CSB14Sh,which is isogenic for its recurrent parent TM-1 except for chromosome 14 short arm,was crossed with TM-1,and the F2 population was produced.A total of 3800 SSR primer pairs covering the whole genome were used ...CSB14Sh,which is isogenic for its recurrent parent TM-1 except for chromosome 14 short arm,was crossed with TM-1,and the F2 population was produced.A total of 3800 SSR primer pairs covering the whole genome were used to screen polymorphism among two parents,TM-1 and CSB14Sh,展开更多
Dendrobium plants are used commonly as tonic herbs and health food in many Asian countries, especially in China. Here we report the genetic map construction of two Dendrobium species with a double pseudo-testcross str...Dendrobium plants are used commonly as tonic herbs and health food in many Asian countries, especially in China. Here we report the genetic map construction of two Dendrobium species with a double pseudo-testcross strategy using random amplified polymorphic DNA （RAPD） and sequence-related amplified polymorphism （SRAP） markers. A F1 mapping population of 90 individuals was developed from a cross between D. officinale and D. hercoglossum. A total of 307 markers, including 209 RAPD and 98 SRAP, were identified and used for genetic linkage group （LG） analysis. The D. officinale linkage map consisted of 11 major linkage groups and 3 doublets, which covered 629.4 cM by a total of 62 markers with an average locus distance of 11.2 cM between two adjacent markers. The D. hercoglos- sum linkage map contained 112 markers mapped on 15 major and 4 minor linkage groups, spanning a total length of 1,304.6 cM with an average distance of I 1.6 cM between two adjacent markers. The maps constructed in this study covered 92.7% and 82.7% of the D. hercoglossum and D. officinale genomes respectively, providing an important basis for the mapping of horticultural and medicinal traits and for the application of marker-assisted selection in Dendrobium breeding program.展开更多
Pacific bluefin tuna (Thunnus orientalis) is one of the most economically important species in the Percomorpha group of teleost fishes. Their migrations are extensive and depend upon continuous swimming at a high rate...Pacific bluefin tuna (Thunnus orientalis) is one of the most economically important species in the Percomorpha group of teleost fishes. Their migrations are extensive and depend upon continuous swimming at a high rate of speed throughout their life. The draft genome sequence of this species has been reported but remains highly fragmented. We constructed a Pacific bluefin tuna genetic linkage map using microsatellite markers developed on each of the scaffolds from the draft genome sequence to link these genome fragments and understand the genomic structure of species in Percomorpha. Of the 606 polymerase chain reaction microsatellite primer pairs tested, 473 were polymorphic in the mapping populations for the linkage analysis. We constructed sex-specific maps for 24 linkage groups consisting of 470 markers, which allowed us to place scaffolds that cumulatively represented 20.8% (153.8 Mb) of the sequenced genome onto the linkage groups. The distribution of orthologous genes on the chromosomes of tuna and four other teleost fish species suggested that the constitution of tuna chromosomes is closest to that of medaka. Both species have the 24 chromosomes of the ancestral teleost, including several chromosomal inversions. The integrated map developed in this study will be useful to construct a complete physical map to conduct comparative teleost genomics and genetic studies on economically useful traits in Pacific bluefin tuna.展开更多
Fenneropaeneus chinensis is an important species in marine fishery resources and aquaculture in China.A genetic linkage map is essential for improving the efficiency of its breeding by marker-as-sisted selection and i...Fenneropaeneus chinensis is an important species in marine fishery resources and aquaculture in China.A genetic linkage map is essential for improving the efficiency of its breeding by marker-as-sisted selection and identifying commercially important genes.Linkage maps of F.chinensis were constructed with an F2 mapping population(110 progenies)using amplified fragment length polymor-phic(AFLP)marker in this study.Fifty-five AFLP primer combinations produced 532 AFLP markers fitting for map strategy in mapping family.The markers with 3:1 segregating ratios were analyzed using F2 intercross model for the common linkage map,while the markers with 1:1 ratio were analyzed using the pseudo-testcross strategy.The maps of male,female and common were constructed.The female map included 103 markers that formed 28 linkage groups,covering a total length of 1090 cM.All mark-ers were linked with the linkage groups.Segregation distortion was observed for 6 of 103 markers in the female map.The average distance between markers was 14.53 cM and ranged from 4.4 to 24.8 cM.The male map included 144 markers that formed 35 linkage groups.Ten markers remained unlinked in male map.Segregation distortion was observed for 7 of 144 markers in the male map.The total dis-tance of male map covered 1617 cM.The average distance between markers was 16.36 cM.The male map was 32.6%longer than the female map,which may reflect sex-specific recombination rates in Chinese shrimp.The common map was composed of 216 markers,including in 44 linkage groups covering a total distance of 1772.1 cM.Two markers remained unlinked.No distorted markers of 216 markers were shown in the common map.The distance between markers was 10.42 cM.An average estimated genome size for the Chinese shrimp was 2420 cM,which was consistent with the relative size of the Penaeid genome.The distribution of AFLP markers was relatively even in chromosomes of Chi-nese shrimp maps.The linkage analysis presented in this work provided some insight into the level of polymorphism and genetic variation of Chinese shrimp.展开更多
This study introduces the construction of the first intraspecific genetic linkage map of the A-genome diploid cotton with newly developed simple sequence repeat （SSR） markers using 189 F2 plants derived from the cro...This study introduces the construction of the first intraspecific genetic linkage map of the A-genome diploid cotton with newly developed simple sequence repeat （SSR） markers using 189 F2 plants derived from the cross of two Asiatic cotton cultivars （Gossypium arboreum L.） Jianglingzhongmlan x Zhejiangxiaoshanl（ishu. Polymorphisms between the two parents were detected using 6 092 pairs of SSR primers. Two-hundred and sixty-eight pairs of SSR primers with better polymorphisms were picked out to analyze the F2 population. In total, 320 polymorphic bands were generated and used to construct a linkage map with JoinMap3.0. Two-hundred and sixty-seven loci, including three phenotypic traits were mapped at a logarithms of odds ratio （LOD）≥ 3.0 on 13 linkage groups. The total length of the map was 2 508.71 cM, and the average distance between adjacent markers was 9.40 cM. Chromosome assignments were according to the association of linkages with our backbone tetraploid specific map using the 89 similar SSR loci. Comparisons among the 13 suites of orthologous linkage groups revealed that the A-genome chromosomes are largely collinear with the At and Dt sub- genome chromosomes. Chromosomes associated with inversions suggested that allopolyploidization was accompanied by homologous chromosomal rearrangement. The inter-chromosomal duplicated loci supply molecular evidence that the A-genome diploid Asiatic cotton is paleopolyploid.展开更多
In this study, we reported the repaid construction of a molecular marker linkage map of rice (Oryza sativa L.). An F-2 population from the cross between Annong S-1 and Nanjing 11 was used to construct a genetic linkag...In this study, we reported the repaid construction of a molecular marker linkage map of rice (Oryza sativa L.). An F-2 population from the cross between Annong S-1 and Nanjing 11 was used to construct a genetic linkage map of rice. Total of 142 newly screened AFLP markers and 30 anchor markers (25 SSR markers and 5 RFLP markers) were mapped on the 12 chromosomes covering 1537.4 cM of rice genome. The average interval between these markers was 9.0 cM. The total work which usually was finished in more than one year was finished within only 3 months by one person. This is the first plant AFLP map developed in China. A new thermosensitive genic male sterile gene in rice, tms5, was Egged and mapped onto chromosome 2 during the development of the linkage map.展开更多
