CN110777197A - Major QTL method for rapidly identifying cotton-related traits through compound BSA-seq - Google Patents
Major QTL method for rapidly identifying cotton-related traits through compound BSA-seq Download PDFInfo
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Abstract
本发明公开了一种复式BSA‑seq快速鉴定棉花相关性状的主效QTL的方法,该方法利用遗传背景相近的姊妹系材料综合性状优良的品种中棉所60和以及纤维品质较差的中棉所60选系EZ60作为母本,分别与共同父本中R014121杂交构建2个各含有1000个单株的F2分离群体,依据相关表型数据分别筛选极端材料,共构建2个群体的纤维长度、强度以及衣分共6组BSA混池,利用高通量重测序技术手段,筛选得到两个群体的共有区段(QTL)qFS‑D02‑1,其为主效QTL,其在物理图谱上的区间为3.15Mb。因此通过复式BSA‑seq可以快速鉴定相关主效位点,挖掘相关基因,为棉花遗传改良奠定基础。The invention discloses a method for rapid identification of major QTLs of cotton-related traits by compound BSA-seq. The method utilizes sister line materials with similar genetic backgrounds, Zhongmiansuo 60 and varieties with excellent comprehensive traits, and Zhongmiansuo 60 with poor fiber quality. The 60 selected lines EZ60 as the female parent were crossed with R014121 in the common male parent to construct two F 2 segregating populations each containing 1000 individual plants. The extreme materials were screened according to the relevant phenotypic data, and the fiber lengths of the two populations were constructed in total. A total of 6 groups of BSA mixed pools were obtained by using high-throughput resequencing technology, and the common segment (QTL) qFS-D02-1 of the two groups was obtained by screening, which is the main QTL, which is on the physical map. The interval is 3.15Mb. Therefore, multiplex BSA-seq can quickly identify relevant major loci, mine relevant genes, and lay the foundation for cotton genetic improvement.
Description
技术领域technical field
本发明属于生物技术应用领域,涉及到复式BSA-seq快速鉴定陆地棉主效QTLs,为棉花主要分子辅助选择鉴定基础。The invention belongs to the application field of biotechnology, and relates to the rapid identification of the main effect QTLs of upland cotton by multiple BSA-seq, which is the basis for the identification of the main molecules of cotton assisted selection.
背景技术Background technique
棉花纤维是由胚珠外珠被表皮单细胞发育形成的毛状体,是研究细胞发育、细胞壁和纤维素合成的理想模式材料,纤维品质和产量由纤维发育过程的4个阶段共同调控,即起始期、伸长期、次生壁加厚期和成熟期。棉花纤维强度等品质性状属于受多基因控制的复杂数量性状,极易受到环境因素的影响,其表现型是由基因型与环境相互作用的结果,且纤维品质和产量性状之间存在较大的负相关,因此对数量性状的遗传操纵能力决定了作物育种的效率。传统育种方法需要的群体大、周期长,而且成本高、预见性差等劣势,因此采用常规育种手段难以实现棉花纤维品质与产量的同步改良。近年来,随着生物技术的发展,为作物性状改良提供了新的途径,通过对纤维强度等相关性状位点的定位,分子标记辅助选择,候选基因的筛选与鉴定等分子手段,加快棉花纤维品质改良。国内外对棉花纤维强度性状形成的遗传基础及分子调控机制研究十分重视,在遗传图谱构建与纤维强度性状QTL定位、重要基因克隆与功能鉴定等方面的研究中均取得了重要进展。Cotton fiber is a trichome formed by the development of a single cell in the epidermis of the outer integument of the ovule. It is an ideal model material for the study of cell development, cell wall and cellulose synthesis. Initial stage, elongation stage, secondary wall thickening stage and mature stage. Quality traits such as cotton fiber strength are complex quantitative traits controlled by multiple genes and are easily affected by environmental factors. are negatively correlated, so the ability to genetically manipulate quantitative traits determines the efficiency of crop breeding. Traditional breeding methods require large populations, long periods, high costs, and poor predictability. Therefore, it is difficult to achieve simultaneous improvement of cotton fiber quality and yield by conventional breeding methods. In recent years, with the development of biotechnology, a new approach has been provided for the improvement of crop traits. Through molecular methods such as the localization of fiber strength and other related traits, molecular marker-assisted selection, and candidate gene screening and identification, cotton fibers can be accelerated. Quality improvement. The research on the genetic basis and molecular regulation mechanism of cotton fiber strength traits has been paid great attention at home and abroad, and important progress has been made in the research of genetic map construction, QTL mapping of fiber strength traits, and important gene cloning and functional identification.
