Stemphylium leaf spot, caused by Stemphylium botryosum f. sp. spinacia, is an important fungal disease of spinach (Spinacia oleracea L.). The aim of this study was to conduct association analysis to identify single nu...Stemphylium leaf spot, caused by Stemphylium botryosum f. sp. spinacia, is an important fungal disease of spinach (Spinacia oleracea L.). The aim of this study was to conduct association analysis to identify single nucleotide polymorphism (SNP) markers associated with Stemphylium leaf spot resistance in spinach. A total of 273 spinach genotypes, including 265 accessions from the USDA spinach germplasm collection and eight commercial cultivars, were used in this study. Phenotyping for Stemphylium leaf spot resistance was evaluated in greenhouse;genotyping was conducted using genotyping by sequencing (GBS) with 787 SNPs;and single marker regression, general linear model, and mixed linear model were used for association analysis of Stemphylium leaf spot. Spinach genotypes showed a skewed distribution for Stemphylium leaf spot resistance, with a range from 0.2% to 23.5% disease severity, suggesting that Stemphylium leaf spot resistance in spinach is a complex, quantitative trait. Association analysis indicated that eight SNP markers, AYZV02052595_115, AYZV02052595_122, AYZV02057770_10404, AYZV02129827_205, AYZV0-2152692_182, AYZV02180153_337, AYZV02225889_197, and AYZV02258563_213 were strongly associated with Stemphylium leaf spot resistance, with a Log of the Odds (LOD) of 2.5 or above. The SNP markers may provide a tool to select for Stemphylium leaf spot resistance in spinach breeding programs through marker-assisted selection (MAS).展开更多
采用基因分型测序(GBS)技术对堇叶紫金牛[Ardisia violacea(T.Suzuki)W.Z.Fang et K.Yao]13个野生居群77份样本进行单核苷酸多态性(SNP)位点挖掘,在此基础上,对13个居群77份样本的遗传多样性、系统发育树、亲缘关系等进行分析。结果表明...采用基因分型测序(GBS)技术对堇叶紫金牛[Ardisia violacea(T.Suzuki)W.Z.Fang et K.Yao]13个野生居群77份样本进行单核苷酸多态性(SNP)位点挖掘,在此基础上,对13个居群77份样本的遗传多样性、系统发育树、亲缘关系等进行分析。结果表明:共获得有效SNP位点246307个,每份样本检测到SNP位点1154~3789个。13个居群的观测杂合度为0.1569~0.4289,多态信息含量为0.0785~0.3244,核苷酸多样性指数为0.0002~0.0007,Tajima’s D值为0.2247~1.0936,Shannon’s多样性指数为0.2175~0.6649,表明堇叶紫金牛整体遗传多样性水平偏低。系统发育树、主成分分析和遗传结构分析结果显示77份样本可划分为6组。亲缘关系分析结果显示:居群内个体间的亲缘关系整体较近;居群间的亲缘关系与地理距离有一定的相关性。遗传分化和基因流分析结果显示:大部分居群间存在较高的遗传分化,各居群间存在一定程度的基因交流。综上所述,堇叶紫金牛13个居群的整体遗传多样性偏低,但居群间的遗传分化程度较高,这与居群间的地理距离较远、基因交流较少有关。建议优先保护安徽省黄山市祁门县牯牛降、浙江省舟山市定海区蔡家岙和浙江省宁波市象山县屠家园村3个遗传多样性较高的居群,并开展相关繁育工作以维持和扩大居群数量。展开更多
Genetic variation developed in plant breeding programs is fundamental to creating new combinations that result in cultivars with enhanced characteristics. Over the years, tomato (Solanum lycopersicum) breeding program...Genetic variation developed in plant breeding programs is fundamental to creating new combinations that result in cultivars with enhanced characteristics. Over the years, tomato (Solanum lycopersicum) breeding programs associated with the Texas A&M University system have developed morphologically diverse lines of tomatoes selected for heat tolerance, fruit quality, and disease resistance to adapt them to Texas growing conditions. Here we explored the intraspecific genetic variations of 322 cultivated tomato genotypes, including 300 breeding lines developed by three Texas A&M breeding programs, as an initial step toward implementing molecular breeding approaches. Genotyping by sequencing using low coverage whole-genome sequencing (SkimGBS) identified 10,236 high-quality single-nucleotide polymorphisms (SNPs) that were used to assess genetic diversity, population structure, and phylogenetic relationship between genotypes and breeding programs. Model-based population structure analysis, phylogenetic tree construction, and principal component