In this study, an RIL （recombinant inbred line） population containing 240 lines was developed by single seed descent method （SSD） based on a parent com- bination of small-grain indica cultivar Kasalath and large-g...In this study, an RIL （recombinant inbred line） population containing 240 lines was developed by single seed descent method （SSD） based on a parent com- bination of small-grain indica cultivar Kasalath and large-grain japanica cultivar TD70 with significant differences in plant type traits, to construct the molecular genetic linkage map. Totally 838 SSR （Simple Sequence Repeat） markers were used for polymorphism screening between parents, 302 SSR markers with polymorphism were detected, with a frequency of 36.04%; 141 SSR markers with clear amplified bands and uniform distribution in the genome were finally used for genotype analysis of the RIL population. According to the experimental results, the frequency of male and female genotype in this RIL population was respectively 53% and 47%, suggesting good balance in population structure. A molecular genetic linkage map of rice was constructed by 141 markers based on a RIL population of 240 lines, with a total genetic distance of about 1 832.47 cM covering all 12 chromosomes, an average genetic distance between markers of 12.70 cM and a range of genetic distance be- tween markers of 0.43-36.11 cM, which is consistent with basic requirements of quantitative trait locus （QTL） mapping. Except for few markers on chromosomes 1 and 8, the order and location of markers is similar to the published sequences of Nipponbare. QTL analysis for the tiller angle was conducted with this RIL population of 240 lines, and results showed that three QTLs controlling tiller angle were detected on chromosome 8, 9 and 11, which were named qTA8, qTA9 and qTA11, with a contribution rate of 4.10%, 26.08% and 4.35%, respectively. To be specific, qTA9 contained Tiller Angle Controlling （TAC1） gene. The construction of this molecular genetic linkage map laid the foundation for genetic analysis and QTL mapping of various traits in the progeny of indica and japonica.展开更多
Non-heading Chinese cabbage （Brassica carnpestris ssp. chinensis Makino） is one of the most important vegetables in eastern China. A genetic linkage map was constructed using 127 doubled haploid （DH） lines, and th...Non-heading Chinese cabbage （Brassica carnpestris ssp. chinensis Makino） is one of the most important vegetables in eastern China. A genetic linkage map was constructed using 127 doubled haploid （DH） lines, and the DH population was derived from a commercial hybrid ＂Hanxiao＂ （lines SW-13 x L-118）. Out of the 614 polyrnorphic markers, 43.49% were not assigned to any of the linkage groups （LGs）. Chi-square tests showed that 42.67% markers were distorted from expected Mendelian segregation ratios, and the direction of distorted segregation was mainly toward the paternal parent L-118. After sequentially removing the markers that had an interval distance smaller than 1 cM from the upper marker, the overall quality of the linkage map was increased. Two hundred and sixty-eight molecular markers were mapped into 10 LGs, which were anchored to the corresponding chromosome of the B. rapa reference map based on com- mon simple sequence repeat （SSR） markers. The map covers 973.38 cM of the genome and the average interval distance between markers was 3.63 cM. The number of markers on each LG ranged from 18 （R08） to 64 （R07）, with an average interval distance within a single LG from 1.70 cM （R07） to 6.71 cM （R06）. Among these mapped markers, 169 were sequence-related amplified polymorphism （SRAP） molecular markers, 50 were SSR markers and 49 were random amplification polymorphic DNA （RAPD） markers. With further saturation to the LG9 the current map offers a genetic tool for loci analysis for important agronomic traits.展开更多
Molecular genetic maps of crop species can be used in a variety of ways in breeding and genomic research such as identification and mapping of genes and quantitative trait loci （QTLs） for morphological, physiologica...Molecular genetic maps of crop species can be used in a variety of ways in breeding and genomic research such as identification and mapping of genes and quantitative trait loci （QTLs） for morphological, physiological and economic traits of crop species. However, a comprehensive genetic linkage map for cultivated peanut has not yet been developed due to the extremely low frequency of DNA polymorphism in cultivated peanut. In this study, 142 recombinant inbred lines （RILs） derived from a cross between Yueyou 13 and Zhenzhuhei were used as mapping population in peanut （Arachis hypogaea L.）. A total 652 pairs of genomic-SSR primer and 392 pairs of EST-SSR primer were used to detect the polymorphisms between the two parents. 141 SSR primer pairs, 127 genomic-SSR and 14 EST-SSR ones, which can be used to detect polymorphisms between the two parents, were selected to analyze the RILs population. Thus, a linkage genetic map which consists of 131 SSR loci in 20 linkage groups, with a coverage of 679 cM and an average of 6.12 cM of inter-maker distance was constructed. The putative functions of 12 EST-SSR markers located on the map were analyzed. Eleven showed homology to gene sequences deposited in GenBank. This is the first report of construction of a comprehensive genetic map with SSR markers in peanut （Arachis hypogaea L.）. The map presented here will provide a genetic framework for mapping the qualitative and quantitative trait in peanut.展开更多
Simple sequence repeat(SSR) markers have been proved to be a very powerful tool for quantitative trait locus(QTL) mapping, marker-assisted selection and comparative genomics research in many crop species. However, a h...Simple sequence repeat(SSR) markers have been proved to be a very powerful tool for quantitative trait locus(QTL) mapping, marker-assisted selection and comparative genomics research in many crop species. However, a high-density SSR genetic linkage map is still lacking because there are only a few SSR markers available in sweet potato. In this study, a total of 2545 simple sequence repeat(SSR) primer pairs, including 1215 genomic SSR(gSSR) primer pairs and 1330 BES-SSR(bSSR) primer pairs designed from the genome sequence and BAC-end sequence of sweet potato, respectively, were screened with sweet potato cultivars Luoxushu 8 and Zhengshu 20 and their randomly sampled two F1 individuals and 571 of them generated polymorphic bands. The selected 571 polymorphic SSR primer pairs and 35 EST-based SSR(eSSR) primer pairs developed at our laboratory were used to genotype 240 F1 individuals derived from a cross between Luoxushu 8 and Zhengshu 20. A double pseudo-test-cross strategy was applied for linkage analysis. The Luoxushu 8 map included 90 linkage groups with 5057 SSR markers and covered 13,299.9 cM with a marker density of 2.6 cM, and the Zhengshu 20 map contained 90 linkage groups with 3009 SSR markers and covered 11,122.9 cM with a marker density of 3.7 cM. Fifteen homologous groups were identified in both parent maps. These are the first SSR linkage maps consisting of the complete 90 linkage groups and 15 homologous groups, which are consistent with the autohexaploid nature of sweetpotato, and are also the linkage maps with the highest SSR marker density reported to date.These results provide a basis for QTL mapping, marker-assisted breeding and comparative genomics research of sweet potato.展开更多
A molecular genetic map of Chinese cabbage was constructed with a 102 recombinant inbred (RI) population from a cross of two cultivated Chinese cabbage lines 177 and 276, using AFLP and RAPD markers. 352 markers inclu...A molecular genetic map of Chinese cabbage was constructed with a 102 recombinant inbred (RI) population from a cross of two cultivated Chinese cabbage lines 177 and 276, using AFLP and RAPD markers. 352 markers including 265 AFLP markers and 87 RAPD markers were integrated into 17 linkage groups. It covered a total of 2 665. 7 cM with an average interval of 7. 6 cM. AFLP marker is efficient for map construction while it easily forms clusters to cause big gaps in map. A total of 13.92 % abnormal segregation markers distributed in the map. The molecular genetic map is fundamental for gene localization, comparative genomics, and QTL mapping of important agronomic traits.展开更多