为了研究棉花纤维强度性状的遗传机制,并利用标记辅助选择改良纤维强度,以陆陆种内群体、海陆种间群体以及其他群体,在遗传连锁图谱构建的基础上,已经定位了一系列纤维强度相关的QTL。Zhang等利用陆地棉种内(0-153×sGK9708)重组自交系群体在11个环境下的表型数据和包括2394个SNP 标记的遗传图谱,一共检测到63个单个环境下的纤维强度QTL,16个多个环境稳定的纤维强度 QTL (Zhang et al. Construction of ahigh-density genetic map and its application to QTL identification for fiberstrength in Upland cotton. Crop Science,2017, 57(2):774.);Ma 等利用 F14重组自交系群体(RIL)与母本回交构建BC群体,在该群体内检测到26个QTL,而在重组自交系群体中检测到37个QTL。其中,在两个群体中均能检测到的QTL只有 7个QTL (Ma et al.QTLsanalysis and validation for fiber quality traits using maternal backcrosspopulation in Upland cotton[J]. Frontiers in Plant Science, 2017, 8:2168);Liu等利用加密后包括2051个SSR标记的高密度遗传图谱和(CCRI35×Yumian 1)重组自交系群体在6个环境下的纤维品质和产量表型数据,一共检测到113个产量和纤维品质QTL,其中,50个QTL 在多个环境下检测到或者该QTL的加性效应值大于环境效应值(Liu etal.Enriching an intraspecifc genetic map and identifying QTL for fiberquality and yield component traits across multiple environments in Uplandcotton (Gossypium hirsutum L.) [J].Mol Genet Genomics,2017,292(6):1281-1306);Diouf等利用CCRI35×NH F2:3群体构建包括 5178个GBS-SNP标记的遗传图谱,结合包括纤维品质在内的11个性状表型数据,共检测到110个 QTL,其中,30个QTL 在2个环境中检测到(Diouf et al. QTL mapping of fiber q uality and yield-related traits in anintra-specific upland cotton using genotype by sequencing (GBS).International journal of molecular sciences, 2018, 19(2): 441);Tan等利用渝棉1号×Acala Maxxa重组自交系群体,通过Cotton SNP80K芯片,结合SSR标记构建陆地棉高密度遗传图谱,获得27个与纤维强度相关的QTL(Tan et al. Genetic Map Constructionand Fiber Quality QTL Mapping Using the CottonSNP80K Array in Upland Cotton.Frontiers inPlant Science, 2018, 9:225. )。Yu等通过陆地棉与海岛棉杂交回交构建的146个BIL 群体,在2个以上环境中检测到的纤维品质相关QTL有2个,1个与纤维强度相关,1个与纤维整齐度相关(Yu et al. 2013. Mapping quantitative trait loci forlint yield and fiber quality across environments in a Gossypium hirsutum×Gossypium barbadense, backcross inbred line population. Theoretical andAppliedGenetics, 126(1):275-287);Yu等利用棉花陆海F2、F2:3和TC等3个群体,分别检测到5、4和5个纤维品质QTL(Yu et al.. Identification of quantitative trait lociacross interspecific F2, F2:3and testcross populations for agronomic andfiber traits in tetraploid cotton. Euphytica, 2013, 191(3):375-389)。Si等利用海岛棉背景下的陆地棉渗入系解析了陆地棉衣分和纤维品质的遗传特性,一共检测到39个QTL,包括4个QTL簇,其中3个QTL簇(纤维长度、比强度和铃重)导入系降低海岛棉品质和产量 (Si et al. Genetic dissection of lint yield and fiber quality traits of G.hirsutum in G. barbadense background[J]. Mol Breeding,2017,37(1):9)。Jia等利用海陆种间重组自交系群体检测到与纤维强度相关的QTL 36个 (Jia et al. QTLdelineation for five fiber quality traits based on an intra-specificGossypium hirsutum L. recombinant inbred line population. Moleculargeneticsand genomics, 2018, 293(4): 831-843)。利用陆地棉背景下的黄褐棉BC3F2、 BC3F2:3和BC3F2:4导入系检测到42个纤维品质QTL,包括15个纤维强度QTL和27个纤维马克隆值QTL(Wanget al. Advanced backcross QTL analysis of fiber strength and fineness ina cross between Gossypium hirsutum and G. mustelinum. Frontiers in PlantScience, 2017, 8:1848。Keerio等利用SLAF-seq对陆地棉与毛棉的107个渐渗系进行分析,共获得3157个高质量的SNP标记,共得到与棉花纤维品质相关的QTLs 30个,与产量性状相关的QTLs 44个(Keerio et al. QTL Mapping for Fiber Quality and Yield TraitsBased on Introgression Lines Derived from Gossypium hirsutum × G. tomentosum[J]. International Journal of Molecular Sciences, 2018, 19(1):243.)。In order to study the genetic mechanism of cotton fiber strength traits and use marker-assisted selection to improve fiber strength, a series of fiber strengths have been located on the basis of genetic linkage map construction in terrestrial and interspecific populations, marine and terrestrial populations, and other populations. Relevant QTL. Zhang et al. used the phenotypic data of the intraspecific (0-153×sGK9708) recombinant inbred line population in Upland cotton in 11 environments and a genetic map including 2394 SNP markers, and detected a total of 63 QTLs for fiber strength in a single environment. , 16 QTLs for multiple environmentally stable fiber strengths (Zhang et al. Construction of a high-density genetic map and its application to QTL identification for fiberstrength in Upland cotton. Crop Science, 2017, 57(2):774.); Ma et al. used the F 14 recombinant inbred line population (RIL) to backcross the parent to construct a BC population, and detected 26 QTLs in this population, while 37 QTLs were detected in the recombinant inbred line population. Among them, only 