High-quality genome information is essential for efficiently deciphering and improving crop traits.Here,we report a highly contiguous and accurate hexaploid genome assembly for the key wheat breeding parent Zhou8425B,...High-quality genome information is essential for efficiently deciphering and improving crop traits.Here,we report a highly contiguous and accurate hexaploid genome assembly for the key wheat breeding parent Zhou8425B,an elite 1BL/1RS translocation line with durable adult plant resistance(APR)against yellow rust(YR)disease.By integrating HiFi and Hi-C sequencing reads,we have generated a 14.75-Gb genome assembly for Zhou8425B with a contig N50 of 70.94 and a scaffold N50 of 735.11 Mb.Comparisons with previously sequenced common wheat cultivars shed light on structural changes in the 1RS chromosome arm,which has been extensively used in wheat improvement.Interestingly,Zhou8425B 1RS carries more genes encoding AP2/ERF-ERF or B3 transcription factors than its counterparts in four previously sequenced wheat and rye genotypes.The Zhou8425B genome assembly aided in the fine mapping of a new APR locus(YrZH3BS)that confers resistance to YR disease and promotes grain yield under field conditions.Notably,pyramiding YrZH3BS with two previously characterized APR loci(YrZH22 and YrZH84)can further reduce YR severity and enhance grain yield,with the triple combination(YrZH3B+YrZH22+YrZH84)having the greatest effect.Finally,the founder genotype effects of Zhou8425B were explored using publicly available genome resequencing data,which reveals the presence of important Zhou8425B genomic blocks in its derivative cultivars.Our data demonstrate the value of the Zhou8425B genome assembly for further study of the structural and functional characteristics of 1RS,the genetic basis of durable YR resistance,and founder genotype effects in wheat breeding.Our resources will facilitate the development of elite wheat cultivars through genomics-assisted breeding.展开更多
On the bases of archaeological discoveries, the earliest domestication of rice has been confirmed in the middle and lower Changjiang River basin, while in the region wild rice populations are found in shallow swamps u...On the bases of archaeological discoveries, the earliest domestication of rice has been confirmed in the middle and lower Changjiang River basin, while in the region wild rice populations are found in shallow swamps under a climate with freezing winter cold. These findings lead us to-examine the past ideas about domestication and differentiation of rice. Historically, in 1930s two sub-species, indica and japonica, were proposed on the basis of sterility in F1 hybrids between them. Soon after that, the two types were classified by the associations of a number of genetically independent traits. The characteristic associations of traits have been explained by the hybrid sterility or reproductive barriers which were assumed to comprise a set of duplicate recessive lethal genes and to be an inner genetic mechanism to lead to the varietal differentiations In 1980s, the hybrid sterility between Indica and Japonica types was analyzed, and Indica, Japonica, and wide-compatibility type which gives fertile hybrids when cross to Indica and Japonica types, are proved to contain an allele, S5＇, S5＇ and S5^n, respectively at a locus on chromosome 6. And those gametes having Sj allele are found to be partially aborted in the hybrid genotypes of S5＇/S5＇ while no gamete abortion occurs in S5＇/S5^n and S5＇/S5^n genotypes. Since then, the gene S5^n has been used in hybrid rice breeding to obtain fertile and vigorous hybrids between subspecies, and the long-disputed problem of hybrid sterility has been solved. Also in such studies the characteristic association of traits found in each of vadetal groups is better explained by founder effects. On the other hand, a large number of native cultivars of rice were surveyed with enzyme polymorphism in 1980s and later with molecular markers. As a result, profound genetic diversity is found in cultivated rice as well as in wild rice. These findings seem to lead us to the idea of multiple independent domestications of rice. However, before reaching such a conclusion, at least two factors, i.e., long-distance-dissemination of some genotypes and the possibilities of introgression by local wild rice to primitive cultivars need to be examined. Taking the two factors as well as the historical events into consideration, it is considered here that the perennial japonica cultivars which are close to wild rice in the Changjiang River basin were disseminated to East India through Assam or along the Bengal Bay, where they were transformed under the introgressions of local wild rice and formed a secondary center, from which some genotypes seem to be disseminated to colonies in Southeast Asia under the influence of Hinduism. Later some of the genotypes were introduced into China and constituted so called Indica type. This may be a reasonable picture for the varietal differentiation.展开更多