analysis indicated that the genotypes were grouped into two main clusters. Genetic distance analysis revealed greater genetic diversity? among the products of the three breeding programs. The germplasm developed at Texas A&M programs at Weslaco, College Station, and by Dr. Paul Leeper exhibited genetic diversity ranges of 0.175 - 0.434, 0.099 - 0.392, and 0.183 - 0.347, respectively, suggesting that there is enough variation within and between the lines from the three programs to perform selection for cultivar development. The SNPs identified here could be used to develop molecular tools for selecting various traits of interest and to select parents for future tomato breeding.展开更多
Maize（Zea mays） root system architecture（RSA）mediates the key functions of plant anchorage and acquisition of nutrients and water. In this study,a set of 204 recombinant inbred lines（RILs） was derived from the w...Maize（Zea mays） root system architecture（RSA）mediates the key functions of plant anchorage and acquisition of nutrients and water. In this study,a set of 204 recombinant inbred lines（RILs） was derived from the widely adapted Chinese hybrid ZD958（Zheng58 Chang7-2）,genotyped by sequencing（GBS） and evaluated as seedlings for 24 RSA related traits divided into primary,seminal and total root classes. Signi ficant differences between the means of the parental phenotypes were detected for 18 traits,and extensive transgressive segregation in the RIL population was observed for all traits. Moderate to strong relationships among the traits were discovered. A total of 62 quantitative trait loci（QTL） were identi fied that individually explained from1.6% to 11.6%（total root dry weight/total seedling shoot dry weight） of the phenotypic variation. Eighteen,24 and 20 QTL were identi fied for primary,seminal and total root classes of traits,respectively. We found hotspots of 5,3,4 and 12 QTL in maize chromosome bins 2.06,3.02-03,9.02-04,and 9.05-06,respectively,implicating the presence of root gene clusters or pleiotropic effects. These results characterized the phenotypic variation and genetic architecture of seedling RSA in a population derived from a successful maize hybrid.展开更多
There is a rapidly rising trend in the development and application of molecular marker assays for gene map- ping and discovery in field crops and trees. Thus far, more than 50 SNP arrays and 15 different types of geno...There is a rapidly rising trend in the development and application of molecular marker assays for gene map- ping and discovery in field crops and trees. Thus far, more than 50 SNP arrays and 15 different types of genotyping-by-sequencing （GBS） platforms have been developed in over 25 crop species and perennial trees. However, much less effort has been made on developing ultra-high-throughput and cost-effective genotyping platforms for applied breeding programs. In this review, we discuss the scientific bottlenecks in existing SNP arrays and GBS technologies and the strategies to develop targeted platforms for crop mo- lecular breeding. We propose that future practical breeding platforms should adopt automated genotyping technologies, either array or sequencing based, target functional polymorphisms underpinning economic traits, and provide desirable prediction accuracy for quantitative traits, with universal applications under wide genetic backgrounds in crops. The development of such platforms faces serious challenges at both the technological level due to cost ineffectiveness, and the knowledge level due to large genotype- phenotype gaps in crop plants. It is expected that such genotyping platforms will be achieved in the next ten years in major crops in consideration