In this study, a population of 119 chromosome segment substitution lines （CSSLs） derived from backcross between indica 9311 and japonica Nipponbare was employed to map quantitative trait loci （QTL） associated with...In this study, a population of 119 chromosome segment substitution lines （CSSLs） derived from backcross between indica 9311 and japonica Nipponbare was employed to map quantitative trait loci （QTL） associated with sheath blight resis-tance in rice with toothpick inoculation method. A total of three sheath blight resis-tance-associated QTLs （qsb8-1, qsb8-2 and qsb8-3） were identified, which were lo-cated on adjacent molecular markers RM3262, RM5485 and RM3496 of chromo-some 8; the genetic interval was 81.7cM-91.7cM, 91.7cM-108.1cM and 108.1cM-119.6cM, respectively. The additive effect of qsb8-2 was negative, indicating that sheath blight resistance of susceptible parent harboring qsb8-2 fragment was en-hanced; additive effects of qsb8-1 and qsb8-3 were positive, indicating that sheath blight resistance of susceptible parent harboring qsb8-1 and qsb8-3 fragments was reduced.展开更多
Drought stress has long been a major constraint in maintaining yield stability of soybean （Glycine max （L.） Merr.） in rainfed ecosystems. The identification of consistent quantitative trait loci （QTL） involving ...Drought stress has long been a major constraint in maintaining yield stability of soybean （Glycine max （L.） Merr.） in rainfed ecosystems. The identification of consistent quantitative trait loci （QTL） involving seed yield per plant （YP） and drought susceptibility index （DSI） in a population across different environments would therefore be important in molecular marker-assisted breeding of soybean cultivars suitable for rainfed regions. The YP of a recombinant line population of 184 F2：7：11 lines from a cross of Kefengl and Nannong1138-2 was studied under water-stressed （WS） and well-watered （WW） conditions in field （F） and greenhouse （G） trials, and DSI for yield was calculated in two trials. Nineteen QTLs associated with YP-WS and YP-WW, and 10 QTLs associated with DSI, were identi- fied. Comparison of these QTL locations with previous findings showed that the majority of these regions control one or more traits re- lated to yield and other agronomic traits. One QTL on molecular linkage group （MLG） K for YP-F, and two QTLs on MLG C2 for YP-G, remained constant across different water regimes. The regions on MLG C2 for YP-WW-F and MLG H for YP-WS-F had a pleiotropic effect on DSI-F, and MLG A1 for YP-WS-G had a pleiotropic effect on DSI-G. The identification of consistent QTLs for YP and DSI across different environments will significantly improve the efficiency of selecting for drought tolerance in soybean.展开更多
It had been demonstrated that the strong and highly significant quantitative trait locus（QTL） can affect protein percentage on Bos Taurus Autosome 3（BTA3） at the position 52 cM, near the microsatellite DIK4353, wi...It had been demonstrated that the strong and highly significant quantitative trait locus（QTL） can affect protein percentage on Bos Taurus Autosome 3（BTA3） at the position 52 cM, near the microsatellite DIK4353, with the 95% confidence interval spanning from 25 to 57 cM in Chinese Holstein population using QTL-express, MQREML, and GRIDQTL softwares. This study herein focused on such region of fine mapping QTLs for milk production and functional traits with 16 microsatellite markers with coverage of 33 cM between the markers BMS2904 and MB099 on BTA3 in a daughter-designed Chinese Holstein population. A total of 1 298 Holstein cows and 7 sires were genotyped for 16 microsatellites with ABI 3700 DNA sequencer. The variance components QTL linkage analysis（LA） and linkage-disequilibrium（LD） analysis（LA/LD） was performed to map QTLs for 7 traits, i.e., 305-d milk yield, fat yield, protein yield, fat percentage, protein percentage, somatic cell score and persistency of milk yield. Four strong and highly significant QTLs were detected for fat yield, fat percentage, protein percentage and somatic cell score at the position 40, 30, 27 and 26 cM, respectively. Two minor QTLs for milk yield and persistency of milk yield were identified at 42 and 46 cM, respectively. These findings provided a general idea for the fine mapping of the causal mutation for milk production and functional traits on BTA3 in the future.展开更多
Fruit quality traits play an important role in consumption of kiwiberry(Actinidia arguta).The genetic basis of fruit quality traits in this woody,perennial and dioecious fruit crop remains largely unknown.This study a...Fruit quality traits play an important role in consumption of kiwiberry(Actinidia arguta).The genetic basis of fruit quality traits in this woody,perennial and dioecious fruit crop remains largely unknown.This study aimed to identify the underlying genetic basis of fruit quality traits in A.arguta,using a single nucleotide polymorphism(SNP)genetic linkage map previously developed in a tetraploid F1 population of‘Ruby-3’בKuiLv-M’.The F1 population was phenotyped over three years(2020–2022)for fruit quality traits,including skin color,flesh color,fruit weight,fruit diameter,total soluble solids,fruit longitudinal diameter and fruit shape index.A total of nine QTLs were detected for five traits,explaining 10%–32%of the trait variation.For fruit color,the support interval of a major QTL on LG9 contained an MYB transcription factor MYB110,which was previously demonstrated to control color regulation in kiwifruit,thus suggesting that the MYB110 is the candidate gene for fruit color in kiwiberry.The linked marker for fruit color was validated in an F1 population and 25 kiwiberry cultivars.In conclusion,the knowledge obtained through the QTL mapping is applicable to improve the efficiency and cost-effectiveness in kiwiberry breeding.展开更多
Stem strength is an important indicator of lodging that significantly influences yield and quality in soybean.Therefore,understanding the regulatory mechanisms underlying stem strength is critical for ensuring soybean...Stem strength is an important indicator of lodging that significantly influences yield and quality in soybean.Therefore,understanding the regulatory mechanisms underlying stem strength is critical for ensuring soybean production.However,the genetic basis underlying this trait remains largely elusive.Here,we explored the key loci and regulators of stem strength by integrating quantitative trait locus(QTL)mapping with genome-wide association study(GWAS)using the recombinant inbred line(RIL)population and natural accessions.Finally,a major QTL covering an interval containing 15 genes was identified.One of these genes encodes a transcription factor related to WUSCHEL-related homeobox 4(GmWOX4-like),a high-confidence candidate for regulating stem strength based on bulk transcriptome deep sequencing and single-cell sequencing.Anatomical analysis of residual heterozygous lines(RHLs)suggested that GmWOX4-like may influence stem strength by modulating cambium differentiation through various pathways.Natural variations in the GmWOX4-like promoter region showed significant correlation with stem strength and lodging ratio across the natural population.These findings provide valuable insights into the molecular mechanisms of stem strength and will contribute to marker-assisted selection for stem strength in soybean breeding.展开更多