Considering the severe impacts of genetic bottlenecks and small numbers of founders in populations of reintroduced animals, it is necessary to study inbreeding and its effect on fitness in species of conservation conc...Considering the severe impacts of genetic bottlenecks and small numbers of founders in populations of reintroduced animals, it is necessary to study inbreeding and its effect on fitness in species of conservation concern. Pere David＇s deer is one of few large mammal species extinct in the wild but safely preserved in captivity. Its specific background gives us the opportunity to study the relationships between heterozygosity and neonatal fitness in relocated populations. We employed five microsatellite loci to explore heterozygosity-fitness correlations in a population of Pere David＇s deer at the Beijing Milu Ecological Research Center. We observed associations between microsatellite-based variables sMLH, IR, MD^2 and HL, and two components of fitness ex- pressed early in life （birth weight and the neonatal mortality of 123 Pere David＇s deer calves born over six consecutive years）. We found that neonatal mortality was 19.1% - 7.6%, not higher than the 19% or 18% reported in other ungulates. The heterozygosity of calves was not associated with neonatal mortality, nor birth weight. Our study implies that low genetic variability of microsa- l：ellite loci has no overt effect on birth weight and neonatal mortality in reintroduced populations of P^re David＇s deer [Current Zoology 59 （2）： 249-256, 2013].展开更多
Recent empirical and theoretical studies suggest that personality and locomotory performance traits linked to dispersal abilities are crucial components of the dispersal syndromes,and that they can evolve during range...Recent empirical and theoretical studies suggest that personality and locomotory performance traits linked to dispersal abilities are crucial components of the dispersal syndromes,and that they can evolve during range expansions and colonization processes.Island colonization is one of the best characterized processes in dispersal biogeography,and its implication in the evolution of phenotypic traits has been investigated over a wide range of temporal scales.However,the effect of island colonization on personality and performance traits of natural populations,and how these traits could drive island colonization,has been little explored.Noteworthy,no studies have addressed these processes in the context of late Pleistocene range expansions.Here,we investigated the contribution of island colonization triggered by postglacial range expansions to intraspecific variation in personality and locomotory performance traits.We compared boldness,exploration,jumping performance,and stickiness abilities in populations from 3 equidistant areas of the Tyrrhenian tree frog Hyla sarda,2 from the main island(Corsica Island),and 1 from the recently colonized island of Elba.Individuals from Elba were significantly bolder than individuals from Corsica,as they emerged sooner from a shelter(P=0.028),while individuals from Corsica showed markedly higher jumping and stickiness performance(both P<0.001),resulting as more performing than those of Elba.We discuss these results in the context of the major microevolutionary processes at play during range expansion,including selection,spatial sorting,founder effects,and their possible interaction with local adaptation processes.展开更多
Genetic changes over space and time provide insights into the relative roles of evolutionary factors in shaping genetic patterns within plant populations. However, compared with spatial genetic structure, few studies ...Genetic changes over space and time provide insights into the relative roles of evolutionary factors in shaping genetic patterns within plant populations. However, compared with spatial genetic structure, few studies have been conducted on genetic changes over time. In this study, we used six polymorphic microsatellite loci to assess genetic variation of six size-classes of the population of Liushan, Cryptomeriajaponica var. sinensis, in the Tianmushan National Nature Reserve, whose origin was debatable. The mean number of alleles per locus and expected heterozygosity were 4.583 and 0.5999 respectively, lower than other conifers with the same life history characteristics. FST was 0.0024-0.003, and the pairwise test revealed no significant differentiation in any pair of size classes. Significant heterozygosity excesses were detected in five size classes except the oldest one, indicating bottleneck event（s）. The above results support the hypothesis that Tianmushan population was introduced and followed by natural regeneration.展开更多
Background:Familial hypomagnesemia with hypercalciuria and nephrocalcinosis(FHHNC)is an autosomal recessive tubular disease caused by mutations in the CLDN16 or CLDN19 gene.Previous studies using microsatellite marker...Background:Familial hypomagnesemia with hypercalciuria and nephrocalcinosis(FHHNC)is an autosomal recessive tubular disease caused by mutations in the CLDN16 or CLDN19 gene.Previous studies using microsatellite markers flanking the CLDN19 locus estimated that p.G20D(c.59G>A),a recurrent mutation in Spanish families,is a founder mutation.In the present study,we assessed the haplotype of Spanish patients using single nucleotide polymorphisms(SNPs).Methods:Twenty-seven FHHNC patients were included in this study.We analyzed four SNPs located in CLDN19 introns 3 and 4 by polymerase chain reaction amplification and DNA sequencing.Results:Three new patients with homozygous p.G20D were identified.The SNP genotyping analysis showed that alleles carrying this mutation shared a common SNP haplotype.Conclusions:Our findings suggest the existence of a founder effect responsible for FHHNC in our cohort.Testing for the presence of mutation p.G20D should be the first genetic screening in Spanish patients.展开更多