In this study,a linkage genetic map was constructed using a F2 population derived from a cross between a elite maize inbred,B73,and its progenitor,Teosinte（Z.mays ssp.mexicana）,through 205 simple sequence repeat（SS...In this study,a linkage genetic map was constructed using a F2 population derived from a cross between a elite maize inbred,B73,and its progenitor,Teosinte（Z.mays ssp.mexicana）,through 205 simple sequence repeat（SSR） markers and one morphological marker.By Mapmaker 3.0,polymorphic markers were clustered into 10 groups,covering 10 chromosomes of maizexteosinte,with a total length of 2 002.4 cM and an average interval of 9.7 cM.Genotyping errors were detected using R/QTL（LOD=2.0） in 109 markers referring to 176 individuals,distributed across all 10 chromosomes with a ratio 1.2%.Projected error loci were re-run and 304 out of the 460 were confirmed as errors and replaced.A new linkage map was constructed,in which markers maintained the same order but the total map length decreased to 1 947.8 cM,with an average interval of 9.4 cM between markers.In total,25.2%（P0.05） markers were identified to have segregation distortion,in which 34.6% deviated towards the pollination parent（B73）,30.8% deviated towards Teosinte,32.7% deviated towards heterozygote and 1.9% deviated towards both parents.This map was also compared with published maizexteosinte and maize IBM map.展开更多
The Chinese shrimp Penaeus (Fenneropaeneus) chinensis is an important species in marine fishery and aquaculture in China. A female Chinese shrimp Penaeus (Fenneropaeneus) chinensis was captured from west coast of the ...The Chinese shrimp Penaeus (Fenneropaeneus) chinensis is an important species in marine fishery and aquaculture in China. A female Chinese shrimp Penaeus (Fenneropaeneus) chinensis was captured from west coast of the Korean peninsula and mated with a "Yellow Sea No. 1" male to produce the first filial generation (F1) 100 F2 full-sib progeny from brother-sister crosses between F1 families was used for the mapping study. A genetic linkage map of the Chinese shrimp was constructed, based on 354 markers, including 300 amplified fragment length polymorphism (AFLP) markers, 42 microsatellite (SSR) markers, and 12 randomly amplified polymorphism (RAPD) markers. Forty-seven linkage groups (LGs) were identified. The total map length was 4 580.5 cM, with an average spacing of 11.3 cM, covering 75.8% of the estimated genome size. The construction of this genetic linkage map was part of a genetic breeding program. This linkage map will contribute to the discovery of genes and quantitative trait loci (QTLs) in Chinese shrimp.展开更多
The construction of high density genetic linkage map provides a powerful tool to detect and map quantitative trait loci(QTLs) controlling agronomically important traits. In this study, simple sequence repeat(SSR) mark...The construction of high density genetic linkage map provides a powerful tool to detect and map quantitative trait loci(QTLs) controlling agronomically important traits. In this study, simple sequence repeat(SSR) markers and Illumina 9K i Select single nucleotide polymorphism(SNP) genechip were employed to construct one genetic linkage map of common wheat(Triticum aestivum L.) using 191 recombinant inbred lines(RILs) derived from cross Yu 8679×Jing 411. This map included 1 901 SNP loci and 178 SSR loci, covering 1 659.9 c M and 1 000 marker bins, with an average interval distance of 1.66 c M. A, B and D genomes covered 719.1, 703.5 and 237.3 c M, with an average interval distance of 1.66, 1.45 and 2.9 c M, respectively. Notably, the genetic linkage map covered 20 chromosomes, with the exception of chromosome 5D. Bioinformatics analysis revealed that 1 754(92.27%) of 1 901 mapped SNP loci could be aligned to 1 215 distinct wheat unigenes, among which 1 184(97.4%) were located on o ne single chromosome, and the rest 31(2.6%) were located on 2 to 3 chromosomes. By performing in silico comparison, 214 chromosome deletion bin-mapped expressed sequence tags(ESTs), 1 043 Brachypodium genes and 1 033 rice genes were further added onto the genetic linkage map. This map not only integrated genetic and physical maps, SSR and SNP loci, respectively, but also provided the information of Brachypodium and rice genes corresponding to 1 754 SNP loci. Therefore, it will be a useful tool for comparative genomics analysis, fine mapping of QTL/gene controlling agronomically important traits and marker-assisted selection breeding in wheat.展开更多
A genetic linkage map of Pacific abalone(Haliotis discus hannai) was constructed using AFLP markers based on a two-way pseudo-testcross strategy in a full-sib family. With 33 primer combinations,a total of 455 markers...A genetic linkage map of Pacific abalone(Haliotis discus hannai) was constructed using AFLP markers based on a two-way pseudo-testcross strategy in a full-sib family. With 33 primer combinations,a total of 455 markers(225 from the female parent and 230 from the male parent) segregated in a 1:1 ratio,corresponding to DNA polymorphism:heterozygous in one parent and null in the other. The female framework map consisted of 174 markers distributed in 18 linkage groups,equivalent to the H. discus hannai haploid chromosome number,and spanning a total length of 2031.4 cM,with an average interval of 13.0 cM between adjacent markers. The male framework map consisted of 195 markers mapped on 19 linkage groups,spanning a total length of 2273.4 cM,with an average spacing of 12.9 cM between adjacent markers. The estimated coverage for the framework linkage maps was 81.2% for the female and 82.1% for the male,on the basis of two estimates of genome length. Fifty-two markers(11.4%) remained unlinked. The level of segregation distortion observed in this cross was 20.4%. These linkage maps will serve as a starting point for linkage studies in the Pacific abalone with potential application for marker-assisted selection in breeding programs.展开更多
Insufficient available phosphorus in soil has become an important limiting factor for the improvement of yield and quality in soybean. The mining of QTLs and candidate genes controlling soybean phosphorus utilization ...Insufficient available phosphorus in soil has become an important limiting factor for the improvement of yield and quality in soybean. The mining of QTLs and candidate genes controlling soybean phosphorus utilization related traits is a necessary strategy to solve this problem. In this study, 11 phosphorus utilization related traits of a natural population of 281 typical soybean germplasms and a recombinant inbred line(RIL) population of 270 lines were evaluated under different phosphorus conditions at two critical stages: the four-leaf stage as the seedling critical stage was designated as the Tstage, and the six-leaf stage as the flowering critical stage was designated as the Tstage. In total, 200 single nucleotide polymorphism(SNP) loci associated with phosphorus utilization related traits were identified in the natural population, including 91 detected at the Tstage, and 109 detected at the Tstage. Among these SNP loci, one SNP cluster(s715611375, ss715611377, ss715611379 and ss715611380) on Gm12 was shown to be significantly associated with plant height under the low phosphorus condition at the Tstage, and the elite haplotype showed significantly greater plant height than the others. Meanwhile, one pleiotropic SNP cluster(ss715606501, ss715606506 and ss715606543) on Gm10 was found to be significantly associated with the ratio of root/shoot, root and total dry weights under the low phosphorus condition at the Tstage, and the elite haplotype also presented significantly higher values for related characteristics under the phosphorus starvation condition. Furthermore, four co-associated SNP loci(ss715597964, ss715607012, ss715622173 and ss715602331) were identified under the low phosphorus condition at both the Tand Tstages, and 12 QTLs were found to be consistent with these genetic loci in the RIL population. More importantly, 14 candidate genes, including MYB transcription factor, purple acid phosphatase, sugar transporter and HSP20-like chaperones superfamily genes, etc., showed differential expression levels after low phosphorus treatment, and three of them were further verified by q RT-PCR. Thus, these genetic loci and candidate genes could be applied in markerassisted selection or map-based gene cloning for the genetic improvement of soybean phosphorus utilization.展开更多