A population of 180 recombinant inbred lines （RILs） was developed by single seed descended from the cross of high yield Upland cotton （Gossypium hirsutum L.） varieties Zhongmiansuo12 （ZMSI2） and 8891, the two pa...A population of 180 recombinant inbred lines （RILs） was developed by single seed descended from the cross of high yield Upland cotton （Gossypium hirsutum L.） varieties Zhongmiansuo12 （ZMSI2） and 8891, the two parents of Xiangzamian2 （XZM2）. A genetic linkage map consisting of 132 loci and covering 865.20 cM was constructed using the RIL population chiefly with SSR markers. Yield and yield components were investigated for RILs in three environments in China. The purpose of the present research was to analyze the relationship between yield and its components and to map QTL for yield and yield components in cotton. QTL were tagged with data sets from single environment （separate analysis） and a set of data from means of the three environments （joint analysis）. A total of 34 QTL for yield and yield components were independently detected in three environments, whereas fifteen QTL were found in joint analysis. Notably, a stable lint percentage QTL qLP-A10-1 was detected both in joint analysis and in two environments of separate analysis, which might be of special value for marker-assisted selection. The QTL detected in the present study provide new information on improving yield and yield components. Results of path analysis showed that bolls/plant had the largest contribution to lint yield, which is consistent with the mid-parent heterosis value in F1. Accordingly, in cotton breeding, bolls/plant can be considered first and other yield components measured as a whole to implement variety enhancement and hybrid selection of cotton.展开更多
Current rice production is usually guaranteed by applying large amount of chemical nitrogen fertilizers to paddy soils. The improvement of nitrogen use efficiency is of great importance not only in rice production its...Current rice production is usually guaranteed by applying large amount of chemical nitrogen fertilizers to paddy soils. The improvement of nitrogen use efficiency is of great importance not only in rice production itself but in environmental protection as well. In this study we performed a molecular marker-based genetic analysis of nitrogen use efficiency for biomass production （NUEp） and several other related traits in a recombinant inbred line （RIL） population, derived from a cross of the parents of Shanyou 63, the most widely cultivated indica hybrid in China. A total of 12 QTLs were detected using interval mapping with a LOD threshold of 2.0, among which one QTL controlling NUEp was located at the marker interval of Waxy-C1496 on chromosome 6, and the rest 11 QTLs associated nitrogen concentration and accumulation in rice plant were positioned on chromosomes 1, 2, 4 and 6, respectively. Correlation between NUEp and other traits was analyzed and the implications of the results with respect to the improvement of the hybrid rice were discussed.展开更多
Oil and protein content and fatty acid composition are quality traits in peanut.Elucidating the genetic mechanisms underlying these traits may help researchers to obtain improved cultivars by molecular breeding.Whole-...Oil and protein content and fatty acid composition are quality traits in peanut.Elucidating the genetic mechanisms underlying these traits may help researchers to obtain improved cultivars by molecular breeding.Whole-genome resequencing of a recombinant inbred population of 318 lines was performed to construct a high-density linkage map and identify QTL for peanut quality.The map,containing 4561 bin markers,covered 2032 c M with a mean marker density of 0.45 c M.A total of 110 QTL for oil and protein content,and fatty acid composition were mapped on the 18 peanut chromosomes.The QTL q A05.1 was detected in four environments and showed a major phenotypic effect on the contents of oil,protein,and six fatty acids.The genomic region spanned by q A05.1,corresponding to a physical interval of approximately 1.5 Mb,contains two SNPs polymorphic between the parents that could cause missense mutations.The two SNP sites were employed as KASP markers and validated using lines with extremely high and low oil contents.These sites may be useful in the marker-assisted breeding of peanut cultivars with high oil contents.展开更多
Tiller is one of the most important agronomic traits which influences quantity and quality of effective panicles and finally influences yield in rice. It is important to understand ＂static＂ and ＂dynamic＂ informati...Tiller is one of the most important agronomic traits which influences quantity and quality of effective panicles and finally influences yield in rice. It is important to understand ＂static＂ and ＂dynamic＂ information of the QTLs for tillers in rice. This work was the first time to simultaneously map unconditional and conditional QTLs for tiller numbers at various stages by using single segment substitution lines in rice. Fourteen QTLs for tiller number, distributing on the corresponding substitution segments of chromosomes 1, 2, 3, 4, 6, 7 and 8 were detected. Both the number and the effect of the QTLs for tiller number were various at different stages, from 6 to 9 in the number and from 1.49 to 3.49 in the effect, respectively. Tiller number QTLs expressed in a time order, mainly detected at three stages of 0-7 d, 14-21 d and 35-42 d after transplanting with 6 positive, 9 random and 6 negative expressing QTLs, respectively. Each of the QTLs expressed one time at least during the whole duration of rice. The tiller number at a specific stage was determined by sum of QTL effects estimated by the unconditional method, while the increasing or decreasing number in a given time interval was controlled by the total of QTL effects estimated by the conditional method. These results demonstrated that it is highly effective and accurate for mapping of the QTLs by using single segment substitution lines and the conditional analysis methodology.展开更多
Asiatic cotton （Gossypium arboreum L.） is an Old World cultivated cotton species. The sinense race was planted extensively in China. Due to the advances in spinning technology during the last century, the species wa...Asiatic cotton （Gossypium arboreum L.） is an Old World cultivated cotton species. The sinense race was planted extensively in China. Due to the advances in spinning technology during the last century, the species was replaced by the New World allotetraploid cotton G. hirsutum L. Gossypium arboreum is still grown in India and Pakistan and also used as an elite in current cotton breeding programs. In addition, G. arboreum serves as a model for genomic research in Gossypium. In the present study, we generated an A-genome diploid cotton intraspecific genetic map including 264 SSR loci with three morphological markers mapped to 13 linkage groups. The map spans 2,508.71 cM with an average distance of 9.4 cM between adjacent loci. A population containing 176 F2：3 families was used to perform quantitative trait loci （QTL） mapping for 17 phenotypes using Multiple QTL Model （MQM） of MapQTL ver 5.0. Overall, 108 QTLs were detected on 13 chromosomes. Thirty-one QTLs for yield and its components were detected in the F2 population. Forty-one QTLs for yield and its components were detected in the F2：3 families with a total of 43 QTLs for fiber qualities. Two QTLs for seed cotton weight/plant and lint index and three QTLs for seed index were consistently detected both in F2 and F2：3. Most QTLs for fiber qualities and yields were located at the same interval or neighboring intervals. These results indicated that the negative correlation between fiber qualities and yield traits may result from either pleiotropic effect of one gene or linkage effects of multiple closely linked genes.展开更多
