program of China(2017YFD0300302 and 2017YFD0300804)the China Agriculture Research System of MOF and MARA(CARS-02-63)the Natural Science Foundation of Inner Mongolia,China(2020MS03053)。
文摘The morphology of the plant and ear is a preliminary selection characteristic in breeding new varieties of maize.As new maize cultivars were developed from the 1950s through the 2010s in China,most had changes in both plant and ear morphological characteristics that contributed substantially to maize yield gains.Over the seven decades,plant and ear height fluctuated with a small increase from the 1950s to 2000s,and then a decrease in the 2010s,while the ear ratio and internodes length below the ear decreased significantly.Leaf angles became significantly more upright,especially for the leaves above the ear,and the leaf area per plant improved markedly.Leaf orientation increased from the 1950s to the 2000s then decreased in the 2010s.Tassel size and the anthesis-silking interval were both reduced substantially.Ear diameter,kernel number,and kernel weight increased from the 1950 to the 2000s,then decreased in the 2010s under the same cultivation conditions.We found that modern maize hybrids have a lower plant height,ear height and ear ratio which increased lodging resistance,a more erect leaf which increased high-density planting tolerance,and smaller ears and kernels which facilitated rapid dehydration during late grain filling.These morphological selection criteria,which are suitable for mechanized operations,are proposed as the focus for future maize breeding.
基金supported by the National Natural Science Foundation of China(32070411,31720103916,31330071,31672494)Natural Science Foundation of Guangdong Province(2019A1515011012)Strategic Priority Research Program of the Chinese Academy of Sciences(XDB11010600)。
文摘The insect brain is the central part of the neurosecretory system,which controls morphology,physiology,and behavior during the insect’s lifecycle.Lepidoptera are holometabolous insects,and their brains develop during the larval period and metamorphosis into the adult form.As the only fully domesticated insect,the Lepidoptera silkworm Bombyx mori experienced changes in larval brain morphology and certain behaviors during the domestication process.Hormonal regulation in insects is a key factor in multiple processes.However,how juvenile hormone(JH)signals regulate brain development in Lepidoptera species,especially in the larval stage,remains elusive.We recently identified the JH receptor Methoprene tolerant 1(Met1)as a putative domestication gene.How artificial selection on Met1 impacts brain and behavioral domestication is another important issue addressing Darwin’s theory on domestication.Here,CRISPR/Cas9-mediated knockout of Bombyx Met1 caused developmental retardation in the brain,unlike precocious pupation of the cuticle.At the whole transcriptomelevel,theecdysteroid(20-hydroxyecdysone,20 E)signaling and downstream pathways were overactivated in the mutant cuticle but not in the brain.Pathways related to cell proliferation and specialization processes,such as extracellular matrix(ECM)-receptor interaction and tyrosine metabolism pathways,were suppressed in the brain.Molecular evolutionary analysis and in vitro assay identified an amino acid replacement located in a novel motif under positive selection in B.mori,which decreased transcriptional binding activity.The B.mori MET1 protein showed a changed structure and dynamic features,as well as a weakened co-expression gene network,compared with B.mandarina.Based on comparative transcriptomic analyses,we proposed a pathway downstream of JH signaling(i.e.,tyrosine metabolism pathway)that likely contributed to silkworm larval brain development and domestication and highlighted the importance of the biogenic amine system in larval evolution during silkworm domestication.
基金supported by the National Key R&D Program of China (2019YFE0119000)National Natural Science Foundation of China (31872561)+1 种基金National Science Fund for Distinguished Young Scholars (32225049)Alliance of International Science Organizations (ANSO-CR-PP-2021-03)。
文摘Common carp are among the oldest domesticated fish in the world.As such,there are many food and ornamental carp strains with abundant phenotypic variations due to natural and artificial selection.Hebao red carp(HB,Cyprinus carpio wuyuanensis),an indigenous strain in China,is renowned for its unique body morphology and reddish skin.To reveal the genetic basis underlying the distinct skin color of HB,we constructed an improved highfidelity(HiFi) HB genome with good contiguity,completeness,and correctness.Genome structure comparison was conducted between HB and a representative wild strain,Yellow River carp(YR,C.carpio haematopterus),to identify structural variants and genes under positive selection.Signatures of artificial selection during domestication were identified in HB and YR populations,while phenotype mapping was performed in a segregating population generated by HB×YR crosses.Body color in HB was associated with regions with fixed mutations.The simultaneous mutation and superposition of a pair of homologous genes(mitfa) in chromosomes A06 and B06 conferred the reddish color in domesticated HB.Transcriptome analysis of common carp with different alleles of the mitfa mutation confirmed that gene duplication can buffer the deleterious effects of mutation in allotetraploids.This study provides new insights into genotype-phenotype associations in allotetraploid species and lays a foundation for future breeding of common carp.