Wheat tiller angle(TA)is an important agronomic trait that contributes to grain production by affecting plant architecture.It also plays a crucial role in high-yield wheat breeding.An association panel and a recombina...Wheat tiller angle(TA)is an important agronomic trait that contributes to grain production by affecting plant architecture.It also plays a crucial role in high-yield wheat breeding.An association panel and a recombinant inbred line(RIL)population were used to map quantitative trait loci(QTL)for TA.Results showed that 470 significant SNPs with 10.4%–28.8%phenotypic variance explained(PVE)were detected in four replicates by a genome-wide association study(GWAS).Haplotype analysis showed that the TA_Hap_4B1 locus on chromosome 4B was a major QTL to regulate wheat TA.Ten QTL were totally detected by linkage mapping with the RIL population,and QTA.hau-4B.1 identified in six environments with the PVE of 7.88%–18.82%was a major and stable QTL.A combined analysis demonstrated that both TA_Hap_4B1 and QTA.hau-4B.1 were co-located on the same region.Moreover,QTA.hau-4B.1 was confirmed by bulked segregant RNA-Seq(BSR-Seq)analysis.Phenotypic analysis showed that QTA.hau-4B.1was also closely related to yield traits.Furthermore,Traes CS4B02G049700 was considered as a candidate gene through analysis of gene sequence and expression.This study can be potentially used in cloning key genes modulating wheat tillering and provides valuable genetic resources for improvement of wheat plant architecture.展开更多
Genetic linkage maps are important for quantitative trait locus(QTL) and marker-assisted selection breeding. The wolfberry(Lycium spp.) is an important food and traditional medicine in China. However, few construction...Genetic linkage maps are important for quantitative trait locus(QTL) and marker-assisted selection breeding. The wolfberry(Lycium spp.) is an important food and traditional medicine in China. However, few construction genetic linkage maps have been reported because of the lack of genomic and genetic resources. In this study, a population of 89 F1 seedings was derived from a cross between two heterozygous parents, L. chinense var. potaninii ‘BF-01’(female)and L. barbarum var. auranticarpum ‘NH-01’(male), in order to construct a genetic linkage map using simple sequence repeat(SSR) and amplified fragment length polymorphism(AFLP) markers based on the double pseudo-test cross mapping strategy. The resulting genetic map consisted of 165 markers(74 AFLPs and 91 SSRs) distributed across 12 linkage groups and spanned a total length of 557.6 cM with an average distance of 3.38 cM between adjacent markers.The 12 linkage groups contained 3 to 21 markers and ranged in length from 8.6 to 58.3 cM. Twenty-nine segregated markers distributed in the map were mainly located on LG4 and LG9 linkage groups at P<0.05. This is the first linkage map of Lycium species using SSR and AFLP markers, which can serve as basis for improving genes and selective breeding of the genome assembly.展开更多
Owing to the limitation of a large genome size(~13 Gb),the genetic and gene mapping studies on faba bean(Vicia faba L.)are lagging far behind those for other legumes.In this study,we selected three purified faba bean ...Owing to the limitation of a large genome size(~13 Gb),the genetic and gene mapping studies on faba bean(Vicia faba L.)are lagging far behind those for other legumes.In this study,we selected three purified faba bean lines(Yundou 8137,H0003712,and H000572)as parents and constructed two F2 populations.These two F2 populations,namely 167 F2 plants in Pop1(Yundou 8137×H0003712)and 204 F2 plants in Pop2(H000572×Yundou 8137),were genotyped using a targeted next-generation sequencing(TNGS)genotyping platform,and two high-density single nucleotide polymorphisms(SNP)genetic linkage maps of faba bean were constructed.The map constructed from Pop1 contained 5103 SNPs with a length of 1333.31 cM and an average marker density of 0.26 cM.The map constructed from Pop2 contained 1904 SNPs with a greater length of 1610.61 cM.In these two F2 populations,QTL mapping identified 98 QTLs for 14 agronomic traits related to the flowers,pods,plant types and grains.The two maps were then merged into an integrated genetic linkage map containing 6895 SNPs,with a length of 3324.48 cM.These results not only lay the foundation for fine mapping and map-based cloning of related genes,but can also accelerate the molecular marker-assisted breeding of faba bean.展开更多
The development and deployment of diverse resistance sources in new wheat cultivars underpin the durable control of stripe rust.In the present study,two loci for adult plant resistance(APR),QYr SM155.1 and QYr SM155.2...The development and deployment of diverse resistance sources in new wheat cultivars underpin the durable control of stripe rust.In the present study,two loci for adult plant resistance(APR),QYr SM155.1 and QYr SM155.2,were identified in the Chinese wheat breeding line Shaanmai 155.QYr SM155.1 was mapped to a 3.0-c M interval between the single-nucleotide polymorphism(SNP)markers AX-109583610 and AX-110907562 on chromosome arm 2 BL.QYr SM155.2 was mapped to a 2.1-c M interval flanked by the SNP markers AX-110378556 and AX-86173526 on chromosome arm 7 AS.A genome-wide association study was used to identify markers associated with APR in a panel of 411 spring wheat lines.Thirteen and 11 SNPs were significantly associated with QYr SM155.1 and QYr SM155.2,respectively,corresponding to physical intervals of 653.75–655.52 Mb on 2 BL and 81.63–83.93 Mb on7 AS.To characterize the haplotype variation and the distribution of these QTL,haplotype analysis was performed based on these SNPs in an independent panel of 1101 worldwide wheat accessions.Three major haplotypes(2 B_h1,2 B_h2,and 2 B_h3)for QYr SM155.1 and four major haplotypes(7 A_h1,7 A_h2,7 A_h3,and 7 A_h4)for QYr SM155.2 were identified.Accessions individually harboring QYr SM155.1_h1 and QYr SM155.2_h1 haplotypes and their combination displayed resistance.Additional assays of 1306 current Chinese cultivars and breeding lines using markers flanking QYr SM155.1 and QYr SM155.2 indicated that the resistance haplotypes of the two QTL were present in respectively 1.45%and 14.16%of lines.Increasing resistance haplotype frequencies at these two loci using marker-assisted selection should benefit wheat production in China.展开更多
文摘CSB14Sh,which is isogenic for its recurrent parent TM-1 except for chromosome 14 short arm,was crossed with TM-1,and the F2 population was produced.A total of 3800 SSR primer pairs covering the whole genome were used to screen polymorphism among two parents,TM-1 and CSB14Sh,
基金funded in part by the National Natural Science Foundation (No.30670199,30870180 and 30770185)the Zhejiang Scientific and Technological Program (No.2008C12081)+1 种基金the Hangzhou Scientific and Technological Program (No.20080432T06)Qianjiang Scholar Program
文摘Dendrobium plants are used commonly as tonic herbs and health food in many Asian countries, especially in China. Here we report the genetic map construction of two Dendrobium species with a double pseudo-testcross strategy using random amplified polymorphic DNA （RAPD） and sequence-related amplified polymorphism （SRAP） markers. A F1 mapping population of 90 individuals was developed from a cross between D. officinale and D. hercoglossum. A total of 307 markers, including 209 RAPD and 98 SRAP, were identified and used for genetic linkage group （LG） analysis. The D. officinale linkage map consisted of 11 major linkage groups and 3 doublets, which covered 629.4 cM by a total of 62 markers with an average locus distance of 11.2 cM between two adjacent markers. The D. hercoglos- sum linkage map contained 112 markers mapped on 15 major and 4 minor linkage groups, spanning a total length of 1,304.6 cM with an average distance of I 1.6 cM between two adjacent markers. The maps constructed in this study covered 92.7% and 82.7% of the D. hercoglossum and D. officinale genomes respectively, providing an important basis for the mapping of horticultural and medicinal traits and for the application of marker-assisted selection in Dendrobium breeding program.