Early seedling vigor(ESV)is a major breeding target in rice,especially under direct seeding.To identify quantitative trait locus(QTL)affecting ESV,a recombinant inbred line population derived from a cross between 0242...Early seedling vigor(ESV)is a major breeding target in rice,especially under direct seeding.To identify quantitative trait locus(QTL)affecting ESV,a recombinant inbred line population derived from a cross between 02428 and YZX,two cultivars differing in vigor during early seedling growth,was used for QTL analysis.Nine traits associated with ESV were examined using a high-density map.Of 16 additive loci identified,three were detected in two generations and thus considered stable.Four epistatic interactions were detected,one of which was repeated in two generations.Further analysis of the pyramiding effect of the three stable QTL showed that the phenotypic value could be effectively improved with an increasing number of QTL.These results were combined with results from our previous QTL analysis of the germination index.The lines G58 and G182 combined all the favourable alleles of all three stable QTL for ESV and three QTL for germination speed.These two lines showed rapid germination and strong ESV.A total of 37 candidate differentially expressed genes were obtained from the regions of the three stable QTL by analysis of the dynamic transcriptomic expression profile during the seedling growth period of the two parents.The QTL are targets for ESV breeding and the candidate genes await functional validation.This study provides a theoretical basis and a genetic resource for the breeding of directseeded rice.展开更多
To gain insight into the molecular and genetic basis of fruit size and shape in cucumber,we conducted Quantitative Trait Locus(QTL)mapping with F2 and BC1F1 populations derived froma cross between the Northern-China t...To gain insight into the molecular and genetic basis of fruit size and shape in cucumber,we conducted Quantitative Trait Locus(QTL)mapping with F2 and BC1F1 populations derived froma cross between the Northern-China type inbred line CNS21 and the Southern-China type inbred line RNS7.Populations were evaluated during two developmental stages,ovary at anthesis and commercial fruit(immature fruit).A total of 13 major-effect QTLs(R2>10%)were detected for six traits,and one of them,fruit shape index 2.1,explained more than 50%of phenotypic variation.All QTLs distributed on chromosome(chr)1 and 2.We constructed a physical map containing almost all of the QTLs with their physical location from previous studies.For fruit size and shape,the highest number of QTLs were mapped on chr1 and chr6,and the fewest number were mapped on chr2 and chr7.At least one consensus region was presented on each chromosome.In addition,three candidate genes were predicted between the long-fruited and round-fruited inbred lines by comparing the sequences of the consensus region of chr3,where many QTLs for marketable fruit length had been detected.Our results provide a base for additional QTLs and molecular markers for fruit size and shape in cucumber breeding.展开更多
Dissecting the genetic relationships among gluten-related traits is important for high quality wheat breeding. Quantita- tive trait loci （QTLs） analysis for gluten strength, as measured by sedimentation volume （SV...Dissecting the genetic relationships among gluten-related traits is important for high quality wheat breeding. Quantita- tive trait loci （QTLs） analysis for gluten strength, as measured by sedimentation volume （SV） and gluten index （GI）, was performed using the QTLNetwork 2.0 software. Recombinant inbred lines （RILs） derived from the winter wheat varieties Shannong 01-35xGaocheng 9411 were used for the study. A total of seven additive QTLs for gluten strength were identi- fied using an unconditional analysis. QGi1D-13 and QSv1D-14 were detected through unconditional and conditional QTLs mapping, which explained 9.15-45.08% of the phenotypic variation. QTLs only identified under conditional QTL mapping were located in three marker intervals： WPT-3743-GLU-D1 （1D）, WPT-7001-WMC258 （1B）, and WPT-8682-WPT-5562 （1B）. Six pairs of epistatic QTLs distributed nine chromosomes were identified. Of these, two main effect QTLs （QGi1D-13 and QSvlD-14） and 12 pairs of epistatic QTLs were involved in interactions with the environment. The results indicated that chromosomes 1B and 1D are important for the improvement of gluten strength in common wheat. The combination of conditional and unconditional QTLs mapping could be useful for a better understanding of the interdependence of different traits at the QTL molecular level.展开更多
To evaluate the possible genetic interrelationships between flour components and the sedimentation volume（SD）,a doubled haploid（DH） population comprising 168 lines were used to identify the conditional quantitativ...To evaluate the possible genetic interrelationships between flour components and the sedimentation volume（SD）,a doubled haploid（DH） population comprising 168 lines were used to identify the conditional quantitative trait loci（QTLs） for SD in three environments.Ten additive QTLs and 15 pairs of epistatic QTLs were detected for SD through unconditional and conditional QTL mapping.Three major additive QTLs were detected for SD conditioned on the seven quality traits.Two additive QTLs were found to be independent of these traits.Three additive QTLs were suppressed by three of the seven traits because of non-detection in unconditional mapping.Three pairs of epistatic QTLs were completely affected by the seven traits because of detection in unconditional mapping but no-detection in conditional mapping.Twelve pairs of epistatic QTLs were detected in conditional mapping.Our results indicated that conditional mapping could contribute to a better understanding of the interdependence of different and closely correlated traits at the QTL molecular level,especially some minor QTLs were found.The conditional mapping approach provides new insights that will make it possible to avoid the disadvantages of different traits by breeding through molecular design.展开更多
Huanglongbing(HLB)is the most devastating disease for citrus worldwide.Candidatus Liberibacter asiaticus(C Las),vectored by Asian citrus psyllid(ACP,Diaphorina citri Kuwayama),is the most common pathogen causing the d...Huanglongbing(HLB)is the most devastating disease for citrus worldwide.Candidatus Liberibacter asiaticus(C Las),vectored by Asian citrus psyllid(ACP,Diaphorina citri Kuwayama),is the most common pathogen causing the disease.Commercial citrus varieties are highly susceptible to HLB,whereas trifoliate orange(Poncirus trifoliata)is considered highly tolerant to HLB.An F1 segregating population and their parent trifoliate orange and sweet orange,which had been exposed to intense HLB pressure for three years,was evaluated for disease symptoms,ACP colonization,C Las titer and tree vigor repeatedly for two to three years.Trifoliate orange and sweet orange showed significant differences for most of the phenotypic traits,and the F1 population exhibited a large variation.A high-density SNP-based genetic map with 1402 markers was constructed for trifoliate orange,which exhibited high synteny and high coverage of its reference genome.A total of 26 quantitative trait locus(QTLs)were identified in four linkage groups LG-t6,LG-t7,LG-t8 and LG-t9,of which four QTL clusters exhibit a clear co-localization of QTLs associated with different traits.Through genome-wide analysis of gene expression in response to C Las infection in‘Flying Dragon’and‘Larger-Flower DPI-50-7’trifoliate orange,85 differentially expressed genes were found located within the QTL clusters.Among them,seven genes were classified as defense or immunity protein which exhibited the highest transcriptional change after C Las infection.Our results indicate a quantitative genetic nature of HLB tolerance and identified candidate genes that should be valuable for searching for genetic solutions to HLB through breeding or genetic engineering.展开更多