of （a） rapid development in gene discovery of important traits, （b） deepened understanding of quantitative traits through new analytical models and population designs, （c） integration of multi-layer -omics data leading to identification of genes and pathways responsible for important breeding traits, and （d） improvement in cost effectiveness of large-scale genotyping. Crop breeding chips and genotyping platforms will provide unprecedented opportunities to accelerate the development of cultivars with desired yield potential, quality, and enhanced adaptation to mitigate the effects of climate change.展开更多
[目的]探究云上黑山羊主配公羊的亲缘关系及近交系数,构建肉羊高效联合育种体系,提升云上黑山羊生产性能和可持续发展力。[方法]采用简化基因组测序(genotyping-by-sequencing,GBS)技术对云上黑山羊5个核心育种场(XD、ZY、ML、SB、TJ)的...[目的]探究云上黑山羊主配公羊的亲缘关系及近交系数,构建肉羊高效联合育种体系,提升云上黑山羊生产性能和可持续发展力。[方法]采用简化基因组测序(genotyping-by-sequencing,GBS)技术对云上黑山羊5个核心育种场(XD、ZY、ML、SB、TJ)的100只主配公羊进行测序,并使用BWA、SAMTOOLS、PLINK v 1.90、Gmatrix v 2、Mega X等软件进行质控后高质量单核苷酸多态性(single nucleotide polymorphism,SNP)位点鉴定、主成分分析(PCA)、状态同源距离矩阵(identical by state,IBS)和G矩阵构建、群体进化树分析、亲缘系数计算及近交系数估计。[结果]GBS质控后共获得215926个高质量SNPs位点;共检测到8692条连续性纯合片段(runs of homozygosity,ROH),长度在10.59~591.23 Mb之间,平均长度245.74 Mb。云上黑山羊主配公羊群体平均IBS遗传距离为0.118±0.011,亲缘关系G矩阵结果与IBS距离矩阵结果一致。结合群体进化树和亲缘关系分析,100只云上黑山羊被分为三大支和28个家系,其中家系2、11、13、14、16、17、18、20、23、24、25仅有1只公羊,XD、ZY、ML、SB、TJ核心育种场分别有18、10、8、5和8个家系;基于ROH的群体平均基因组近交系数为0.099641,29只公羊的近交系数<0.0625,39只公羊的近交系数在0.0625~0.125之间,32只公羊近交系数>0.125,存在较大的近交累积。[结论]100只云上黑山羊主配公羊被分为28个家系,其中11个家系仅有1只公羊,应加强繁育防止其血统的流失,配种方案制定中应关注近交系数>0.125的个体,防止近交衰退,同时根据不同的育种目标合理进行种公羊的交换。展开更多
Hordeum bulbosum L., a wild relative of barley （Hordeum vulgare L.）, has been considered as a valuable source of genetic diversity for barley improvement. Since the 1990s, a considerable number of barley/H, bulbosum...Hordeum bulbosum L., a wild relative of barley （Hordeum vulgare L.）, has been considered as a valuable source of genetic diversity for barley improvement. Since the 1990s, a considerable number of barley/H, bulbosum introgression lines （IL）s has been generated, with segments introgressed from H. bulbosum harboring a diverse set of desirable traits. However, the efficient utilization of these ILs has been hampered, largely due to the lack of suitable molecular tools for their genetic characterization and highly reduced interspecific recombination frequencies in the region of the introgression. In the present study, we utilized genotyping-by-sequencing for the detailed molecular characterization of 145 ILs. Genotypic information allows the genetic diversity within the set of ILs to be determined and a strategy was outlined to tackle the obstacle of reduced recombination frequencies. Furthermore, we compiled exome capture re-sequencing information of barley and H. bulbosum and designed an integrated barley/ H. bulbosum sequence resource with polymorphism information on interspecific and intraspecific sequence variations of both species. The integrated sequence will be valuable for marker development in barley/H, bulbosum ILs derived from any barley and H. bulbosum donors. This study provides the tools for the widespread utilization of barley/H, bulbosum ILs in applied barley breeding and academic research.展开更多
为构建多鳞[鱼喜](Sillago sihama)遗传连锁图谱并鉴定生长等重要经济性状数量性状位点(QTL),实验通过基因分型测序(GBS)技术对163个多鳞[鱼喜]个体(2个亲本和161个全同胞家系F1代)进行测序及标记分型,并通过复合区间定位法对该物种的...为构建多鳞[鱼喜](Sillago sihama)遗传连锁图谱并鉴定生长等重要经济性状数量性状位点(QTL),实验通过基因分型测序(GBS)技术对163个多鳞[鱼喜]个体(2个亲本和161个全同胞家系F1代)进行测序及标记分型,并通过复合区间定位法对该物种的体重、体高、体厚、眼径、体长和背鳍前长6个生长性状进行QTL定位分析。结果显示,多鳞[鱼喜]首张高密度遗传连锁图谱全长2 154.803 c M,标记间平均遗传距离0.455 c M,共有4 735个SNP标记分配到24个连锁群。QTL定位分析结果发现在6个生长性状中共检测到20个生长显著相关QTL位点,分布在8个连锁群上,单个QTL的LOD值范围为3.02~4.23,可解释的表型变异范围为0.14%~8.42%。其中,在连锁群LG08聚集了8个生长性状显著相关的QTL。通过对候选QTL区间内的基因进行功能注释,共筛选到了19个潜在生长调控相关基因,包含igf1、igf2、sstr5、sst1a、tgfbr2、gas1、igfals、gfg6、gfg20、bmp7、kdm5c、tti1以及rbm10等。实验获得的遗传标记及相关候选基因是多鳞[鱼喜]生长相关性状标记辅助选择(MAS)的有用基因资源,为进一步研究鱼类生长调控机制提供了更多的理论依据。展开更多