文摘Pacific bluefin tuna (Thunnus orientalis) is one of the most economically important species in the Percomorpha group of teleost fishes. Their migrations are extensive and depend upon continuous swimming at a high rate of speed throughout their life. The draft genome sequence of this species has been reported but remains highly fragmented. We constructed a Pacific bluefin tuna genetic linkage map using microsatellite markers developed on each of the scaffolds from the draft genome sequence to link these genome fragments and understand the genomic structure of species in Percomorpha. Of the 606 polymerase chain reaction microsatellite primer pairs tested, 473 were polymorphic in the mapping populations for the linkage analysis. We constructed sex-specific maps for 24 linkage groups consisting of 470 markers, which allowed us to place scaffolds that cumulatively represented 20.8% (153.8 Mb) of the sequenced genome onto the linkage groups. The distribution of orthologous genes on the chromosomes of tuna and four other teleost fish species suggested that the constitution of tuna chromosomes is closest to that of medaka. Both species have the 24 chromosomes of the ancestral teleost, including several chromosomal inversions. The integrated map developed in this study will be useful to construct a complete physical map to conduct comparative teleost genomics and genetic studies on economically useful traits in Pacific bluefin tuna.
基金the National‘948’Project(Grant No.2006-G55(B))the National High Technology Research and Development Program of China(Grant No.2006AA10A406)
文摘Fenneropaeneus chinensis is an important species in marine fishery resources and aquaculture in China.A genetic linkage map is essential for improving the efficiency of its breeding by marker-as-sisted selection and identifying commercially important genes.Linkage maps of F.chinensis were constructed with an F2 mapping population(110 progenies)using amplified fragment length polymor-phic(AFLP)marker in this study.Fifty-five AFLP primer combinations produced 532 AFLP markers fitting for map strategy in mapping family.The markers with 3:1 segregating ratios were analyzed using F2 intercross model for the common linkage map,while the markers with 1:1 ratio were analyzed using the pseudo-testcross strategy.The maps of male,female and common were constructed.The female map included 103 markers that formed 28 linkage groups,covering a total length of 1090 cM.All mark-ers were linked with the linkage groups.Segregation distortion was observed for 6 of 103 markers in the female map.The average distance between markers was 14.53 cM and ranged from 4.4 to 24.8 cM.The male map included 144 markers that formed 35 linkage groups.Ten markers remained unlinked in male map.Segregation distortion was observed for 7 of 144 markers in the male map.The total dis-tance of male map covered 1617 cM.The average distance between markers was 16.36 cM.The male map was 32.6%longer than the female map,which may reflect sex-specific recombination rates in Chinese shrimp.The common map was composed of 216 markers,including in 44 linkage groups covering a total distance of 1772.1 cM.Two markers remained unlinked.No distorted markers of 216 markers were shown in the common map.The distance between markers was 10.42 cM.An average estimated genome size for the Chinese shrimp was 2420 cM,which was consistent with the relative size of the Penaeid genome.The distribution of AFLP markers was relatively even in chromosomes of Chi-nese shrimp maps.The linkage analysis presented in this work provided some insight into the level of polymorphism and genetic variation of Chinese shrimp.
基金the grants from the Project of the Changjiang Scholars andInnovative Research Team in University (IRT0432)the 111 Project(B08025)the Ministry of Education of China
文摘This study introduces the construction of the first intraspecific genetic linkage map of the A-genome diploid cotton with newly developed simple sequence repeat （SSR） markers using 189 F2 plants derived from the cross of two Asiatic cotton cultivars （Gossypium arboreum L.） Jianglingzhongmlan x Zhejiangxiaoshanl（ishu. Polymorphisms between the two parents were detected using 6 092 pairs of SSR primers. Two-hundred and sixty-eight pairs of SSR primers with better polymorphisms were picked out to analyze the F2 population. In total, 320 polymorphic bands were generated and used to construct a linkage map with JoinMap3.0. Two-hundred and sixty-seven loci, including three phenotypic traits were mapped at a logarithms of odds ratio （LOD）≥ 3.0 on 13 linkage groups. The total length of the map was 2 508.71 cM, and the average distance between adjacent markers was 9.40 cM. Chromosome assignments were according to the association of linkages with our backbone tetraploid specific map using the 89 similar SSR loci. Comparisons among the 13 suites of orthologous linkage groups revealed that the A-genome chromosomes are largely collinear with the At and Dt sub- genome chromosomes. Chromosomes associated with inversions suggested that allopolyploidization was accompanied by homologous chromosomal rearrangement. The inter-chromosomal duplicated loci supply molecular evidence that the A-genome diploid Asiatic cotton is paleopolyploid.
文摘In this study, we reported the repaid construction of a molecular marker linkage map of rice (Oryza sativa L.). An F-2 population from the cross between Annong S-1 and Nanjing 11 was used to construct a genetic linkage map of rice. Total of 142 newly screened AFLP markers and 30 anchor markers (25 SSR markers and 5 RFLP markers) were mapped on the 12 chromosomes covering 1537.4 cM of rice genome. The average interval between these markers was 9.0 cM. The total work which usually was finished in more than one year was finished within only 3 months by one person. This is the first plant AFLP map developed in China. A new thermosensitive genic male sterile gene in rice, tms5, was Egged and mapped onto chromosome 2 during the development of the linkage map.