General combining abilities （GCAs） are very important in utilization of heterosis in maize breeding. However, its genetic basis is unclear. In the present study, a set of 118 doubled haploid （DH） lines were induce...General combining abilities （GCAs） are very important in utilization of heterosis in maize breeding. However, its genetic basis is unclear. In the present study, a set of 118 doubled haploid （DH） lines were induced from F1 generations produced from the cross between the inbred line Zheng 58 and the inbred line W499 belonging to the Reid subgroup. Using the MaizeSNP50 BeadChip, a high-density genetic map was constructed based on the DH population which included 1 147 bin markers with an average interval length of 2.00 cM. Meanwhile, the DH population was crossed with three testers including W16-5, HD568, and W556, which belong to the Sipingtou subgroup. The GCAs of the ear height （EH）, the kernel moisture content （KMC）, the kernel ratio （KR）, and the yield per plant （YPP） were estimated using these hybrids in three environments. Combining the high-density genetic map and the GCAs, a total of 14 QTLs were detected for the GCAs of the four traits. Especially, one pleiotropic QTL was identified on chromosome 1 between the SNP SYN16067 and the SNP PZE-101169244 which was simultaneously associated with the GCAs of the EH, the KR, and the YPP. These QTLs pave the way for further dissecting the genetic architecture underlying GCAs of the traits, and they may be used to enhance GCAs of inbred lines under the fixed heterotic pattern ReidxSipingtou in China through a marker-assisted selection approach.展开更多
The QTL qTGW3-1 was located on chromosome 3 of rice （Oryza sativa L.） and associated with the 1 000-grain weight （TGW） according to the result of our earlier study. With the objective of fine mapping of this locus...The QTL qTGW3-1 was located on chromosome 3 of rice （Oryza sativa L.） and associated with the 1 000-grain weight （TGW） according to the result of our earlier study. With the objective of fine mapping of this locus, we developed a F2 population consisting of 3 428 plants derived from the cross between TGW-related near isogenic line DL017 （BC3F4 generation of GSL 156×Nipponbare） and the recurrent parent Nipponbare. Using six microsatellites, this QTL was delimited between RM5477 and RM6417. Markers MM 1455 and MM 1456 within this region were used for further mapping of this QTL. Finally, qTGW3-1 was fine-mapped into a 89-kb interval between RM5477 and MM1456, which locates in the BAC clone AC107226 harboring five putative candidate genes.展开更多
Red tilapia(Oreochromis spp.)is one of the most popular fish in China due to its bright red appearance,fast growth rate,and strong adaptability.Understanding the sex determination mechanisms is of vital importance for...Red tilapia(Oreochromis spp.)is one of the most popular fish in China due to its bright red appearance,fast growth rate,and strong adaptability.Understanding the sex determination mechanisms is of vital importance for the selection of all-male lines to increase aquacultural production of red tilapia.In this research,the genetic architecture for sex from four mapping populations(n=1090)of red tilapia was analyzed by quantitative trait loci(QTL)-seq,linkage-based QTL mapping,and linkage disequilibrium(LD)-based genome-wide association studies.Two genome-wide significant QTL intervals associated with sex were identified on ChrLG1(22.4-23.9 Mb)and ChrLG23(32.0-35.9 Mb),respectively.The QTL on ChrLG1 was detected in family 1(FAM1),FAM2,and FAM4,and the other QTL on ChrLG23 was detected in FAM3 and FAM4.Four microsatellite markers located within the QTL were successfully developed for marker-assisted selection.Interestingly,three(Ipp,sox14,and amh)of the 12 candidate genes located near or on the two QTL intervals were abundantly expressed in males,while the remaining genes were more highly expressed in females.Seven genes(scly,ube3a,Ipp,gpr17,oca2,cog4,and atp10a)were significantly differentially expressed between the male and female groups.Furthermore,LD block analysis suggested that a cluster of genes on ChrLG23 may participate in regulating sex development in red tilapia.Our study provides important information on the genetic architecture of sex in red tilapia and should facilitate further exploration of sex determination mechanisms in this species.展开更多
Genetic segregation analysis for mature seed culturability was conducted using recombinant inbred lines derived from a cross of indica rice, Yangdao 6 and Pei＇ai 64s. Three indices of seed culturability, the frequenc...Genetic segregation analysis for mature seed culturability was conducted using recombinant inbred lines derived from a cross of indica rice, Yangdao 6 and Pei＇ai 64s. Three indices of seed culturability, the frequency of callus induction, the frequency of brown callus and the increase of callus weight were investigated. A combined genetic map constructed with simple sequence repeat （SSR）, sequence tag site （STS）, cleaved amplified polymorphic sequences （CAPS） and single nucleotide polymorphism （SNP） markers covered a total distance of 1 732.5 cM, averaging approximately 12 cM between two neighboring loci. Three QTLs on chromosomes 7, 7 and 10 were detected for the frequency of callus induction; three QTLs on chromosomes 6, 7 and 9 were detected for the frequency of brown callus; and two QTLs on chromosomes 5 and 7 were detected for the increase of callus weight. Common QTLs mapped at the interval flanking RM5481 and RM6835 on chromosome 7 were identified to be involved in the frequency of callus induction and the frequency of brown callus, explaining 7.29% and 12.52% of phenotypic variation, respectively. A total of 14 epistatic effects were detected for the three indices of mature seed culturability. ~展开更多
Seed number per silique(SNPS)is one of seed yield components in rapeseed,but its genetic mechanism remains elusive.Here a double haploid(DH)population derived from a hybrid between female 6Q006with 35–40 SNPS and mal...Seed number per silique(SNPS)is one of seed yield components in rapeseed,but its genetic mechanism remains elusive.Here a double haploid(DH)population derived from a hybrid between female 6Q006with 35–40 SNPS and male 6W26 with 10–15 SNPS was investigated for SNPS in the year 2017,2018,2019 and 2021,and genotyped with Brassica 60K Illumina Infinium SNP array.An overlapping major QTL(qSNPS.C09)explaining 51.50%of phenotypic variance on average was narrowed to a 0.90 Mb region from 44.87 Mb to 45.77 Mb on chromosome C09 by BSA-seq.Subsequently,two DEGs in this interval were detected between extreme individuals in DH and F_2populations by transcriptome sequencing at7 and 14 days after pollination siliques.Of which,BnaC09g45400D encoded an adenine phosphoribosyltransferase 5(APT5)has a 48-bp InDel variation in the promoter of two parents.Candidate gene association analysis showed that this InDel variation was associated with SNPS in a nature population of rapeseed,where 54 accessions carrying the same haplotype as parent 6Q006 had higher SNPS than103 accessions carrying the same haplotype as parent 6W26.Collectively,the findings are helpful for rapeseed molecular breeding of SNPS,and provide new insight into the genetic and molecular mechanism of SNPS in rapeseed.展开更多
基金Supported by Specific Fund for the Independent Innovation of Agricultural Science and Technology[CX(11)1020]~~
文摘In this study, a population of 119 chromosome segment substitution lines （CSSLs） derived from backcross between indica 9311 and japonica Nipponbare was employed to map quantitative trait loci （QTL） associated with sheath blight resis-tance in rice with toothpick inoculation method. A total of three sheath blight resis-tance-associated QTLs （qsb8-1, qsb8-2 and qsb8-3） were identified, which were lo-cated on adjacent molecular markers RM3262, RM5485 and RM3496 of chromo-some 8; the genetic interval was 81.7cM-91.7cM, 91.7cM-108.1cM and 108.1cM-119.6cM, respectively. The additive effect of qsb8-2 was negative, indicating that sheath blight resistance of susceptible parent harboring qsb8-2 fragment was en-hanced; additive effects of qsb8-1 and qsb8-3 were positive, indicating that sheath blight resistance of susceptible parent harboring qsb8-1 and qsb8-3 fragments was reduced.