Litchi chinensis Sonn is widely cultivated in subtropical regions and has an important economic value.A high-density genetic map is a valuable tool for mapping quantitative trait loci(QTL)and marker-assisted breeding ...Litchi chinensis Sonn is widely cultivated in subtropical regions and has an important economic value.A high-density genetic map is a valuable tool for mapping quantitative trait loci(QTL)and marker-assisted breeding programs.In this study,a single nucleotide polymorphism(SNP)-based high-density linkage map was constructed by a genotyping-by-sequencing(GBS)protocol using an F1 population of 178 progenies between two commercial litchi cultivars,‘Ziniangxi’(dwarf)and‘Feizixiao’(vigorous).The genetic map consisted of 3027 SNP markers with a total length of 1711.97 cM in 15 linkage groups(LGs)and an average marker distance of 0.57 cM.Based on this high-density linkage map and three years of phenotyping,a total of 37 QTLs were detected for eight dwarf-related traits,including length of new branch(LNB),diameter of new branch(DNB),length of common petiole(LCP),diameter of common petiole(DCP),length of internode(LI),length of single leaf(LSL),width of single leaf(WSL),and plant height(PH).These QTLs could explain 8.0 to 14.7%(mean=9.7%)of the phenotypic variation.Among them,several QTL clusters were observed,particularly on LG04 and LG11,which might show enrichment for genes regulating the dwarf-related traits in litchi.There were 126 candidate genes identified within the QTL regions,55 of which are differentially expressed genes by RNA-seq analysis between‘Ziniangxi’and‘Feizixiao’.These DEGs were found to participate in the regulation of cell development,material transportation,signal transduction,and plant morphogenesis,so they might play important roles in regulating plant dwarf-related traits.The high-density genetic map and QTLs identification related to dwarf traits can provide a valuable genetic resource and a basis for marker-assisted selection and genomic studies of litchi.展开更多
文摘Stemphylium leaf spot, caused by Stemphylium botryosum f. sp. spinacia, is an important fungal disease of spinach (Spinacia oleracea L.). The aim of this study was to conduct association analysis to identify single nucleotide polymorphism (SNP) markers associated with Stemphylium leaf spot resistance in spinach. A total of 273 spinach genotypes, including 265 accessions from the USDA spinach germplasm collection and eight commercial cultivars, were used in this study. Phenotyping for Stemphylium leaf spot resistance was evaluated in greenhouse;genotyping was conducted using genotyping by sequencing (GBS) with 787 SNPs;and single marker regression, general linear model, and mixed linear model were used for association analysis of Stemphylium leaf spot. Spinach genotypes showed a skewed distribution for Stemphylium leaf spot resistance, with a range from 0.2% to 23.5% disease severity, suggesting that Stemphylium leaf spot resistance in spinach is a complex, quantitative trait. Association analysis indicated that eight SNP markers, AYZV02052595_115, AYZV02052595_122, AYZV02057770_10404, AYZV02129827_205, AYZV0-2152692_182, AYZV02180153_337, AYZV02225889_197, and AYZV02258563_213 were strongly associated with Stemphylium leaf spot resistance, with a Log of the Odds (LOD) of 2.5 or above. The SNP markers may provide a tool to select for Stemphylium leaf spot resistance in spinach breeding programs through marker-assisted selection (MAS).