基金Supported by Fund for Agricultural Science and Technology Innovation in Jiangsu Province(CX[12]1003)Science Technology Pillar Program in Jiangsu Province(BK2013303)Supper Rice Breeding and Demonstration Program of the Ministry ofAgriculture~~
文摘In this study, an RIL （recombinant inbred line） population containing 240 lines was developed by single seed descent method （SSD） based on a parent com- bination of small-grain indica cultivar Kasalath and large-grain japanica cultivar TD70 with significant differences in plant type traits, to construct the molecular genetic linkage map. Totally 838 SSR （Simple Sequence Repeat） markers were used for polymorphism screening between parents, 302 SSR markers with polymorphism were detected, with a frequency of 36.04%; 141 SSR markers with clear amplified bands and uniform distribution in the genome were finally used for genotype analysis of the RIL population. According to the experimental results, the frequency of male and female genotype in this RIL population was respectively 53% and 47%, suggesting good balance in population structure. A molecular genetic linkage map of rice was constructed by 141 markers based on a RIL population of 240 lines, with a total genetic distance of about 1 832.47 cM covering all 12 chromosomes, an average genetic distance between markers of 12.70 cM and a range of genetic distance be- tween markers of 0.43-36.11 cM, which is consistent with basic requirements of quantitative trait locus （QTL） mapping. Except for few markers on chromosomes 1 and 8, the order and location of markers is similar to the published sequences of Nipponbare. QTL analysis for the tiller angle was conducted with this RIL population of 240 lines, and results showed that three QTLs controlling tiller angle were detected on chromosome 8, 9 and 11, which were named qTA8, qTA9 and qTA11, with a contribution rate of 4.10%, 26.08% and 4.35%, respectively. To be specific, qTA9 contained Tiller Angle Controlling （TAC1） gene. The construction of this molecular genetic linkage map laid the foundation for genetic analysis and QTL mapping of various traits in the progeny of indica and japonica.
基金supported by the National High-tech R&D Program (863 Program) (No.2006AA10Z1C9)the National Natural Science Foundation (No.30671420)
文摘Non-heading Chinese cabbage （Brassica carnpestris ssp. chinensis Makino） is one of the most important vegetables in eastern China. A genetic linkage map was constructed using 127 doubled haploid （DH） lines, and the DH population was derived from a commercial hybrid ＂Hanxiao＂ （lines SW-13 x L-118）. Out of the 614 polyrnorphic markers, 43.49% were not assigned to any of the linkage groups （LGs）. Chi-square tests showed that 42.67% markers were distorted from expected Mendelian segregation ratios, and the direction of distorted segregation was mainly toward the paternal parent L-118. After sequentially removing the markers that had an interval distance smaller than 1 cM from the upper marker, the overall quality of the linkage map was increased. Two hundred and sixty-eight molecular markers were mapped into 10 LGs, which were anchored to the corresponding chromosome of the B. rapa reference map based on com- mon simple sequence repeat （SSR） markers. The map covers 973.38 cM of the genome and the average interval distance between markers was 3.63 cM. The number of markers on each LG ranged from 18 （R08） to 64 （R07）, with an average interval distance within a single LG from 1.70 cM （R07） to 6.71 cM （R06）. Among these mapped markers, 169 were sequence-related amplified polymorphism （SRAP） molecular markers, 50 were SSR markers and 49 were random amplification polymorphic DNA （RAPD） markers. With further saturation to the LG9 the current map offers a genetic tool for loci analysis for important agronomic traits.
基金the National Natural Science Foundation of China(30571179)National 863 Program of China(2006AA0Z156,2006AA10A115)
文摘Molecular genetic maps of crop species can be used in a variety of ways in breeding and genomic research such as identification and mapping of genes and quantitative trait loci （QTLs） for morphological, physiological and economic traits of crop species. However, a comprehensive genetic linkage map for cultivated peanut has not yet been developed due to the extremely low frequency of DNA polymorphism in cultivated peanut. In this study, 142 recombinant inbred lines （RILs） derived from a cross between Yueyou 13 and Zhenzhuhei were used as mapping population in peanut （Arachis hypogaea L.）. A total 652 pairs of genomic-SSR primer and 392 pairs of EST-SSR primer were used to detect the polymorphisms between the two parents. 141 SSR primer pairs, 127 genomic-SSR and 14 EST-SSR ones, which can be used to detect polymorphisms between the two parents, were selected to analyze the RILs population. Thus, a linkage genetic map which consists of 131 SSR loci in 20 linkage groups, with a coverage of 679 cM and an average of 6.12 cM of inter-maker distance was constructed. The putative functions of 12 EST-SSR markers located on the map were analyzed. Eleven showed homology to gene sequences deposited in GenBank. This is the first report of construction of a comprehensive genetic map with SSR markers in peanut （Arachis hypogaea L.）. The map presented here will provide a genetic framework for mapping the qualitative and quantitative trait in peanut.
基金supported by the National Key Research and Development Program of China (2018YFD1000706/2018YFD1000700)China Agriculture Research System (CARS-10, Sweet potato)。
文摘Simple sequence repeat(SSR) markers have been proved to be a very powerful tool for quantitative trait locus(QTL) mapping, marker-assisted selection and comparative genomics research in many crop species. However, a high-density SSR genetic linkage map is still lacking because there are only a few SSR markers available in sweet potato. In this study, a total of 2545 simple sequence repeat(SSR) primer pairs, including 1215 genomic SSR(gSSR) primer pairs and 1330 BES-SSR(bSSR) primer pairs designed from the genome sequence and BAC-end sequence of sweet potato, respectively, were screened with sweet potato cultivars Luoxushu 8 and Zhengshu 20 and their randomly sampled two F1 individuals and 571 of them generated polymorphic bands. The selected 571 polymorphic SSR primer pairs and 35 EST-based SSR(eSSR) primer pairs developed at our laboratory were used to genotype 240 F1 individuals derived from a cross between Luoxushu 8 and Zhengshu 20. A double pseudo-test-cross strategy was applied for linkage analysis. The Luoxushu 8 map included 90 linkage groups with 5057 SSR markers and covered 13,299.9 cM with a marker density of 2.6 cM, and the Zhengshu 20 map contained 90 linkage groups with 3009 SSR markers and covered 11,122.9 cM with a marker density of 3.7 cM. Fifteen homologous groups were identified in both parent maps. These are the first SSR linkage maps consisting of the complete 90 linkage groups and 15 homologous groups, which are consistent with the autohexaploid nature of sweetpotato, and are also the linkage maps with the highest SSR marker density reported to date.These results provide a basis for QTL mapping, marker-assisted breeding and comparative genomics research of sweet potato.
文摘A molecular genetic map of Chinese cabbage was constructed with a 102 recombinant inbred (RI) population from a cross of two cultivated Chinese cabbage lines 177 and 276, using AFLP and RAPD markers. 352 markers including 265 AFLP markers and 87 RAPD markers were integrated into 17 linkage groups. It covered a total of 2 665. 7 cM with an average interval of 7. 6 cM. AFLP marker is efficient for map construction while it easily forms clusters to cause big gaps in map. A total of 13.92 % abnormal segregation markers distributed in the map. The molecular genetic map is fundamental for gene localization, comparative genomics, and QTL mapping of important agronomic traits.