7 QTLs could be detected in both populations (Ma et al.QTLsanalysis and validation for fiber quality traits using maternal backcrosspopulation in Upland cotton[J]. Frontiers in Plant Science, 2017, 8:2168) Liu et al. used the encrypted high-density genetic map including 2051 SSR markers and the fiber quality and yield phenotype data of the (CCRI35×Yumian 1) recombinant inbred line population in 6 environments, and detected a total of 113 yield and fiber phenotypes. Quality QTLs, of which 50 QTLs were detected in multiple environments or the QTL had an additive effect value greater than the environmental effect value (Liu et al. Enriching an intraspecifc genetic map and identifying QTL for fiber quality and yield component traits across multiple environments in Uplandcotton ( Gossypium hirsutum L.) [J].Mol Genet Genomics, 2017, 292(6):1281-1306); Diouf et al constructed a genetic map including 5178 GBS-SNP markers using the CCRI35×NHF 2:3 population, combined with A total of 110 QTLs were detected in the phenotypic data of 11 traits including fiber quality, of which 30 QTLs were detected in 2 environments (Diouf et al. QTL mapping of fiber quality and yield-related traits in anintra). -specific upland cotton using genotype by sequencing (GBS). International journal of molecular sciences, 2018, 19(2): 441); Tan et al. used Yumian No. 1 × Acala Maxxa recombinant inbred line population, through Cotton SNP80K chip, combined with SSR markers constructed a high-density genetic map of upland cotton, and obtained 27 QTLs related to fiber strength (Tan et al. Genetic Map Construction and Fiber Quality QTL Mapping Us ing the CottonSNP80K Array in Upland Cotton. Frontiers in Plant Science, 2018, 9:225.). Yu et al. constructed 146 BIL populations by backcrossing upland cotton and sea island cotton. There were 2 QTLs related to fiber quality detected in more than 2 environments, one related to fiber strength and one related to fiber uniformity ( Yu et al. 2013. Mapping quantitative trait loci forlint yield and fiber quality across environments in a Gossypium hirsutum×Gossypium barbadense, backcross inbred line population. Theoretical and Applied Genetics, 126(1):275-287); 2 , F2 :3 and TC, 5, 4 and 5 fiber quality QTLs were detected respectively (Yu et al.. Identification of quantitative trait lociacross interspecific F2, F2:3 and testcross populations for agronomic and fiber traits in tetraploid cotton. Euphytica, 2013, 191(3):375-389). Si et al. analyzed the genetic characteristics of upland cotton lint content and fiber quality using the upland cotton infiltration line under the background of sea island cotton. A total of 39 QTLs were detected, including 4 QTL clusters, of which 3 QTL clusters (fiber length, specific strength and boll quality) Heavy) introduced line reduces the quality and yield of sea island cotton (Si et al. Genetic dissection of lint yield and fiber quality traits of G. hirsutum in G. barbadense background[J]. Mol Breeding, 2017, 37(1):9). Jia et al. detected 36 QTLs related to fiber strength using recombinant inbred line populations between marine and terrestrial species (Jia et al. QTLdelineation for five fiber quality traits based on an intra-specific Gossypium hirsutum L. recombinant inbred line population. Moleculargenetics and genomics, 2018 , 293(4): 831-843). 42 fiber quality QTLs, including 15 fiber strength QTLs and 27 fiber micronaire values, were detected using the BC 3 F 2 , BC 3 F 2:3 and BC 3 F 2:4 introductory lines in the upland cotton background QTL (Wanget al. Advanced backcross QTL analysis of fiber strength and fineness ina cross between Gossypium hirsutum and G. mustelinum. Frontiers in PlantScience, 2017, 8:1848. Keerio et al. used SLAF-seq to analyze the 107 gradients of upland cotton and wool cotton. A total of 3157 high-quality SNP markers were obtained, including 30 QTLs related to cotton fiber quality and 44 QTLs related to yield traits (Keerio et al. QTL Mapping for Fiber Quality and Yield TraitsBased on Introgression). Lines Derived from Gossypium hirsutum × G. tomentosum [J]. International Journal of Molecular Sciences, 2018, 19(1):243.).