基金supported in part by the National High-Tech Program (No.2006AA10Z1C1)National Basic Research Program (No.2004CB117206 and 2009CB118400)+2 种基金the National Natural Science Foundation of China (No.30471094)the Key Project of Science and Technology of Shanxi Province (No.051017)the Scientific Research Foundation for Youth Academic Leaders from University in Shanxi Province (No.200425)
文摘Drought stress has long been a major constraint in maintaining yield stability of soybean （Glycine max （L.） Merr.） in rainfed ecosystems. The identification of consistent quantitative trait loci （QTL） involving seed yield per plant （YP） and drought susceptibility index （DSI） in a population across different environments would therefore be important in molecular marker-assisted breeding of soybean cultivars suitable for rainfed regions. The YP of a recombinant line population of 184 F2：7：11 lines from a cross of Kefengl and Nannong1138-2 was studied under water-stressed （WS） and well-watered （WW） conditions in field （F） and greenhouse （G） trials, and DSI for yield was calculated in two trials. Nineteen QTLs associated with YP-WS and YP-WW, and 10 QTLs associated with DSI, were identi- fied. Comparison of these QTL locations with previous findings showed that the majority of these regions control one or more traits re- lated to yield and other agronomic traits. One QTL on molecular linkage group （MLG） K for YP-F, and two QTLs on MLG C2 for YP-G, remained constant across different water regimes. The regions on MLG C2 for YP-WW-F and MLG H for YP-WS-F had a pleiotropic effect on DSI-F, and MLG A1 for YP-WS-G had a pleiotropic effect on DSI-G. The identification of consistent QTLs for YP and DSI across different environments will significantly improve the efficiency of selecting for drought tolerance in soybean.
基金supported by the High Technology Research and Development Program of China(2013AA102504)the Beijing Innovation Team of Technology System in the National Dairy Industry+2 种基金the National Key Technologies R&D Program of China(2011BAD28B02,2012BAD12B01)the Beijing Research and Technology Program,China(D121100003312001)the Program for Changjiang Scholar and Innovation Research Team in University,China(IRT1191)
文摘It had been demonstrated that the strong and highly significant quantitative trait locus（QTL） can affect protein percentage on Bos Taurus Autosome 3（BTA3） at the position 52 cM, near the microsatellite DIK4353, with the 95% confidence interval spanning from 25 to 57 cM in Chinese Holstein population using QTL-express, MQREML, and GRIDQTL softwares. This study herein focused on such region of fine mapping QTLs for milk production and functional traits with 16 microsatellite markers with coverage of 33 cM between the markers BMS2904 and MB099 on BTA3 in a daughter-designed Chinese Holstein population. A total of 1 298 Holstein cows and 7 sires were genotyped for 16 microsatellites with ABI 3700 DNA sequencer. The variance components QTL linkage analysis（LA） and linkage-disequilibrium（LD） analysis（LA/LD） was performed to map QTLs for 7 traits, i.e., 305-d milk yield, fat yield, protein yield, fat percentage, protein percentage, somatic cell score and persistency of milk yield. Four strong and highly significant QTLs were detected for fat yield, fat percentage, protein percentage and somatic cell score at the position 40, 30, 27 and 26 cM, respectively. Two minor QTLs for milk yield and persistency of milk yield were identified at 42 and 46 cM, respectively. These findings provided a general idea for the fine mapping of the causal mutation for milk production and functional traits on BTA3 in the future.
基金support from the National Natural Science Foundation of China(Grant No.32001995)the Major Science and Technology Project of Henan Province(Grant No.221100110400)+3 种基金the China Agriculture Research System of MOF and MARA(Grant No.CARS-26)the Special Engineering Science and Technology Innovation,CAAS(Grant No.CAAS-ASTIP-2024-ZFRI).Part of this research was funded under the TKI project:“Novel genetic and genomic tools for polyploid crops”(KV 1605-020BO 26.03009004,BO 50002022)and USDA's National Institute of Food and Agriculture(NIFA)Specialty Crop Research Initiative project“Tools for genomics assisted breeding in polyploids:Development of a community resource”(Grant No.2020-51181-32156/SCRI)received a scholarship from China Scholarship Council(Grant No.202303250034).
文摘Fruit quality traits play an important role in consumption of kiwiberry(Actinidia arguta).The genetic basis of fruit quality traits in this woody,perennial and dioecious fruit crop remains largely unknown.This study aimed to identify the underlying genetic basis of fruit quality traits in A.arguta,using a single nucleotide polymorphism(SNP)genetic linkage map previously developed in a tetraploid F1 population of‘Ruby-3’בKuiLv-M’.The F1 population was phenotyped over three years(2020–2022)for fruit quality traits,including skin color,flesh color,fruit weight,fruit diameter,total soluble solids,fruit longitudinal diameter and fruit shape index.A total of nine QTLs were detected for five traits,explaining 10%–32%of the trait variation.For fruit color,the support interval of a major QTL on LG9 contained an MYB transcription factor MYB110,which was previously demonstrated to control color regulation in kiwifruit,thus suggesting that the MYB110 is the candidate gene for fruit color in kiwiberry.The linked marker for fruit color was validated in an F1 population and 25 kiwiberry cultivars.In conclusion,the knowledge obtained through the QTL mapping is applicable to improve the efficiency and cost-effectiveness in kiwiberry breeding.
基金supported by the National Natural Science Foundation of China(32322062 and 32441057)the Natural Science Foundation of Shandong Province(ZR2023JQ009)+2 种基金the Agricultural Variety Improvement Project of Shandong Province(2024LZGC010,2024LZGC030)the National Key Research and Development Program of China(2021YFF1001100)the Modern Agro-industry Technology Research System of Shandong Province(SDAIT-28-01,SDAIT-28-06).
文摘Stem strength is an important indicator of lodging that significantly influences yield and quality in soybean.Therefore,understanding the regulatory mechanisms underlying stem strength is critical for ensuring soybean production.However,the genetic basis underlying this trait remains largely elusive.Here,we explored the key loci and regulators of stem strength by integrating quantitative trait locus(QTL)mapping with genome-wide association study(GWAS)using the recombinant inbred line(RIL)population and natural accessions.Finally,a major QTL covering an interval containing 15 genes was identified.One of these genes encodes a transcription factor related to WUSCHEL-related homeobox 4(GmWOX4-like),a high-confidence candidate for regulating stem strength based on bulk transcriptome deep sequencing and single-cell sequencing.Anatomical analysis of residual heterozygous lines(RHLs)suggested that GmWOX4-like may influence stem strength by modulating cambium differentiation through various pathways.Natural variations in the GmWOX4-like promoter region showed significant correlation with stem strength and lodging ratio across the natural population.These findings provide valuable insights into the molecular mechanisms of stem strength and will contribute to marker-assisted selection for stem strength in soybean breeding.
基金This work was supported by the National Science Foundation for Outstanding Youth Scholars (No. 30025029), Chinese National Programs for High Technology Research and Development (No. 2002AA207006), the Teaching and Research Award Program for Outstanding Young Teachers in Higher Education Institutions, and Program for Changjiang Scholars and Innovative Research Team in University of MOE, China.