基金supported by the National High-Tech R&D Program of China(2006AA10Z183,2006AA10A107)
文摘In this study,a linkage genetic map was constructed using a F2 population derived from a cross between a elite maize inbred,B73,and its progenitor,Teosinte（Z.mays ssp.mexicana）,through 205 simple sequence repeat（SSR） markers and one morphological marker.By Mapmaker 3.0,polymorphic markers were clustered into 10 groups,covering 10 chromosomes of maizexteosinte,with a total length of 2 002.4 cM and an average interval of 9.7 cM.Genotyping errors were detected using R/QTL（LOD=2.0） in 109 markers referring to 176 individuals,distributed across all 10 chromosomes with a ratio 1.2%.Projected error loci were re-run and 304 out of the 460 were confirmed as errors and replaced.A new linkage map was constructed,in which markers maintained the same order but the total map length decreased to 1 947.8 cM,with an average interval of 9.4 cM between markers.In total,25.2%（P0.05） markers were identified to have segregation distortion,in which 34.6% deviated towards the pollination parent（B73）,30.8% deviated towards Teosinte,32.7% deviated towards heterozygote and 1.9% deviated towards both parents.This map was also compared with published maizexteosinte and maize IBM map.
基金Supported by National Key Technology R&D Program(No.2006BAD01A13)National Special Research Fund for Nonprofit Sector(Agriculture)(No.nyhyzx07-042)the Earmarked Fund for Modern Agro-industry Technology Research System(No.nycytx-46)
文摘The Chinese shrimp Penaeus (Fenneropaeneus) chinensis is an important species in marine fishery and aquaculture in China. A female Chinese shrimp Penaeus (Fenneropaeneus) chinensis was captured from west coast of the Korean peninsula and mated with a "Yellow Sea No. 1" male to produce the first filial generation (F1) 100 F2 full-sib progeny from brother-sister crosses between F1 families was used for the mapping study. A genetic linkage map of the Chinese shrimp was constructed, based on 354 markers, including 300 amplified fragment length polymorphism (AFLP) markers, 42 microsatellite (SSR) markers, and 12 randomly amplified polymorphism (RAPD) markers. Forty-seven linkage groups (LGs) were identified. The total map length was 4 580.5 cM, with an average spacing of 11.3 cM, covering 75.8% of the estimated genome size. The construction of this genetic linkage map was part of a genetic breeding program. This linkage map will contribute to the discovery of genes and quantitative trait loci (QTLs) in Chinese shrimp.
基金financially supported by the National Natural Science Foundation of China (91435204, 31271710)the National 863 Program of China (2012AA10A309)the Program of Conservation and Sustainable Utilization of Wild Relatives of Crops by the Ministry of Agriculture of China (201003021)
文摘The construction of high density genetic linkage map provides a powerful tool to detect and map quantitative trait loci(QTLs) controlling agronomically important traits. In this study, simple sequence repeat(SSR) markers and Illumina 9K i Select single nucleotide polymorphism(SNP) genechip were employed to construct one genetic linkage map of common wheat(Triticum aestivum L.) using 191 recombinant inbred lines(RILs) derived from cross Yu 8679×Jing 411. This map included 1 901 SNP loci and 178 SSR loci, covering 1 659.9 c M and 1 000 marker bins, with an average interval distance of 1.66 c M. A, B and D genomes covered 719.1, 703.5 and 237.3 c M, with an average interval distance of 1.66, 1.45 and 2.9 c M, respectively. Notably, the genetic linkage map covered 20 chromosomes, with the exception of chromosome 5D. Bioinformatics analysis revealed that 1 754(92.27%) of 1 901 mapped SNP loci could be aligned to 1 215 distinct wheat unigenes, among which 1 184(97.4%) were located on o ne single chromosome, and the rest 31(2.6%) were located on 2 to 3 chromosomes. By performing in silico comparison, 214 chromosome deletion bin-mapped expressed sequence tags(ESTs), 1 043 Brachypodium genes and 1 033 rice genes were further added onto the genetic linkage map. This map not only integrated genetic and physical maps, SSR and SNP loci, respectively, but also provided the information of Brachypodium and rice genes corresponding to 1 754 SNP loci. Therefore, it will be a useful tool for comparative genomics analysis, fine mapping of QTL/gene controlling agronomically important traits and marker-assisted selection breeding in wheat.
基金The study was supported by grants from the Chinese Ministry of Education(NCET-04-0640)the National Natural Science Foundation of China(No.30571442).
文摘A genetic linkage map of Pacific abalone(Haliotis discus hannai) was constructed using AFLP markers based on a two-way pseudo-testcross strategy in a full-sib family. With 33 primer combinations,a total of 455 markers(225 from the female parent and 230 from the male parent) segregated in a 1:1 ratio,corresponding to DNA polymorphism:heterozygous in one parent and null in the other. The female framework map consisted of 174 markers distributed in 18 linkage groups,equivalent to the H. discus hannai haploid chromosome number,and spanning a total length of 2031.4 cM,with an average interval of 13.0 cM between adjacent markers. The male framework map consisted of 195 markers mapped on 19 linkage groups,spanning a total length of 2273.4 cM,with an average spacing of 12.9 cM between adjacent markers. The estimated coverage for the framework linkage maps was 81.2% for the female and 82.1% for the male,on the basis of two estimates of genome length. Fifty-two markers(11.4%) remained unlinked. The level of segregation distortion observed in this cross was 20.4%. These linkage maps will serve as a starting point for linkage studies in the Pacific abalone with potential application for marker-assisted selection in breeding programs.
基金funded by the Project of Hebei Province Science and Technology Support Program,China(17927670H and 16227516D-1)。
文摘Insufficient available phosphorus in soil has become an important limiting factor for the improvement of yield and quality in soybean. The mining of QTLs and candidate genes controlling soybean phosphorus utilization related traits is a necessary strategy to solve this problem. In this study, 11 phosphorus utilization related traits of a natural population of 281 typical soybean germplasms and a recombinant inbred line(RIL) population of 270 lines were evaluated under different phosphorus conditions at two critical stages: the four-leaf stage as the seedling critical stage was designated as the Tstage, and the six-leaf stage as the flowering critical stage was designated as the Tstage. In total, 200 single nucleotide polymorphism(SNP) loci associated with phosphorus utilization related traits were identified in the natural population, including 91 detected at the Tstage, and 109 detected at the Tstage. Among these SNP loci, one SNP cluster(s715611375, ss715611377, ss715611379 and ss715611380) on Gm12 was shown to be significantly associated with plant height under the low phosphorus condition at the Tstage, and the elite haplotype showed significantly greater plant height than the others. Meanwhile, one pleiotropic SNP cluster(ss715606501, ss715606506 and ss715606543) on Gm10 was found to be significantly associated with the ratio of root/shoot, root and total dry weights under the low phosphorus condition at the Tstage, and the elite haplotype also presented significantly higher values for related characteristics under the phosphorus starvation condition. Furthermore, four co-associated SNP loci(ss715597964, ss715607012, ss715622173 and ss715602331) were identified under the low phosphorus condition at both the Tand Tstages, and 12 QTLs were found to be consistent with these genetic loci in the RIL population. More importantly, 14 candidate genes, including MYB transcription factor, purple acid phosphatase, sugar transporter and HSP20-like chaperones superfamily genes, etc., showed differential expression levels after low phosphorus treatment, and three of them were further verified by q RT-PCR. Thus, these genetic loci and candidate genes could be applied in markerassisted selection or map-based gene cloning for the genetic improvement of soybean phosphorus utilization.