基金supported by the Ministry of Science and Technology(China)of China(2021YFF1000200)the National Science Foundation of China(32372132)+1 种基金the Natural Science Foundation of Henan Province(232300421033)the Science and Technology Funds of Zhengzhou City,and China Postdoctoral Funds(GZC20230727)。
文摘High-quality genome information is essential for efficiently deciphering and improving crop traits.Here,we report a highly contiguous and accurate hexaploid genome assembly for the key wheat breeding parent Zhou8425B,an elite 1BL/1RS translocation line with durable adult plant resistance(APR)against yellow rust(YR)disease.By integrating HiFi and Hi-C sequencing reads,we have generated a 14.75-Gb genome assembly for Zhou8425B with a contig N50 of 70.94 and a scaffold N50 of 735.11 Mb.Comparisons with previously sequenced common wheat cultivars shed light on structural changes in the 1RS chromosome arm,which has been extensively used in wheat improvement.Interestingly,Zhou8425B 1RS carries more genes encoding AP2/ERF-ERF or B3 transcription factors than its counterparts in four previously sequenced wheat and rye genotypes.The Zhou8425B genome assembly aided in the fine mapping of a new APR locus(YrZH3BS)that confers resistance to YR disease and promotes grain yield under field conditions.Notably,pyramiding YrZH3BS with two previously characterized APR loci(YrZH22 and YrZH84)can further reduce YR severity and enhance grain yield,with the triple combination(YrZH3B+YrZH22+YrZH84)having the greatest effect.Finally,the founder genotype effects of Zhou8425B were explored using publicly available genome resequencing data,which reveals the presence of important Zhou8425B genomic blocks in its derivative cultivars.Our data demonstrate the value of the Zhou8425B genome assembly for further study of the structural and functional characteristics of 1RS,the genetic basis of durable YR resistance,and founder genotype effects in wheat breeding.Our resources will facilitate the development of elite wheat cultivars through genomics-assisted breeding.
文摘On the bases of archaeological discoveries, the earliest domestication of rice has been confirmed in the middle and lower Changjiang River basin, while in the region wild rice populations are found in shallow swamps under a climate with freezing winter cold. These findings lead us to-examine the past ideas about domestication and differentiation of rice. Historically, in 1930s two sub-species, indica and japonica, were proposed on the basis of sterility in F1 hybrids between them. Soon after that, the two types were classified by the associations of a number of genetically independent traits. The characteristic associations of traits have been explained by the hybrid sterility or reproductive barriers which were assumed to comprise a set of duplicate recessive lethal genes and to be an inner genetic mechanism to lead to the varietal differentiations In 1980s, the hybrid sterility between Indica and Japonica types was analyzed, and Indica, Japonica, and wide-compatibility type which gives fertile hybrids when cross to Indica and Japonica types, are proved to contain an allele, S5＇, S5＇ and S5^n, respectively at a locus on chromosome 6. And those gametes having Sj allele are found to be partially aborted in the hybrid genotypes of S5＇/S5＇ while no gamete abortion occurs in S5＇/S5^n and S5＇/S5^n genotypes. Since then, the gene S5^n has been used in hybrid rice breeding to obtain fertile and vigorous hybrids between subspecies, and the long-disputed problem of hybrid sterility has been solved. Also in such studies the characteristic association of traits found in each of vadetal groups is better explained by founder effects. On the other hand, a large number of native cultivars of rice were surveyed with enzyme polymorphism in 1980s and later with molecular markers. As a result, profound genetic diversity is found in cultivated rice as well as in wild rice. These findings seem to lead us to the idea of multiple independent domestications of rice. However, before reaching such a conclusion, at least two factors, i.e., long-distance-dissemination of some genotypes and the possibilities of introgression by local wild rice to primitive cultivars need to be examined. Taking the two factors as well as the historical events into consideration, it is considered here that the perennial japonica cultivars which are close to wild rice in the Changjiang River basin were disseminated to East India through Assam or along the Bengal Bay, where they were transformed under the introgressions of local wild rice and formed a secondary center, from which some genotypes seem to be disseminated to colonies in Southeast Asia under the influence of Hinduism. Later some of the genotypes were introduced into China and constituted so called Indica type. This may be a reasonable picture for the varietal differentiation.