混池分组测序(BSA-seq):针对研究的目标性状,选择表型极端差异的亲本构建混池,对亲本及极端混池进行DNA测序,检测与性状相关联的位点,快速挖掘候选基因的方法。早在1991 年,Michelmore等(1991)首次采用混池分组分析(BSA)方法在莴苣分离群体中成功筛选到 3个与霜霉病抗性基因 Dm5/8紧密连锁的标记(Michelmore et al.Identification of markers linked to disease-resistance genes by bulkedsegregant analysis: a rapid method to detect markers in specific genomicregions by using segregating populations. Proceedings of the National Academyof Sciences of the United States of America, 1991, 88: 9828);近年来,基于高通量测序技术的BSA 方法,即 BSA-seq技术已被成功用于作物重要农艺性状相关QTL的精细定位和候选基因鉴别(Ogiso et al. Detection of novel QTLs qDTH4.5 and qDTH6.3,which confer late heading under short-day conditions, by SSR marker-based andQTL-seq analysis. Breeding Science, 2017, 67: 101.;Pandey et al. QTL-seqapproach identified genomic regions and diagnostic markers for rust and lateleaf spot resistance in groundnut (Arachis hypogaea L.). Plant BiotechnologyJournal, 2017,15: 927.;Shu et al. QTL-seq for rapid identification ofcandidate genes for flowering time in broccoli×cabbage. Theoretical andApplied Genetics. 2018, 101:1-12)。BSA-seq技术可实现对作物重要性状相关 QTL/关键基因区段高效、准确的精细定位,但是在棉花中主要是与质量性状相关的精细定位报道。Chen 等(2015)利用BSA-seq技术将隐性无限分支基因gb_nb1定位到16号染色体上600 kb左右的2个SNP 标记间(Chen et al. Genetic mapping of the nulliplex-branch gene(gb_nb1) in cotton using next-generation sequencing. Theoretical & AppliedGenetics,2015, 128:539-547)。Zhu等(2017)利用陆BSA-seq技术精细定位芽黄基因virescent-1,成功鉴别候选基因 GhCHL1(Zhu et al. Rapid mapping and cloning ofthe virescent-1 gene in cotton by bulked segregant analysis-next generationsequencing and virus-induced gene silencing strategies. Journal ofExperimental Botany,2017, 68: 4125)。Marina等(2017)利用BSA-seq技术发现了与Li性状完全连锁的SNP位点,群体验证后得到超短纤维Li1基因。利用该技术对棉花纤维强度等数量性状相关 QTL进行定位的研究报道很少,Zhang等(2015)通过BSA方法和SSR标记,构建了陆地棉25号染色体遗传图谱,发掘了棉花纤维长度、强度以及马克隆值的QTL(ZhangZhen, Li Junwen, Muhammad Jamshed, et al. High Resolution Consensus Mappingof Quantitative Trait Loci for Fiber Strength, Length and Micronaire onChromosome 25 of the Upland Cotton (Gossypium hirsutum L.). PLoS ONE, 2015,10(8): e0135430)。通过利用姊妹系为母本构建的分离大群体,根据相关性状构建复试BSA混池,通过高通量重测序技术,快速获得共有区段,确定为候选QTL,还没有报导。Pooled pool sequencing (BSA-seq): For the target traits of the study, select the parents with extreme differences in phenotype to construct pooled pools, perform DNA sequencing on the parents and extreme pooled pools, detect loci associated with traits, and quickly mine candidate genes Methods. As early as 1991, Michelmore et al. (1991) successfully screened three markers closely linked to the downy mildew resistance gene Dm5/8 in the lettuce segregated population by using the pooled pool analysis (BSA) method for the first time (Michelmore et al. of markers linked to disease-resistance genes by bulkedsegregant analysis: a rapid method to detect markers in specific genomic regions by using segregating populations. Proceedings of the National Academy of Sciences of the United States of America, 1991, 88: 9828); The BSA method of high-throughput sequencing technology, namely BSA-seq technology, has been successfully used for fine mapping and candidate gene identification of QTLs related to important agronomic traits in crops (Ogiso et al. Detection of novel QTLs qDTH4.5 and qDTH6.3, which confer late heading under short-day conditions, by SSR marker-based and QTL-seq analysis. Breeding Science, 2017, 67: 101.; Pandey et al. QTL-seqapproach identified genomic regions and diagnostic markers for rust and lateleaf spot resistance in groundnut (Arachis hypogaea L.). Plant Biotechnology Journal, 2017, 15: 927.; Shu et al. QTL-seq for rapid identification of candidate genes for flowering time in broccoli×cabbage. Theoretical and Applied Genetics. 2018, 101:1-12). BSA-seq technology can achieve efficient and accurate fine-mapping of QTL/key gene segments related to important crop traits, but in cotton, the fine-mapping reports are mainly related to quality traits. Chen et al. (2015) used BSA-seq technology to map the recessive infinite branch gene gb_nb1 between two SNP markers about 600 kb on chromosome 16 (Chen et al. Genetic mapping of the nulliplex-branch gene (gb_nb1) in cotton using next-generation sequencing. Theoretical & Applied Genetics, 2015, 128:539-547). Zhu et al. (2017) used Lu BSA-seq technology to fine-map the virescent-1 gene in bud yellow and successfully identified the candidate gene GhCHL1 (Zhu et al. Rapid mapping and cloning of the virescent-1 gene in cotton by bulked segregant analysis-next generationsequencing and virus -induced gene silencing strategies. Journal of Experimental Botany, 2017, 68: 4125). Marina et al. (2017) used BSA-seq technology to discover SNP loci that were completely linked to the Li trait, and obtained the ultrashort fiber Li1 gene after population verification. There are few reports on the mapping of QTLs related to quantitative traits such as cotton fiber strength using this technology. Zhang et al. (2015) constructed a genetic map of upland cotton chromosome 25 through BSA and SSR markers, and explored cotton fiber length, strength and QTL for micronaire value (ZhangZhen, Li Junwen, Muhammad Jamshed, et al. High Resolution Consensus Mapping of Quantitative Trait Loci for Fiber Strength, Length and Micronaire on Chromosome 25 of the Upland Cotton (Gossypium hirsutum L.). PLoS ONE, 2015,10 (8): e0135430). By using the segregated large population constructed by the sister line as the female parent, the retest BSA pool was constructed according to the related traits, and the consensus segment was quickly obtained by high-throughput resequencing technology, which was identified as a candidate QTL, which has not been reported yet.