基金funded by the National Natural Science Foundation of China(31971947 and 32072057)Henan Major Science and Technology Projects(201300110800,201300111600)Key Scientific and Technological Project of Henan Province(222102110026)。
文摘Wheat tiller angle(TA)is an important agronomic trait that contributes to grain production by affecting plant architecture.It also plays a crucial role in high-yield wheat breeding.An association panel and a recombinant inbred line(RIL)population were used to map quantitative trait loci(QTL)for TA.Results showed that 470 significant SNPs with 10.4%–28.8%phenotypic variance explained(PVE)were detected in four replicates by a genome-wide association study(GWAS).Haplotype analysis showed that the TA_Hap_4B1 locus on chromosome 4B was a major QTL to regulate wheat TA.Ten QTL were totally detected by linkage mapping with the RIL population,and QTA.hau-4B.1 identified in six environments with the PVE of 7.88%–18.82%was a major and stable QTL.A combined analysis demonstrated that both TA_Hap_4B1 and QTA.hau-4B.1 were co-located on the same region.Moreover,QTA.hau-4B.1 was confirmed by bulked segregant RNA-Seq(BSR-Seq)analysis.Phenotypic analysis showed that QTA.hau-4B.1was also closely related to yield traits.Furthermore,Traes CS4B02G049700 was considered as a candidate gene through analysis of gene sequence and expression.This study can be potentially used in cloning key genes modulating wheat tillering and provides valuable genetic resources for improvement of wheat plant architecture.
基金financially supported by the National Natural Science Foundation of China(31760218)the Third Batch of Ningxia Youth Talents Supporting Program(TJGC2018022)the Whole Industry Chain Innovation Demonstration Project of Ningxia Academy of Agriculture and Forestry Sciences,China(ERS-2016-0405)。
文摘Genetic linkage maps are important for quantitative trait locus(QTL) and marker-assisted selection breeding. The wolfberry(Lycium spp.) is an important food and traditional medicine in China. However, few construction genetic linkage maps have been reported because of the lack of genomic and genetic resources. In this study, a population of 89 F1 seedings was derived from a cross between two heterozygous parents, L. chinense var. potaninii ‘BF-01’(female)and L. barbarum var. auranticarpum ‘NH-01’(male), in order to construct a genetic linkage map using simple sequence repeat(SSR) and amplified fragment length polymorphism(AFLP) markers based on the double pseudo-test cross mapping strategy. The resulting genetic map consisted of 165 markers(74 AFLPs and 91 SSRs) distributed across 12 linkage groups and spanned a total length of 557.6 cM with an average distance of 3.38 cM between adjacent markers.The 12 linkage groups contained 3 to 21 markers and ranged in length from 8.6 to 58.3 cM. Twenty-nine segregated markers distributed in the map were mainly located on LG4 and LG9 linkage groups at P<0.05. This is the first linkage map of Lycium species using SSR and AFLP markers, which can serve as basis for improving genes and selective breeding of the genome assembly.
基金supported by the National Key R&D Program of China(2019YFD1001300 and 2019YFD1001303)the Construction of Molecular Database of Faba Bean and Pea and Identification of Maize Germplasm Project,Ministry of Agriculture and Rural Affairs,China(19200030)+3 种基金the Yunnan Key R&D Program,China(202202AE090003)the earmarked fund for China Agriculture Research System(CARS-08)the Crop Germplasm Resources Protection(2130135)the Major Agricultural Science and Technology Program of Chinese Academy of Agricultural Sciences(CAAS-XTCX20190025)。
文摘Owing to the limitation of a large genome size(~13 Gb),the genetic and gene mapping studies on faba bean(Vicia faba L.)are lagging far behind those for other legumes.In this study,we selected three purified faba bean lines(Yundou 8137,H0003712,and H000572)as parents and constructed two F2 populations.These two F2 populations,namely 167 F2 plants in Pop1(Yundou 8137×H0003712)and 204 F2 plants in Pop2(H000572×Yundou 8137),were genotyped using a targeted next-generation sequencing(TNGS)genotyping platform,and two high-density single nucleotide polymorphisms(SNP)genetic linkage maps of faba bean were constructed.The map constructed from Pop1 contained 5103 SNPs with a length of 1333.31 cM and an average marker density of 0.26 cM.The map constructed from Pop2 contained 1904 SNPs with a greater length of 1610.61 cM.In these two F2 populations,QTL mapping identified 98 QTLs for 14 agronomic traits related to the flowers,pods,plant types and grains.The two maps were then merged into an integrated genetic linkage map containing 6895 SNPs,with a length of 3324.48 cM.These results not only lay the foundation for fine mapping and map-based cloning of related genes,but can also accelerate the molecular marker-assisted breeding of faba bean.
基金financially the National Natural Science Foundation of China(31871611 and31971890)the National Science Foundation for Young Scientistsin China(31901494 and 31901869)+1 种基金International Cooperation and Exchange of the National Natural Science Foundation of China(31961143019)the Integrated Extension Project of Agricultural Science and Technology Innovation in Shaanxi Province(NYKJ-2021-YL(XN)15)。
文摘The development and deployment of diverse resistance sources in new wheat cultivars underpin the durable control of stripe rust.In the present study,two loci for adult plant resistance(APR),QYr SM155.1 and QYr SM155.2,were identified in the Chinese wheat breeding line Shaanmai 155.QYr SM155.1 was mapped to a 3.0-c M interval between the single-nucleotide polymorphism(SNP)markers AX-109583610 and AX-110907562 on chromosome arm 2 BL.QYr SM155.2 was mapped to a 2.1-c M interval flanked by the SNP markers AX-110378556 and AX-86173526 on chromosome arm 7 AS.A genome-wide association study was used to identify markers associated with APR in a panel of 411 spring wheat lines.Thirteen and 11 SNPs were significantly associated with QYr SM155.1 and QYr SM155.2,respectively,corresponding to physical intervals of 653.75–655.52 Mb on 2 BL and 81.63–83.93 Mb on7 AS.To characterize the haplotype variation and the distribution of these QTL,haplotype analysis was performed based on these SNPs in an independent panel of 1101 worldwide wheat accessions.Three major haplotypes(2 B_h1,2 B_h2,and 2 B_h3)for QYr SM155.1 and four major haplotypes(7 A_h1,7 A_h2,7 A_h3,and 7 A_h4)for QYr SM155.2 were identified.Accessions individually harboring QYr SM155.1_h1 and QYr SM155.2_h1 haplotypes and their combination displayed resistance.Additional assays of 1306 current Chinese cultivars and breeding lines using markers flanking QYr SM155.1 and QYr SM155.2 indicated that the resistance haplotypes of the two QTL were present in respectively 1.45%and 14.16%of lines.Increasing resistance haplotype frequencies at these two loci using marker-assisted selection should benefit wheat production in China.