文摘Considering the severe impacts of genetic bottlenecks and small numbers of founders in populations of reintroduced animals, it is necessary to study inbreeding and its effect on fitness in species of conservation concern. Pere David＇s deer is one of few large mammal species extinct in the wild but safely preserved in captivity. Its specific background gives us the opportunity to study the relationships between heterozygosity and neonatal fitness in relocated populations. We employed five microsatellite loci to explore heterozygosity-fitness correlations in a population of Pere David＇s deer at the Beijing Milu Ecological Research Center. We observed associations between microsatellite-based variables sMLH, IR, MD^2 and HL, and two components of fitness ex- pressed early in life （birth weight and the neonatal mortality of 123 Pere David＇s deer calves born over six consecutive years）. We found that neonatal mortality was 19.1% - 7.6%, not higher than the 19% or 18% reported in other ungulates. The heterozygosity of calves was not associated with neonatal mortality, nor birth weight. Our study implies that low genetic variability of microsa- l：ellite loci has no overt effect on birth weight and neonatal mortality in reintroduced populations of P^re David＇s deer [Current Zoology 59 （2）： 249-256, 2013].
基金supported by a grant from the Italian Ministry of Education,University and Research(PRIN project 2017KLZ3MA).
文摘Recent empirical and theoretical studies suggest that personality and locomotory performance traits linked to dispersal abilities are crucial components of the dispersal syndromes,and that they can evolve during range expansions and colonization processes.Island colonization is one of the best characterized processes in dispersal biogeography,and its implication in the evolution of phenotypic traits has been investigated over a wide range of temporal scales.However,the effect of island colonization on personality and performance traits of natural populations,and how these traits could drive island colonization,has been little explored.Noteworthy,no studies have addressed these processes in the context of late Pleistocene range expansions.Here,we investigated the contribution of island colonization triggered by postglacial range expansions to intraspecific variation in personality and locomotory performance traits.We compared boldness,exploration,jumping performance,and stickiness abilities in populations from 3 equidistant areas of the Tyrrhenian tree frog Hyla sarda,2 from the main island(Corsica Island),and 1 from the recently colonized island of Elba.Individuals from Elba were significantly bolder than individuals from Corsica,as they emerged sooner from a shelter(P=0.028),while individuals from Corsica showed markedly higher jumping and stickiness performance(both P<0.001),resulting as more performing than those of Elba.We discuss these results in the context of the major microevolutionary processes at play during range expansion,including selection,spatial sorting,founder effects,and their possible interaction with local adaptation processes.
基金the Program for New Century Excellent Talents in University (NCET-05-0431)funding from the Commission of Science and Technol-ogy of Lin'an City to XY Chen
文摘Genetic changes over space and time provide insights into the relative roles of evolutionary factors in shaping genetic patterns within plant populations. However, compared with spatial genetic structure, few studies have been conducted on genetic changes over time. In this study, we used six polymorphic microsatellite loci to assess genetic variation of six size-classes of the population of Liushan, Cryptomeriajaponica var. sinensis, in the Tianmushan National Nature Reserve, whose origin was debatable. The mean number of alleles per locus and expected heterozygosity were 4.583 and 0.5999 respectively, lower than other conifers with the same life history characteristics. FST was 0.0024-0.003, and the pairwise test revealed no significant differentiation in any pair of size classes. Significant heterozygosity excesses were detected in five size classes except the oldest one, indicating bottleneck event（s）. The above results support the hypothesis that Tianmushan population was introduced and followed by natural regeneration.
基金supported by a research grant(PI11/00342)from Fondo de Investigacion Sanitaria(co-funded by the European Regional Development Fund,"A way to build Europe")to F.C.M.This funding was granted as coordinated project Renaltube
文摘Background:Familial hypomagnesemia with hypercalciuria and nephrocalcinosis(FHHNC)is an autosomal recessive tubular disease caused by mutations in the CLDN16 or CLDN19 gene.Previous studies using microsatellite markers flanking the CLDN19 locus estimated that p.G20D(c.59G>A),a recurrent mutation in Spanish families,is a founder mutation.In the present study,we assessed the haplotype of Spanish patients using single nucleotide polymorphisms(SNPs).Methods:Twenty-seven FHHNC patients were included in this study.We analyzed four SNPs located in CLDN19 introns 3 and 4 by polymerase chain reaction amplification and DNA sequencing.Results:Three new patients with homozygous p.G20D were identified.The SNP genotyping analysis showed that alleles carrying this mutation shared a common SNP haplotype.Conclusions:Our findings suggest the existence of a founder effect responsible for FHHNC in our cohort.Testing for the presence of mutation p.G20D should be the first genetic screening in Spanish patients.