发明内容SUMMARY OF THE INVENTION
棉花纤维强度与长度成正相关,与衣分成负相关,因此结合性状间的相关性,本发明是利用遗传背景相近的姊妹系材料与共同父本分别构建分离大群体,选择各性状的极端材料分别构建高性状值和低性状值的BSA混池,利用高通量测序技术,快速获得主效QTL。Cotton fiber strength is positively correlated with length and negatively correlated with lint. Therefore, in combination with the correlation between traits, the present invention uses sister line materials with similar genetic backgrounds and common male parents to construct separate large groups, and select extreme materials for each trait. Construct a mixed pool of BSA with high trait value and low trait value, and use high-throughput sequencing technology to quickly obtain major QTL.
本发明提供的技术方案是:本发明提供一种复式BSA-seq快速鉴定棉花相关性状的主效QTL的方法:利用遗传背景相近的姊妹系材料综合性状优良的品种中棉所60以及纤维品质较差的中棉所60选系EZ60(以下简称EZ60)(国家棉花种质中期库,国家种质统一库编号:M116025,河南省安阳开市发区黄河大道38号,邮编:455000)与共同父本中R014121(国家棉花种质中期库,国家种质统一库编号:ZM115357)分别构建含有1000个单株的F2分离群体,是研究数量性状遗传的理想材料,可有效消除群体内遗传背景的干扰,可提高复杂农艺性状基因定位的准确性。棉花纤维强度与长度成正相关,与衣分成负相关,因此结合具有相关性状间极端材料分别构建混池,共构建中棉所60×中R014121 F2群体纤维强度、纤维长度以及衣分混池,和EZ60×中R014121 F2群体纤维强度、纤维长度以及衣分混池,共6组混池。利用高通量测序技术,快速获得主效QTL。The technical scheme provided by the invention is as follows: the invention provides a method for rapid identification of major QTLs of cotton-related traits by compound BSA-seq: using sister line materials with similar genetic backgrounds, Zhongmiansuo 60, a variety with excellent comprehensive traits, and a relatively high fiber quality The poor China Cotton Research Institute 60 selected line EZ60 (hereinafter referred to as EZ60) (National Cotton Germplasm Mid-term Bank, National Germplasm Unified Bank No.: M116025, No. 38 Huanghe Avenue, Development District, Anyang City, Henan Province, zip code: 455000) and the common parent In this paper, R014121 (National Cotton Germplasm Medium-term Bank, National Germplasm Unified Bank No.: ZM115357) respectively constructs F 2 segregating populations containing 1000 individual plants, which are ideal materials for the study of quantitative trait inheritance, which can effectively eliminate the genetic background in the population. Interference can improve the accuracy of gene mapping of complex agronomic traits. Cotton fiber strength is positively correlated with length and negatively correlated with lint. Therefore, combined with extreme materials with related traits, mixed pools were constructed respectively. A total of 60×medium R014121 F 2 populations of China Cotton Research Institute were constructed. The fiber strength, fiber length and lint of the R014121 F 2 population in EZ60×medium were mixed, with a total of 6 groups of mixed pools. Use high-throughput sequencing technology to quickly obtain major QTLs.