文摘Animal behavior is remarkably variable at all taxonomic levels. Over the last decades, research on animal behavior has focused on understanding ultimate processes. Yet, it has progressively become more evident that to fully understand beha- vioral variation, ultimate explanations need to be complemented with proximate ones. In particular, the mechanisms generating variation in sexual behavior remain an open question. Variation in aspects of brain morphology has been suggested as a plausible mechanism underlying this variation. However, our knowledge of this potential association is based almost exclusively on com- parative analyses. Experimental studies are needed to establish causality and bridge the gap between micro- and macroevolutio- nary mechanisms concerning the link between brain and sexual behavior. We used male guppies that had been artificially selected for large or small relative brain size to study this association. We paired males with females and scored the full known set of male and female sexual behaviors described in guppies. We found several previously demonstrated associations between male traits, male behavior and female behavior. Females responded more strongly towards males that courted more and males with more orange coloration. Also, larger males and males with less conspicuous coloration attempted more coerced copulations. However, courting, frequency of coerced copulation attempts, total intensity of sexual behavior, and female response did not differ between large- and small-brained males. Our data suggest that relative brain size is an unlikely mechanism underlying variation in sexual behavior of the male guppy. We discuss these findings in the context of the conditions under which relative brain size might affect male sexual behavior .
文摘Producing sperm is costly and males have been selected to strategically adjust their sperm produc- tion and/or expenditure according to the fitness return associated with a specific mating. For exam- ple, males respond to fluctuations in the mating opportunities by adjusting the number of ＂ready＂ sperm. This phenomenon is known as ＂sperm priming＂ and is interpreted as a strategy to econo- mize the investment in sperm. The cost and benefits of the sperm priming response, however, are expected to depend on a male＇s baseline sperm production （BSP） in the absence of females, because of the different risk of sperm depletion and the nonlinearly increasing costs of sperm pro- duction. We tested this prediction in 2 replicated lines of male guppies Poecilia reticulata that were artificially selected for high and low BSP. BSP has a large genetic variance and a high sire heritabil- ity in guppies, and males respond to the perceived mating opportunities by increasing the number of ＂ready＂ sperm. We investigated whether males with a different BSP differed in their sperm pri- ming response. We found that when the perceived mating opportunities increased, males from low-sperm lines had a stronger sperm priming response than those from high-sperm lines. This result suggests that adaptive plasticity in sperm priming has the potential to evolve in response to different levels of BSP. The comparison between guppy populations with different levels of sperm production would allow to test whether the pattern reported here is also observed at the interpopulation level.
基金supported by the National Key Research and Development Program of China(2016YFD0300301)the China Agriculture Research System of MOF and MARA+1 种基金the Education Department Funds(190233)the Natural Science Funds of Jiangxi Province(20202BABL215004)。
文摘Screening for agronomic traits associated with grain moisture is important for mechanical grainharvesting of maize. Cob color as a visual indicator has received limited attention, though it has been subjected to artificial selection, and may have some association with threshability. To investigate the relationships between cob color and grain moisture and other agronomic traits, field experiments were conducted during 2016–2017 using 23 commercial hybrids with red or white cobs. Kernels of red-cob hybrids dehydrated faster, showing lower moisture content at harvest than white-cob hybrids. A cob color index(CCI) was established as a quantitative measure of cob color in the hybrid panel. Ranging from0(whitest) to 17.98(reddest), CCI correlated well with grain dehydration and other agronomic traits associated with growth ontogeny, plant morphology, and plant N content. Strong selection of red cob for recently released hybrids suitable for mechanical grain-harvesting indirectly validated the observed link between cob color and grain dehydration. We propose that cob color and CCI could be used in future selection of maize cultivars bred for mechanical grain-harvesting.