文摘采用基因分型测序(GBS)技术对堇叶紫金牛[Ardisia violacea(T.Suzuki)W.Z.Fang et K.Yao]13个野生居群77份样本进行单核苷酸多态性(SNP)位点挖掘,在此基础上,对13个居群77份样本的遗传多样性、系统发育树、亲缘关系等进行分析。结果表明:共获得有效SNP位点246307个,每份样本检测到SNP位点1154~3789个。13个居群的观测杂合度为0.1569~0.4289,多态信息含量为0.0785~0.3244,核苷酸多样性指数为0.0002~0.0007,Tajima’s D值为0.2247~1.0936,Shannon’s多样性指数为0.2175~0.6649,表明堇叶紫金牛整体遗传多样性水平偏低。系统发育树、主成分分析和遗传结构分析结果显示77份样本可划分为6组。亲缘关系分析结果显示:居群内个体间的亲缘关系整体较近;居群间的亲缘关系与地理距离有一定的相关性。遗传分化和基因流分析结果显示:大部分居群间存在较高的遗传分化,各居群间存在一定程度的基因交流。综上所述,堇叶紫金牛13个居群的整体遗传多样性偏低,但居群间的遗传分化程度较高,这与居群间的地理距离较远、基因交流较少有关。建议优先保护安徽省黄山市祁门县牯牛降、浙江省舟山市定海区蔡家岙和浙江省宁波市象山县屠家园村3个遗传多样性较高的居群,并开展相关繁育工作以维持和扩大居群数量。
文摘Genetic variation developed in plant breeding programs is fundamental to creating new combinations that result in cultivars with enhanced characteristics. Over the years, tomato (Solanum lycopersicum) breeding programs associated with the Texas A&M University system have developed morphologically diverse lines of tomatoes selected for heat tolerance, fruit quality, and disease resistance to adapt them to Texas growing conditions. Here we explored the intraspecific genetic variations of 322 cultivated tomato genotypes, including 300 breeding lines developed by three Texas A&M breeding programs, as an initial step toward implementing molecular breeding approaches. Genotyping by sequencing using low coverage whole-genome sequencing (SkimGBS) identified 10,236 high-quality single-nucleotide polymorphisms (SNPs) that were used to assess genetic diversity, population structure, and phylogenetic relationship between genotypes and breeding programs. Model-based population structure analysis, phylogenetic tree construction, and principal component analysis indicated that the genotypes were grouped into two main clusters. Genetic distance analysis revealed greater genetic diversity? among the products of the three breeding programs. The germplasm developed at Texas A&M programs at Weslaco, College Station, and by Dr. Paul Leeper exhibited genetic diversity ranges of 0.175 - 0.434, 0.099 - 0.392, and 0.183 - 0.347, respectively, suggesting that there is enough variation within and between the lines from the three programs to perform selection for cultivar development. The SNPs identified here could be used to develop molecular tools for selecting various traits of interest and to select parents for future tomato breeding.
基金supported by 863 Project (2012AA10A305)Chinese Universities Scientific Fund (2014XJ036)+1 种基金NSF (31301321)948 Project (2011-G15)
文摘Maize（Zea mays） root system architecture（RSA）mediates the key functions of plant anchorage and acquisition of nutrients and water. In this study,a set of 204 recombinant inbred lines（RILs） was derived from the widely adapted Chinese hybrid ZD958（Zheng58 Chang7-2）,genotyped by sequencing（GBS） and evaluated as seedlings for 24 RSA related traits divided into primary,seminal and total root classes. Signi ficant differences between the means of the parental phenotypes were detected for 18 traits,and extensive transgressive segregation in the RIL population was observed for all traits. Moderate to strong relationships among the traits were discovered. A total of 62 quantitative trait loci（QTL） were identi fied that individually explained from1.6% to 11.6%（total root dry weight/total seedling shoot dry weight） of the phenotypic variation. Eighteen,24 and 20 QTL were identi fied for primary,seminal and total root classes of traits,respectively. We found hotspots of 5,3,4 and 12 QTL in maize chromosome bins 2.06,3.02-03,9.02-04,and 9.05-06,respectively,implicating the presence of root gene clusters or pleiotropic effects. These results characterized the phenotypic variation and genetic architecture of seedling RSA in a population derived from a successful maize hybrid.