文摘A population of 180 recombinant inbred lines （RILs） was developed by single seed descended from the cross of high yield Upland cotton （Gossypium hirsutum L.） varieties Zhongmiansuo12 （ZMSI2） and 8891, the two parents of Xiangzamian2 （XZM2）. A genetic linkage map consisting of 132 loci and covering 865.20 cM was constructed using the RIL population chiefly with SSR markers. Yield and yield components were investigated for RILs in three environments in China. The purpose of the present research was to analyze the relationship between yield and its components and to map QTL for yield and yield components in cotton. QTL were tagged with data sets from single environment （separate analysis） and a set of data from means of the three environments （joint analysis）. A total of 34 QTL for yield and yield components were independently detected in three environments, whereas fifteen QTL were found in joint analysis. Notably, a stable lint percentage QTL qLP-A10-1 was detected both in joint analysis and in two environments of separate analysis, which might be of special value for marker-assisted selection. The QTL detected in the present study provide new information on improving yield and yield components. Results of path analysis showed that bolls/plant had the largest contribution to lint yield, which is consistent with the mid-parent heterosis value in F1. Accordingly, in cotton breeding, bolls/plant can be considered first and other yield components measured as a whole to implement variety enhancement and hybrid selection of cotton.
基金This research was financially supported by the National Natural Science Foundation of China(NSFC)fund from the Education Committee of Jiangsu Province,China.The recombinant inbred line(RIL)population,derived from a cross of the parents of Shanyou 63,and relevant genetic information were provided by the National Key Lab for Crop Genetic Improvement of China.
文摘Current rice production is usually guaranteed by applying large amount of chemical nitrogen fertilizers to paddy soils. The improvement of nitrogen use efficiency is of great importance not only in rice production itself but in environmental protection as well. In this study we performed a molecular marker-based genetic analysis of nitrogen use efficiency for biomass production （NUEp） and several other related traits in a recombinant inbred line （RIL） population, derived from a cross of the parents of Shanyou 63, the most widely cultivated indica hybrid in China. A total of 12 QTLs were detected using interval mapping with a LOD threshold of 2.0, among which one QTL controlling NUEp was located at the marker interval of Waxy-C1496 on chromosome 6, and the rest 11 QTLs associated nitrogen concentration and accumulation in rice plant were positioned on chromosomes 1, 2, 4 and 6, respectively. Correlation between NUEp and other traits was analyzed and the implications of the results with respect to the improvement of the hybrid rice were discussed.
基金supported by the National Basic Research Program of ChinaSpecial Project for National Supercomputing Zhengzhou Center Innovation Ecosystem Construction(201400210600)+4 种基金Outstanding Young Scientists of Henan Academy of Agricultural Sciences(2020YQ08)Fund for Distinguished Young Scholars from Henan Academy of Agricultural Sciences(2019JQ02)China Agriculture Research System(CARS-13)Henan Provincial Agriculture Research System,China(S2012-5)Henan Provincial Young Talents Supporting Project(2020HYTP044)。
文摘Oil and protein content and fatty acid composition are quality traits in peanut.Elucidating the genetic mechanisms underlying these traits may help researchers to obtain improved cultivars by molecular breeding.Whole-genome resequencing of a recombinant inbred population of 318 lines was performed to construct a high-density linkage map and identify QTL for peanut quality.The map,containing 4561 bin markers,covered 2032 c M with a mean marker density of 0.45 c M.A total of 110 QTL for oil and protein content,and fatty acid composition were mapped on the 18 peanut chromosomes.The QTL q A05.1 was detected in four environments and showed a major phenotypic effect on the contents of oil,protein,and six fatty acids.The genomic region spanned by q A05.1,corresponding to a physical interval of approximately 1.5 Mb,contains two SNPs polymorphic between the parents that could cause missense mutations.The two SNP sites were employed as KASP markers and validated using lines with extremely high and low oil contents.These sites may be useful in the marker-assisted breeding of peanut cultivars with high oil contents.
基金supported by the grants from the National.Basic Research Program of China(2006CB 101700)the National Natural Science Foundation of China(30330370).
文摘Tiller is one of the most important agronomic traits which influences quantity and quality of effective panicles and finally influences yield in rice. It is important to understand ＂static＂ and ＂dynamic＂ information of the QTLs for tillers in rice. This work was the first time to simultaneously map unconditional and conditional QTLs for tiller numbers at various stages by using single segment substitution lines in rice. Fourteen QTLs for tiller number, distributing on the corresponding substitution segments of chromosomes 1, 2, 3, 4, 6, 7 and 8 were detected. Both the number and the effect of the QTLs for tiller number were various at different stages, from 6 to 9 in the number and from 1.49 to 3.49 in the effect, respectively. Tiller number QTLs expressed in a time order, mainly detected at three stages of 0-7 d, 14-21 d and 35-42 d after transplanting with 6 positive, 9 random and 6 negative expressing QTLs, respectively. Each of the QTLs expressed one time at least during the whole duration of rice. The tiller number at a specific stage was determined by sum of QTL effects estimated by the unconditional method, while the increasing or decreasing number in a given time interval was controlled by the total of QTL effects estimated by the conditional method. These results demonstrated that it is highly effective and accurate for mapping of the QTLs by using single segment substitution lines and the conditional analysis methodology.
基金supported by the Project of the Changjiang Scholars and Innovative Research Team in University, the Ministry of Education of China (No.IRT0432)the 111 Project (No.B08025)
文摘Asiatic cotton （Gossypium arboreum L.） is an Old World cultivated cotton species. The sinense race was planted extensively in China. Due to the advances in spinning technology during the last century, the species was replaced by the New World allotetraploid cotton G. hirsutum L. Gossypium arboreum is still grown in India and Pakistan and also used as an elite in current cotton breeding programs. In addition, G. arboreum serves as a model for genomic research in Gossypium. In the present study, we generated an A-genome diploid cotton intraspecific genetic map including 264 SSR loci with three morphological markers mapped to 13 linkage groups. The map spans 2,508.71 cM with an average distance of 9.4 cM between adjacent loci. A population containing 176 F2：3 families was used to perform quantitative trait loci （QTL） mapping for 17 phenotypes using Multiple QTL Model （MQM） of MapQTL ver 5.0. Overall, 108 QTLs were detected on 13 chromosomes. Thirty-one QTLs for yield and its components were detected in the F2 population. Forty-one QTLs for yield and its components were detected in the F2：3 families with a total of 43 QTLs for fiber qualities. Two QTLs for seed cotton weight/plant and lint index and three QTLs for seed index were consistently detected both in F2 and F2：3. Most QTLs for fiber qualities and yields were located at the same interval or neighboring intervals. These results indicated that the negative correlation between fiber qualities and yield traits may result from either pleiotropic effect of one gene or linkage effects of multiple closely linked genes.