文摘The Great Spotted Woodpecker Dendrocopos major （L.）, one of the natural predators of Anoplophora glabripennis （Motsch.） （Coleoptera： Cerambycidae）, is resident to Wulate Qianqi County of the Inner Mongolia and widely found in shelter plantations. In August 2005 and 2006, 174 and 153 nest-cavities of Great Spotted Woodpeckers were found respectively in Wulate Qianqi County and 22 breeding nest-cavities were investigated in 2007. The results showed that mostly willow species were selected for nesting by the Great Spotted Woodpecker, but mature poplar trees also could be chosen. Nest cavities were often found with a protuberance above the cavity entrance or with a downward sloping gradient, or both. The selection of the height of the nest-cavity height was not significant. The vertical diameter of the nest-cavity entrance （VDE） and the horizontal diameter of the nest-cavity entrance （HDE） ranged from 5.0 to 5.8 cm. The results also indicated that the compass orientation of more than 60% of nest-cavities were towards the north, northeast and east. This study suggests a convergence of some nest-cavity characteristics of the Great Spotted Woodpecker in shelter plantations and will help us to make artificial nest for conserving the woodpecker and, as well, use the bird for controlling pests.
基金the Young Scientists Fund of the National Natural Science Foundation of China(Grant No.32200244)the National Key Research and Development Program of China(Grant No.2020YFA0509901-1)for financial support。
文摘In the face of accelerating global climate change,developing crops that can withstand extreme environmental conditions,such as cold temperatures at high latitudes,has become a critical challenge for ensuring global food security.In addition,as the population increases,it is essential to expand planting areas to northern regions with lower accumulated yearly temperatures.Natural variations of crops are artificially selected to adapt to extreme temperature environments during their domestication.For the temperate crops like maize and rice,striking a tradeoff between growth development and cold tolerance is essential for breeding.
基金supported by the National Natural Science Foundation of China(grant nos.32090065 and 32001508 to L.D.,32090064 and 31725021 to F.K.,31930083 to B.L,31901568 to Q.C,32022062 to S.Lu.,32001502 to Y,Z)and also supported by the Major Program of Guangdong Basic and Applied FResearch(grant no.2019B030302006 to F.K.andB.L).
文摘Photoperiod responsiveness is a key factor limiting the geographic distribution of cultivated soybean and its wild ancestor.In particular,the genetic basis of the adaptation in wild soybean remains poorly understood.In this study,by combining whole-genome resequencing and genome-wide association studies we identified a novel locus,Time of Flowering 5(Tof5),which promotes flowering and enhances adaptation to high latitudes in both wild and cultivated soybean.By genomic,genetic and transgenic analyses we showed that Tof5 en-codes a homolog of Arabidopsis thaliana FRUITFULL(FUL).Importantly,further analyses suggested that different alleles of Tof5 have undergone parallel selection.The Tof5H1 allele was strongly selected by humans after the early domestication of cultivated soybean,while Tof5H2 allele was naturally selected in wild soybean,and in each case facilitating adaptation to high latitudes.Moreover,we found that the key flowering repressor E1 suppresses the transcription of Tof5 by binding to its promoter.In turn,Tof5 physically associates with the promoters of two important FLOWERING LOCUS T(FT),FT2a and FT5a,to upregulate their transcription and promote flowering under long photoperiods.Collectively,ourfindings provide insights into how wild soybean adapted to high latitudes through natural selection and indicate that cultivated soybean underwent changes in the same gene but evolved a distinct allele that was artificially selected after domestication.
基金supported by a grant from the Citrus Research and Development Foundation and USDA APHIS MAC funding to LLS。
文摘Imidacloprid is a neonicotinoid insecticide used for managing the Asian citrus psyllid,Diaphorina citri Kuwayama,which serves as vector of phytopathogens causing citrus greening.However,development of resistance to neonicotinoids among populations of D.citri has coincided with occasional control failures in the field.The objectives of this research were to(1)survey current levels of imidacloprid resistance in Florida citrus;(2)compare feeding behavior between imidacloprid-resistant and susceptible D.citri using electrical penetration graph recordings,and(3)investigate the possible amplification of insecticide hormoligosis associated with resistance.Field surveys confirmed that the susceptibility of D.citri populations to imidacloprid has decreased in commercial Florida citrus groves compared with a laboratory-susceptible population.Following 12 generations of selection,resistance to imidacloprid increased by 438 fold compared with the susceptible strain.Imidacloprid-susceptible D.citri feeding on citrus exhibited significantly more bouts associated with intercellular pathway(C),phloem penetration(D),phloem salivation(E1),and nonprobing(Np)activities than imidacloprid-resistant counterparts.However,there were no differences observed in the frequency or duration of phloem ingestion or xylem feeding between susceptible and resistant D.citri.There was no statistical difference in fecundity between resistant and susceptible strains.However,the fecundity of imidacloprid-susceptible female D.citri treated with a sublethal concentration of imidacloprid(LC_(25))increased significantly compared with controls,while such hormoligosis was less pronounced among imidacloprid-resistant psyllids.Our results suggest that imidacloprid-resistant psyllids may cease feeding sooner than susceptible counterparts following sublethal exposure to this insecticide,indicative of a behavioral resistance mechanism.