基金This study was supported by the National Key Research and Development Program of China （2016YFD0101802 and 2016YFE0108600） and National Natural Science Foundation of China （31550110212）.
文摘There is a rapidly rising trend in the development and application of molecular marker assays for gene map- ping and discovery in field crops and trees. Thus far, more than 50 SNP arrays and 15 different types of genotyping-by-sequencing （GBS） platforms have been developed in over 25 crop species and perennial trees. However, much less effort has been made on developing ultra-high-throughput and cost-effective genotyping platforms for applied breeding programs. In this review, we discuss the scientific bottlenecks in existing SNP arrays and GBS technologies and the strategies to develop targeted platforms for crop mo- lecular breeding. We propose that future practical breeding platforms should adopt automated genotyping technologies, either array or sequencing based, target functional polymorphisms underpinning economic traits, and provide desirable prediction accuracy for quantitative traits, with universal applications under wide genetic backgrounds in crops. The development of such platforms faces serious challenges at both the technological level due to cost ineffectiveness, and the knowledge level due to large genotype- phenotype gaps in crop plants. It is expected that such genotyping platforms will be achieved in the next ten years in major crops in consideration of （a） rapid development in gene discovery of important traits, （b） deepened understanding of quantitative traits through new analytical models and population designs, （c） integration of multi-layer -omics data leading to identification of genes and pathways responsible for important breeding traits, and （d） improvement in cost effectiveness of large-scale genotyping. Crop breeding chips and genotyping platforms will provide unprecedented opportunities to accelerate the development of cultivars with desired yield potential, quality, and enhanced adaptation to mitigate the effects of climate change.
文摘[目的]探究云上黑山羊主配公羊的亲缘关系及近交系数,构建肉羊高效联合育种体系,提升云上黑山羊生产性能和可持续发展力。[方法]采用简化基因组测序(genotyping-by-sequencing,GBS)技术对云上黑山羊5个核心育种场(XD、ZY、ML、SB、TJ)的100只主配公羊进行测序,并使用BWA、SAMTOOLS、PLINK v 1.90、Gmatrix v 2、Mega X等软件进行质控后高质量单核苷酸多态性(single nucleotide polymorphism,SNP)位点鉴定、主成分分析(PCA)、状态同源距离矩阵(identical by state,IBS)和G矩阵构建、群体进化树分析、亲缘系数计算及近交系数估计。[结果]GBS质控后共获得215926个高质量SNPs位点;共检测到8692条连续性纯合片段(runs of homozygosity,ROH),长度在10.59~591.23 Mb之间,平均长度245.74 Mb。云上黑山羊主配公羊群体平均IBS遗传距离为0.118±0.011,亲缘关系G矩阵结果与IBS距离矩阵结果一致。结合群体进化树和亲缘关系分析,100只云上黑山羊被分为三大支和28个家系,其中家系2、11、13、14、16、17、18、20、23、24、25仅有1只公羊,XD、ZY、ML、SB、TJ核心育种场分别有18、10、8、5和8个家系;基于ROH的群体平均基因组近交系数为0.099641,29只公羊的近交系数<0.0625,39只公羊的近交系数在0.0625~0.125之间,32只公羊近交系数>0.125,存在较大的近交累积。[结论]100只云上黑山羊主配公羊被分为28个家系,其中11个家系仅有1只公羊,应加强繁育防止其血统的流失,配种方案制定中应关注近交系数>0.125的个体,防止近交衰退,同时根据不同的育种目标合理进行种公羊的交换。
文摘Hordeum bulbosum L., a wild relative of barley （Hordeum vulgare L.）, has been considered as a valuable source of genetic diversity for barley improvement. Since the 1990s, a considerable number of barley/H, bulbosum introgression lines （IL）s has been generated, with segments introgressed from H. bulbosum harboring a diverse set of desirable traits. However, the efficient utilization of these ILs has been hampered, largely due to the lack of suitable molecular tools for their genetic characterization and highly reduced interspecific recombination frequencies in the region of the introgression. In the present study, we utilized genotyping-by-sequencing for the detailed molecular characterization of 145 ILs. Genotypic information allows the genetic diversity within the set of ILs to be determined and a strategy was outlined to tackle the obstacle of reduced recombination frequencies. Furthermore, we compiled exome capture re-sequencing information of barley and H. bulbosum and designed an integrated barley/ H. bulbosum sequence resource with polymorphism information on interspecific and intraspecific sequence variations of both species. The integrated sequence will be valuable for marker development in barley/H, bulbosum ILs derived from any barley and H. bulbosum donors. This study provides the tools for the widespread utilization of barley/H, bulbosum ILs in applied barley breeding and academic research.