基金This research was supported by the Breeding New Varieties of Rice Suitable for Light and Simple Cultivation and Mechanized Production Project(2017YFD0100104)the Research and Development Plan for Key Areas in Guangdong Province(2018B020206002)+1 种基金the China Agriculture Research System(CARS-01-17)Special thanks are due to the South China Agricultural University Doctoral Innovative Talents(Domestic Training)Cultivation Program(CX2019N044)。
文摘Early seedling vigor(ESV)is a major breeding target in rice,especially under direct seeding.To identify quantitative trait locus(QTL)affecting ESV,a recombinant inbred line population derived from a cross between 02428 and YZX,two cultivars differing in vigor during early seedling growth,was used for QTL analysis.Nine traits associated with ESV were examined using a high-density map.Of 16 additive loci identified,three were detected in two generations and thus considered stable.Four epistatic interactions were detected,one of which was repeated in two generations.Further analysis of the pyramiding effect of the three stable QTL showed that the phenotypic value could be effectively improved with an increasing number of QTL.These results were combined with results from our previous QTL analysis of the germination index.The lines G58 and G182 combined all the favourable alleles of all three stable QTL for ESV and three QTL for germination speed.These two lines showed rapid germination and strong ESV.A total of 37 candidate differentially expressed genes were obtained from the regions of the three stable QTL by analysis of the dynamic transcriptomic expression profile during the seedling growth period of the two parents.The QTL are targets for ESV breeding and the candidate genes await functional validation.This study provides a theoretical basis and a genetic resource for the breeding of directseeded rice.
基金supported by the National Natural Science Foundation of China(Grant Nos.31672170,31872950 and 31222048)the Natural Science Foundation of Shandong Province(Grant No.JQ201309),the Shandong“Double Tops”Program(Grant No.SYL2017YSTD06)the‘Taishan Scholar’Foundation of the People’s Government of Shandong Province(Grant No.ts20130932).
文摘To gain insight into the molecular and genetic basis of fruit size and shape in cucumber,we conducted Quantitative Trait Locus(QTL)mapping with F2 and BC1F1 populations derived froma cross between the Northern-China type inbred line CNS21 and the Southern-China type inbred line RNS7.Populations were evaluated during two developmental stages,ovary at anthesis and commercial fruit(immature fruit).A total of 13 major-effect QTLs(R2>10%)were detected for six traits,and one of them,fruit shape index 2.1,explained more than 50%of phenotypic variation.All QTLs distributed on chromosome(chr)1 and 2.We constructed a physical map containing almost all of the QTLs with their physical location from previous studies.For fruit size and shape,the highest number of QTLs were mapped on chr1 and chr6,and the fewest number were mapped on chr2 and chr7.At least one consensus region was presented on each chromosome.In addition,three candidate genes were predicted between the long-fruited and round-fruited inbred lines by comparing the sequences of the consensus region of chr3,where many QTLs for marketable fruit length had been detected.Our results provide a base for additional QTLs and molecular markers for fruit size and shape in cucumber breeding.
基金support from the Natural Science Foundation of Shandong Province,China (ZR2015CM036)the Molecular Foundation of Main Crop Quality,the Ministry of Science and Technology of China (2016YFD0100500)+1 种基金the Project of Science and Technology of Shandong “Wheat Breeding by Molecular Design”,China (2016LZGC023)the Research Fund for Agricultural Big Data Project,China
文摘Dissecting the genetic relationships among gluten-related traits is important for high quality wheat breeding. Quantita- tive trait loci （QTLs） analysis for gluten strength, as measured by sedimentation volume （SV） and gluten index （GI）, was performed using the QTLNetwork 2.0 software. Recombinant inbred lines （RILs） derived from the winter wheat varieties Shannong 01-35xGaocheng 9411 were used for the study. A total of seven additive QTLs for gluten strength were identi- fied using an unconditional analysis. QGi1D-13 and QSv1D-14 were detected through unconditional and conditional QTLs mapping, which explained 9.15-45.08% of the phenotypic variation. QTLs only identified under conditional QTL mapping were located in three marker intervals： WPT-3743-GLU-D1 （1D）, WPT-7001-WMC258 （1B）, and WPT-8682-WPT-5562 （1B）. Six pairs of epistatic QTLs distributed nine chromosomes were identified. Of these, two main effect QTLs （QGi1D-13 and QSvlD-14） and 12 pairs of epistatic QTLs were involved in interactions with the environment. The results indicated that chromosomes 1B and 1D are important for the improvement of gluten strength in common wheat. The combination of conditional and unconditional QTLs mapping could be useful for a better understanding of the interdependence of different traits at the QTL molecular level.
基金supported by the Natural Science Foundation of Shandong Province,China(ZR2009DQ009)the National Natural Science Foundation of China(30971764 and 31171554)the National Major Projects of Cultivated Transgenic New Varieties Foundation of China(2011ZX08002-003 and 2009ZX08002-017B)
文摘To evaluate the possible genetic interrelationships between flour components and the sedimentation volume（SD）,a doubled haploid（DH） population comprising 168 lines were used to identify the conditional quantitative trait loci（QTLs） for SD in three environments.Ten additive QTLs and 15 pairs of epistatic QTLs were detected for SD through unconditional and conditional QTL mapping.Three major additive QTLs were detected for SD conditioned on the seven quality traits.Two additive QTLs were found to be independent of these traits.Three additive QTLs were suppressed by three of the seven traits because of non-detection in unconditional mapping.Three pairs of epistatic QTLs were completely affected by the seven traits because of detection in unconditional mapping but no-detection in conditional mapping.Twelve pairs of epistatic QTLs were detected in conditional mapping.Our results indicated that conditional mapping could contribute to a better understanding of the interdependence of different and closely correlated traits at the QTL molecular level,especially some minor QTLs were found.The conditional mapping approach provides new insights that will make it possible to avoid the disadvantages of different traits by breeding through molecular design.
基金supported by grants from the Citrus Research and Development Foundation,USA(Grant No.CRDF#15-010)the New Varieties Development and Management Corporation(NVDMC),on behalf of the Florida citrus industry,USA,the Fundamental Research Funds for the Central Universities,China(Grant No.2022CDJXY-004)from the USDA-NIFA-SCRI,USA(Grant No.2015-70016-2302).
文摘Huanglongbing(HLB)is the most devastating disease for citrus worldwide.Candidatus Liberibacter asiaticus(C Las),vectored by Asian citrus psyllid(ACP,Diaphorina citri Kuwayama),is the most common pathogen causing the disease.Commercial citrus varieties are highly susceptible to HLB,whereas trifoliate orange(Poncirus trifoliata)is considered highly tolerant to HLB.An F1 segregating population and their parent trifoliate orange and sweet orange,which had been exposed to intense HLB pressure for three years,was evaluated for disease symptoms,ACP colonization,C Las titer and tree vigor repeatedly for two to three years.Trifoliate orange and sweet orange showed significant differences for most of the phenotypic traits,and the F1 population exhibited a large variation.A high-density SNP-based genetic map with 1402 markers was constructed for trifoliate orange,which exhibited high synteny and high coverage of its reference genome.A total of 26 quantitative trait locus(QTLs)were identified in four linkage groups LG-t6,LG-t7,LG-t8 and LG-t9,of which four QTL clusters exhibit a clear co-localization of QTLs associated with different traits.Through genome-wide analysis of gene expression in response to C Las infection in‘Flying Dragon’and‘Larger-Flower DPI-50-7’trifoliate orange,85 differentially expressed genes were found located within the QTL clusters.Among them,seven genes were classified as defense or immunity protein which exhibited the highest transcriptional change after C Las infection.Our results indicate a quantitative genetic nature of HLB tolerance and identified candidate genes that should be valuable for searching for genetic solutions to HLB through breeding or genetic engineering.