基金Supported by the National Natural Science Foundation of China （30500049, 30470119 and 30300033）. Tian Tang is supported by International Foundation for Science （IFS）. Publication of this paper is supported by the National Natural Science Foundation of China （30624808）.Acknowledgements We thank Chung-1 Wu at the University of Chicago for many thoughtful comments.
文摘Domestication is a selection process that genetically modifies species to meet human needs. A most intriguing feature of domestication is the extreme phenotypic diversification among breeds. What could be the ultimate source of such genetic variations？ Another notable outcome of artificial selection is the reduction In the fitness of domesticated species when they live In the wild without human assistance. The complete sequences of the two subspecies of rice cultlvars provide an opportunity to address these questions. Between the two subspecies, we found much higher rates of non-synonymous （N） than synonymous （S） substitutions and the N/S ratios are higher between cultivars than between wild species. Most interestingly, substitutions of highly dissimilar amino acids that are deleterious and uncommon between natural species are disproportionately common between the two subspecies of rice. We suggest strong selection in the absence of effective recombination may be the driving force, which we called the domestication-associated Hill-Robertson effect. These hitchhiking mutations may contribute to some fitness reduction in cultivars. Comparisons of the two genomes also reveal the existence of highly divergent regions in the genomes. Haplotypes in these regions often form highly polymorphic linkage blocks that are much older than speciation between wild species. Genes from such regions could contribute to the differences between indica and japonica and are likely to be involved in the diversifying selection under domestication. Their existence suggests that the amount of genetic variation within the single progenitor species Oryza rufipogon may be insufficient to account for the variation among rice cultivars, which may come from a more inclusive gene pool comprising most of the A-genome wild species. Genes from the highly polymorphic regions also provide strong support for the Independent domestication of the two subspecies. The genomic variation in rice has revealing implications for studying the genetic basis of indica-japonica differentiation under rice domestication and subsequent improvement.
基金supported by grants from the National Natural Science Foundation of China(91331104)the 973 Program(2013CB835200,2013CB835204)Bureau of Science and Technology of Yunnan Province(2015FA026)。
文摘Body size is the most important economic trait for animal production and breeding.Several hundreds of loci have been reported to be associated with growth trait and body weight in chickens.The loci are mapped to large genomic regions due to the low density and limited number of genetic markers in previous studies.Herein,we employed comparative population genomics to identify genetic basis underlying the small body size of Yuanbao chicken(a famous ornamental chicken)based on 89 whole genomes.The most significant signal was mapped to the BMP10 gene,whose expression was upregulated in the Yuanbao chicken.Overexpression of BMP10 induced a significant decrease in body length by inhibiting angiogenic vessel development in zebrafish.In addition,three other loci on chromosomes 1,2,and 24 were also identified to be potentially involved in the development of body size.Our results provide a paradigm shift in identification of novel loci controlling body size variation,availing a fast and efficient strategy.These loci,particularly BMP10,add insights into ongoing research of the evolution of body size under artificial selection and have important implications for future chicken breeding.
基金supported by the National Natural Science Foundation of China(Grant Nos.31771415 and 31801054)the Bureau of Science and Technology of Yunnan Province,China(Grant No.2015FA026)+1 种基金the Youth Innovation Promotion Association,Chinese Academy of Sciencesthe support of the CAS-TWAS President’s Fellowship Program for Doctoral Candidates。
文摘Piao chicken,a rare Chinese native poultry breed,lacks primary tail structures,such as pygostyle,caudal vertebra,uropygial gland,and tail feathers.So far,the molecular mechanisms underlying tail absence in this breed remain unclear.In this study,we comprehensively employed comparative transcriptomic and genomic analyses to unravel potential genetic underpinnings of rumplessness in Piao chicken.Our results reveal many biological factors involved in tail development and several genomic regions under strong positive selection in this breed.These regions contain candidate genes associated with rumplessness,including Irx4,Il18,Hspb2,and Cryab.Retrieval of quantitative trait loci(QTL)and gene functions implies that rumplessness might be consciously or unconsciously selected along with the high-yield traits in Piao chicken.We hypothesize that strong selection pressures on regulatory elements might lead to changes in gene activity in mesenchymal stem cells of the tail bud.The ectopic activity could eventually result in tail truncation by impeding differentiation and proliferation of the stem cells.Our study provides fundamental insights into early initiation and genetic basis of the rumpless phenotype in Piao chicken.