文摘为构建多鳞[鱼喜](Sillago sihama)遗传连锁图谱并鉴定生长等重要经济性状数量性状位点(QTL),实验通过基因分型测序(GBS)技术对163个多鳞[鱼喜]个体(2个亲本和161个全同胞家系F1代)进行测序及标记分型,并通过复合区间定位法对该物种的体重、体高、体厚、眼径、体长和背鳍前长6个生长性状进行QTL定位分析。结果显示,多鳞[鱼喜]首张高密度遗传连锁图谱全长2 154.803 c M,标记间平均遗传距离0.455 c M,共有4 735个SNP标记分配到24个连锁群。QTL定位分析结果发现在6个生长性状中共检测到20个生长显著相关QTL位点,分布在8个连锁群上,单个QTL的LOD值范围为3.02~4.23,可解释的表型变异范围为0.14%~8.42%。其中,在连锁群LG08聚集了8个生长性状显著相关的QTL。通过对候选QTL区间内的基因进行功能注释,共筛选到了19个潜在生长调控相关基因,包含igf1、igf2、sstr5、sst1a、tgfbr2、gas1、igfals、gfg6、gfg20、bmp7、kdm5c、tti1以及rbm10等。实验获得的遗传标记及相关候选基因是多鳞[鱼喜]生长相关性状标记辅助选择(MAS)的有用基因资源,为进一步研究鱼类生长调控机制提供了更多的理论依据。
基金funded by the Key-Area of Research and Development Program of Guangdong Province,China(2018B020202011)the National Natural Science Foundation of China(31701885)+2 种基金the China Agriculture Research System of MOF and MARA(CARS-32-05)the State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources,China(SKLCUSA-b201716)the YangFan Innovative&Entrepreneurial Research Team Project,China(2014YT02H013)。
文摘Litchi chinensis Sonn is widely cultivated in subtropical regions and has an important economic value.A high-density genetic map is a valuable tool for mapping quantitative trait loci(QTL)and marker-assisted breeding programs.In this study,a single nucleotide polymorphism(SNP)-based high-density linkage map was constructed by a genotyping-by-sequencing(GBS)protocol using an F1 population of 178 progenies between two commercial litchi cultivars,‘Ziniangxi’(dwarf)and‘Feizixiao’(vigorous).The genetic map consisted of 3027 SNP markers with a total length of 1711.97 cM in 15 linkage groups(LGs)and an average marker distance of 0.57 cM.Based on this high-density linkage map and three years of phenotyping,a total of 37 QTLs were detected for eight dwarf-related traits,including length of new branch(LNB),diameter of new branch(DNB),length of common petiole(LCP),diameter of common petiole(DCP),length of internode(LI),length of single leaf(LSL),width of single leaf(WSL),and plant height(PH).These QTLs could explain 8.0 to 14.7%(mean=9.7%)of the phenotypic variation.Among them,several QTL clusters were observed,particularly on LG04 and LG11,which might show enrichment for genes regulating the dwarf-related traits in litchi.There were 126 candidate genes identified within the QTL regions,55 of which are differentially expressed genes by RNA-seq analysis between‘Ziniangxi’and‘Feizixiao’.These DEGs were found to participate in the regulation of cell development,material transportation,signal transduction,and plant morphogenesis,so they might play important roles in regulating plant dwarf-related traits.The high-density genetic map and QTLs identification related to dwarf traits can provide a valuable genetic resource and a basis for marker-assisted selection and genomic studies of litchi.