本发明所述的复式BSA-seq快速鉴定棉花相关性状的主效QTL的方法,该方法包括以步骤:The method for rapidly identifying the main effect QTL of cotton-related traits by compound BSA-seq of the present invention comprises the following steps:
(1)利用遗传背景相近的姊妹系材料综合性状优良的品种以及纤维品质较差的品系与其共同父本分别构建两个陆地棉的杂交组合,其中,组合Ⅰ:综合性状优良的品种×父本 ,组合Ⅱ:纤维品质较差的品系×父本,获得各包含1000个单株的F2分离群体以及F2:3,F2:4群体,并准确鉴定F2,F2:3,F2:4群体的表型数据;(1) Two hybrid combinations of upland cotton were constructed by using sister line materials with similar genetic backgrounds with excellent comprehensive traits and lines with poor fiber quality and their common male parents. Among them, Combination I: varieties with excellent comprehensive traits × male parent , Combination II: line with poor fiber quality × male parent, obtain F 2 segregation population and F 2:3 , F 2: 4 population each containing 1000 individual plants, and accurately identify F 2 , F 2:3 , F 2:4 population phenotypic data;
(2)依据棉花纤维强度与长度成正相关,与衣分成负相关的特点,分别筛选综合性状优良的品种×父本以及纤维品质较差的品系×父本的F2群体中高强材料单株、低强单株材料;长度较长的单株材料、长度较短单株材料;衣分较高单株材料以及衣分较低单株材料,提取叶片基因组DNA;(2) According to the characteristics that cotton fiber strength is positively correlated with length and negatively correlated with lint content, the F 2 populations of varieties with excellent comprehensive traits × male parent and lines with poor fiber quality × male parent were screened for high-strength materials per plant, Low-strength single-plant material; longer-length single-plant material, shorter-length single-plant material; higher-lint single-plant material and lower-lint single-plant material, extract leaf genomic DNA;
(3)将所述两个群体的高强单株、低强单株;长度较长单株、长度较短单株;衣分较高单株以及衣分较低单株的基因组DNA等量混合,构建六组BSA混池;(3) Mixing equal amounts of genomic DNAs of high-strength individual plants and low-strength individual plants; longer-length individual plants and shorter-length individual plants; higher-lint individual plants and lower-lint individual plants of the two populations , build six groups of BSA mixed pools;
(4)利用高通量重测序技术对混池DNA进行测序,每个混池的测序深度为棉花基因组DNA的30倍,利用QTL-seqr软件包对结果进行分析,六组BSA混池结果共同指向一个共有区段qFS-chrD02-1,其为陆地棉纤维强度主效基因位点。(4) High-throughput resequencing technology was used to sequence the DNA of the mixed pools. The sequencing depth of each pool was 30 times that of cotton genomic DNA. The QTL-seqr software package was used to analyze the results. The results of the six groups of BSA mixed pools were the same. Points to a consensus segment qFS-chrD02-1, which is the major gene locus for upland cotton fiber strength.
所述的复式BSA快速鉴定棉花相关性状的主效QTL的方法,具体地,步骤(1)中,所述综合性状优良的品种是中棉所60,纤维品质较差的品系是中棉所60选系EZ60,共同父本为中R014121,组合Ⅰ:中棉所60×中R014121 ,组合Ⅱ:EZ60×中R014121。本发明方法提供的一个具体实施例如下:The method for rapidly identifying the main QTL of cotton-related traits by compound BSA, specifically, in step (1), the variety with excellent comprehensive traits is China Cotton Research Institute 60, and the line with poor fiber quality is China Cotton Research Institute 60 The line EZ60 is selected, and the common male parent is Zhong R014121. Combination I: China Cotton Research Institute 60 × Zhong R014121, and combination II: EZ60 × Zhong R014121. A specific embodiment provided by the method of the present invention is as follows:
(1)利用遗传背景相近的姊妹系材料综合性状优良的品种中棉所60以及纤维品质较差的品系EZ60与共同父本中R014121分别构建两个陆地棉的杂交组合,其中,组合Ⅰ:中棉所60×中R014121 ,组合Ⅱ:EZ60×中R014121,获得1000个单株的F2分离群体,并鉴定F2,F2:3,F2:4群体的表型数据;(1) Two crosses of upland cotton were constructed using sister line materials with similar genetic backgrounds, Zhongmiansuo 60 with excellent comprehensive traits, and EZ60 with poor fiber quality and common male parent Zhong R014121. Among them, Combination I: Medium Cotton Institute 60×ZhongR014121, Combination II: EZ60×ZhongR014121, 1000 individual F 2 segregated populations were obtained, and the phenotypic data of F 2 , F 2:3 and F 2:4 populations were identified;
(2)依据棉花纤维强度与长度成正相关,与衣分成负相关的特点,分别筛选出中棉所60×中R014121 的F2群体中纤维高强材料、低强材料;长度较长的材料、长度较短材料;衣分较高材料,衣分较低材料各30株; EZ60×中R014121的F2群体中纤维高强材料、低强材料;长度较长的材料、长度较短材料;衣分较高材料,衣分较低材料各30株;提取其叶片基因组DNA;(2) According to the characteristics that cotton fiber strength is positively correlated with length and negatively correlated with clothing fraction, the fiber high-strength materials and low-strength materials in the F 2 group of 60×zhong R014121 of the China Cotton Research Institute were screened out respectively; Shorter materials; materials with higher lint content and 30 plants with lower lint content; fiber high-strength materials and low-strength materials in the F 2 population of EZ60×medium R014121; materials with longer lengths and materials with shorter lengths; 30 plants with high material and 30 plants with low lint content; extract genomic DNA from leaves;
(3)将两个群体的高强单株、低强单株;长度较长单株、长度较短单株;衣分较高单株以及衣分较低单株的基因组DNA分别等量混合,构建6组BSA混池;(3) The genomic DNAs of high-strength individual plants and low-strength plants of the two populations; longer-length individual plants and shorter-length individual plants; higher-lint individual plants and lower-lint individual plants were mixed in equal amounts, respectively. Build 6 groups of BSA mixed pools;
(4)利用高通量重测序技术对各混池DNA进行测序,每个混池测序深度为棉花基因组DNA的 30×,利用R语言中QTL-seqr软件包对结果进行分析,六组混池结果共同指向一个共有区段(QTL)qFS-chrD02-1(FS表示纤维强度,chrD02 表示D02染色体,QTL)qFS-chrD02-1表示在D02染色体上定位到的第一个与纤维强度相关的QTL),其为陆地棉纤维强度主效基因位点。(4) High-throughput resequencing technology was used to sequence the DNA of each pooled pool. The sequencing depth of each pooled pool was 30× that of cotton genomic DNA. The results were analyzed using the QTL-seqr software package in R language. Six groups of pooled pools were used. The results collectively point to a consensus segment (QTL) qFS-chrD02-1 (FS indicates fiber strength, chrD02 indicates D02 chromosome, QTL) qFS-chrD02-1 indicates the first fiber strength-related QTL mapped on D02 chromosome ), which is the main gene locus of upland cotton fiber strength.