基金financially supported by the National Key Research and Development Plan of China(2016YFD0101200)
文摘General combining abilities （GCAs） are very important in utilization of heterosis in maize breeding. However, its genetic basis is unclear. In the present study, a set of 118 doubled haploid （DH） lines were induced from F1 generations produced from the cross between the inbred line Zheng 58 and the inbred line W499 belonging to the Reid subgroup. Using the MaizeSNP50 BeadChip, a high-density genetic map was constructed based on the DH population which included 1 147 bin markers with an average interval length of 2.00 cM. Meanwhile, the DH population was crossed with three testers including W16-5, HD568, and W556, which belong to the Sipingtou subgroup. The GCAs of the ear height （EH）, the kernel moisture content （KMC）, the kernel ratio （KR）, and the yield per plant （YPP） were estimated using these hybrids in three environments. Combining the high-density genetic map and the GCAs, a total of 14 QTLs were detected for the GCAs of the four traits. Especially, one pleiotropic QTL was identified on chromosome 1 between the SNP SYN16067 and the SNP PZE-101169244 which was simultaneously associated with the GCAs of the EH, the KR, and the YPP. These QTLs pave the way for further dissecting the genetic architecture underlying GCAs of the traits, and they may be used to enhance GCAs of inbred lines under the fixed heterotic pattern ReidxSipingtou in China through a marker-assisted selection approach.
基金supported by the National Basic Research Program of China (2010CB129504)the National Key Technologies R&D Program of China (2009BADA2B01)the 948 Project of MOA, China (2011-G2B)
文摘The QTL qTGW3-1 was located on chromosome 3 of rice （Oryza sativa L.） and associated with the 1 000-grain weight （TGW） according to the result of our earlier study. With the objective of fine mapping of this locus, we developed a F2 population consisting of 3 428 plants derived from the cross between TGW-related near isogenic line DL017 （BC3F4 generation of GSL 156×Nipponbare） and the recurrent parent Nipponbare. Using six microsatellites, this QTL was delimited between RM5477 and RM6417. Markers MM 1455 and MM 1456 within this region were used for further mapping of this QTL. Finally, qTGW3-1 was fine-mapped into a 89-kb interval between RM5477 and MM1456, which locates in the BAC clone AC107226 harboring five putative candidate genes.
基金supported by the Guangdong Provincial Key R&D Program(2021B0202020001)Independent Research and Development Projects of Maoming Laboratory(2021ZZ007)+1 种基金National Natural Science Foundation of China(32072970)Special Science and Technology Program of Maoming,Guangdong,China(2019S002004)。
文摘Red tilapia(Oreochromis spp.)is one of the most popular fish in China due to its bright red appearance,fast growth rate,and strong adaptability.Understanding the sex determination mechanisms is of vital importance for the selection of all-male lines to increase aquacultural production of red tilapia.In this research,the genetic architecture for sex from four mapping populations(n=1090)of red tilapia was analyzed by quantitative trait loci(QTL)-seq,linkage-based QTL mapping,and linkage disequilibrium(LD)-based genome-wide association studies.Two genome-wide significant QTL intervals associated with sex were identified on ChrLG1(22.4-23.9 Mb)and ChrLG23(32.0-35.9 Mb),respectively.The QTL on ChrLG1 was detected in family 1(FAM1),FAM2,and FAM4,and the other QTL on ChrLG23 was detected in FAM3 and FAM4.Four microsatellite markers located within the QTL were successfully developed for marker-assisted selection.Interestingly,three(Ipp,sox14,and amh)of the 12 candidate genes located near or on the two QTL intervals were abundantly expressed in males,while the remaining genes were more highly expressed in females.Seven genes(scly,ube3a,Ipp,gpr17,oca2,cog4,and atp10a)were significantly differentially expressed between the male and female groups.Furthermore,LD block analysis suggested that a cluster of genes on ChrLG23 may participate in regulating sex development in red tilapia.Our study provides important information on the genetic architecture of sex in red tilapia and should facilitate further exploration of sex determination mechanisms in this species.
基金supported by grants from the Natural Science Fund for Distinguished Young ScholarsZhejiang Province+2 种基金China(Grant No.LR12C06001)Project of Transgenic CropsChina(Grant No.2011ZX08001)
文摘Genetic segregation analysis for mature seed culturability was conducted using recombinant inbred lines derived from a cross of indica rice, Yangdao 6 and Pei＇ai 64s. Three indices of seed culturability, the frequency of callus induction, the frequency of brown callus and the increase of callus weight were investigated. A combined genetic map constructed with simple sequence repeat （SSR）, sequence tag site （STS）, cleaved amplified polymorphic sequences （CAPS） and single nucleotide polymorphism （SNP） markers covered a total distance of 1 732.5 cM, averaging approximately 12 cM between two neighboring loci. Three QTLs on chromosomes 7, 7 and 10 were detected for the frequency of callus induction; three QTLs on chromosomes 6, 7 and 9 were detected for the frequency of brown callus; and two QTLs on chromosomes 5 and 7 were detected for the increase of callus weight. Common QTLs mapped at the interval flanking RM5481 and RM6835 on chromosome 7 were identified to be involved in the frequency of callus induction and the frequency of brown callus, explaining 7.29% and 12.52% of phenotypic variation, respectively. A total of 14 epistatic effects were detected for the three indices of mature seed culturability. ~
基金supported by the National Basic Research Program of China(2015CB150201)the Natural Science Foundation of Chongqing(cstc2019jcyj-bshX0055,cstc2019jcyj-zdxmX0012cstc2020jcyj-msxmX0461)。
文摘Seed number per silique(SNPS)is one of seed yield components in rapeseed,but its genetic mechanism remains elusive.Here a double haploid(DH)population derived from a hybrid between female 6Q006with 35–40 SNPS and male 6W26 with 10–15 SNPS was investigated for SNPS in the year 2017,2018,2019 and 2021,and genotyped with Brassica 60K Illumina Infinium SNP array.An overlapping major QTL(qSNPS.C09)explaining 51.50%of phenotypic variance on average was narrowed to a 0.90 Mb region from 44.87 Mb to 45.77 Mb on chromosome C09 by BSA-seq.Subsequently,two DEGs in this interval were detected between extreme individuals in DH and F_2populations by transcriptome sequencing at7 and 14 days after pollination siliques.Of which,BnaC09g45400D encoded an adenine phosphoribosyltransferase 5(APT5)has a 48-bp InDel variation in the promoter of two parents.Candidate gene association analysis showed that this InDel variation was associated with SNPS in a nature population of rapeseed,where 54 accessions carrying the same haplotype as parent 6Q006 had higher SNPS than103 accessions carrying the same haplotype as parent 6W26.Collectively,the findings are helpful for rapeseed molecular breeding of SNPS,and provide new insight into the genetic and molecular mechanism of SNPS in rapeseed.