本发明的具有如下优点:The present invention has the following advantages:
本发明中应用的是利用遗传背景相近的姊妹系材料综合性状优良的品种中棉所60以及纤维品质较差的品系EZ60与共同父本中R014121分别构建含有1000个单株的F2分离群体。棉花纤维强度与长度成正相关,与衣分成负相关,因此结合具有相关性状间极端材料分别构建混池,通过复式BSA-seq技术,快速获得共有区段(QTL)。The application of the present invention is to use sister line materials with similar genetic backgrounds, Zhongmiansuo 60, a variety with excellent comprehensive traits, and a line EZ60 with poor fiber quality and a common male parent Zhong R014121 to construct F2 segregated populations containing 1000 individual plants respectively. Cotton fiber strength is positively correlated with length and negatively correlated with lint. Therefore, combined with extreme materials with correlated traits, mixed pools were constructed respectively, and the common segment (QTL) was quickly obtained by double BSA-seq technology.
本发明所用的中棉所60以及品系EZ60是遗传背景相近的姊妹系材料,与共同父本中R014121 构建F2分离群体,研究数量性状遗传的理想材料,可有效消除群体内遗传背景的干扰,可提高复杂农艺性状基因定位的准确性。The China Cotton Research Institute 60 and the line EZ60 used in the present invention are sister line materials with similar genetic backgrounds, and the F2 segregated population is constructed with R014121 in the common male parent, ideal materials for studying the inheritance of quantitative traits, which can effectively eliminate the interference of genetic backgrounds in the population, It can improve the accuracy of gene mapping of complex agronomic traits.
基于姊妹系材料构建分离群体,结合相关性状间极端材料的复式BSA-seq 技术和RNA-seq 数据高效、准确进行纤维强度 qFS-D02-1 的精细定位,本发明方法在棉花数量性状 QTL 定位中尚未报道,属于首创。The isolated population was constructed based on the sister line materials, combined with the duplex BSA-seq technology and RNA-seq data of the extreme materials between related traits to efficiently and accurately perform fine mapping of fiber strength qFS-D02-1. The method of the present invention is used in cotton quantitative trait QTL mapping Not yet reported, it is a first.
附图说明Description of drawings
图1为本发明中棉所60×中R014121F2长度极端混池G-value值以及SNP-index结果;Fig. 1 is the G-value value and SNP-index result of the 60× medium R014121F 2 length extreme mixed pool of the present invention;
图2为本发明中棉所60×中R014121F2强度极端混池G-value值以及SNP-index结果;Fig. 2 is the G-value value and SNP-index result of the 60× medium R014121F 2 intensity extreme mixed pool of the present invention;
图3为本发明EZ60×中R014121 F2长度极端混池G-value值以及SNP-index结果;Fig. 3 is the G-value value and SNP-index result of the extreme mixed pool of R014121 F 2 length in EZ60× of the present invention;
图4为本发明中棉所60×中R014121 F2衣分极端混池G-value值以及SNP-index结果;Fig. 4 is the G-value value and SNP-index result of 60× middle R014121 F 2 lint extreme mixed pool of China Cotton Research Institute of the present invention;
这些共有的峰值图指向D02染色体。These shared peak profiles point to the D02 chromosome.
具体实施方式Detailed ways
下面通过具体实施方式的详细描述来进一步阐明本发明:The present invention is further illustrated below by the detailed description of specific embodiments:
本发明复式BSA-seq快速鉴定棉花相关性状的主效QTL的方法,具体步骤如下:The method for rapidly identifying the main effect QTL of cotton-related traits by compound BSA-seq of the present invention has the following specific steps:
(1)用于复式BSA-seq快速鉴定棉花相关性状的主效QTL的F2群体的培育方法及过程:分别以中国农业科学院棉花研究所培育的陆地棉品种中棉所60及其选系EZ60为母本,以中国农业科学院棉花研究所培育的纤维品质优异的大铃材料中R014121为共同父本,在2015年夏天于中国农业科学院棉花研究所(河南安阳)试验农场分别配制杂交组合,2016年在安阳种植F1,2017年在安阳种植1000个单株组成的F2群体,自交后获得F2:3家系,分别选取中棉所60×中R014121组合的300个F2:3家系以及EZ60×中R014121组合的200个F2:3家系,并结合冬季海南加代繁殖,家系内每单株各选一个自交铃,混收直获得F2:4。F2群体按单株收花,F2:3以及F2:4按家系收花,分别考种获得衣分数据,并取12-15g纤维样品用于纤维品质的测定。对相关表型(强度、长度及衣分),综合考虑F2,F2:3,F2:4群体的极端材料表型数据,极端表型表现一致的单株筛选为目的材料,用于后续的BSA-seq分析。(1) Breeding method and process of F 2 population for rapid identification of major QTLs for cotton-related traits by multiplex BSA-seq: Upland cotton cultivar Zhongmian 60 and its selected line EZ60 bred by Cotton Research Institute of Chinese Academy of Agricultural Sciences were used respectively. As the female parent, R014121 of the boll material with excellent fiber quality cultivated by the Cotton Research Institute of the Chinese Academy of Agricultural Sciences was used as the common male parent. In the summer of 2015, the hybrid combinations were prepared at the experimental farm of the Cotton Research Institute of the Chinese Academy of Agricultural Sciences (Anyang, Henan), respectively, 2016 F 1 was planted in Anyang in 2017, and an F 2 population consisting of 1000 individual plants was planted in Anyang in 2017. After selfing, F 2: 3 families were obtained, and 300 F 2: 3 families of the combination of 60×Zhong R014121 of China Cotton Research Institute were selected respectively. As well as 200 F 2:3 families of EZ60×R014121 combination, and combined with Hainan for breeding in winter, one self-crossing boll was selected for each individual plant in the family, and F 2:4 was obtained by mixing. The F 2 population was harvested according to a single plant, and the F 2:3 and F 2:4 were harvested according to the family. For related phenotypes (strength, length and lint), the extreme material phenotype data of F 2 , F 2:3 and F 2:4 populations were comprehensively considered, and the single plant with consistent extreme phenotype was selected as the target material for Subsequent BSA-seq analysis.
本发明中,中棉所60选系EZ60和中R014121来源于国家棉花种质中期库(地址:河南省安阳开市发区黄河大道38号,邮编:455000),国家种质统一库编号分别为:M116025、ZM115357。In the present invention, the 60 selected lines of China Cotton Research Institute EZ60 and China R014121 are from the National Cotton Germplasm Mid-term Bank (Address: No. 38, Huanghe Avenue, Development District, Anyang City, Henan Province, zip code: 455000), and the national germplasm unified bank numbers are respectively : M116025, ZM115357.
(2)取F2群体的叶片样本,采用CTAB法分别提取中棉所60×中R014121组合的1000个单株、EZ60×中R014121组合的1000个单株和三个亲本中棉所60、EZ60以及中R014121的DNA。(2) Take the leaf samples of the F 2 population, and use the CTAB method to extract 1000 individual plants of the combination of CMI 60×Zhong R014121, 1000 individual plants of the combination of EZ60×Zhong R014121 and the three parents CMI 60, EZ60 as well as the DNA of R014121.
(3)将步骤(1)中筛选的极端单株的DNA提取出来,通过琼脂糖凝胶电泳以及NANODROP 2000检测DNA的完整度以及浓度,按照不同的群体不同性状组建混池(中棉所60×中R014121 的F2群体中纤维高强材料、低强材料;长度较长的材料、长度较短材料;衣分较高材料,衣分较低材料共计3组混池;EZ60×中R014121的F2群体中纤维高强材料、低强材料;长度较长的材料、长度较短材料;衣分较高材料,衣分较低材料共3组混池),混池中的每份DNA等量混合,共构建6组混池。(3) Extract the DNA of the extreme individual plants screened in step (1), detect the integrity and concentration of DNA by agarose gel electrophoresis and NANODROP 2000, and set up mixed pools (China Cotton Research Institute 60) according to different characteristics of different groups. ×Middle R014121 F 2 group medium fiber high-strength material, low-strength material; longer-length material, shorter-length material; higher lint material, lower lint material, a total of 3 groups of mixed pools; EZ60 × F of middle R014121 2 groups of fiber high-strength materials, low-strength materials; longer-length materials, shorter-length materials; higher lint materials, lower lint materials (a total of 3 groups of mixed pools), each DNA in the mixed pool is mixed in equal amounts , a total of 6 groups of mixed pools were constructed.
(4)利用高通量重测序技术对6组混池DNA以及三个亲本DNA进行测序,利用BWA软件将测序数据比对到参考基因组,利用GATK软件检测SNP以及INDEL位点。(4) High-throughput resequencing technology was used to sequence 6 groups of mixed pool DNA and three parental DNAs. BWA software was used to compare the sequencing data to the reference genome, and GATK software was used to detect SNP and INDEL sites.
(5)利用QTL-seqr软件包对步骤(4)结果进行分析,六组混池结果共同指向一个共有主效位点qFS-chrD02-1(图1),其在物理图谱上的区间为3.15Mb(表1),该区段也包含了陆地棉纤维长度(图2、图3)、和衣分(图4)主效基因位点。(5) Using the QTL-seqr software package to analyze the results of step (4), the results of the six groups of pooled pools point to a common main site qFS-chrD02-1 (Figure 1), and its interval on the physical map is 3.15 Mb (Table 1), this segment also contains the major gene loci for upland cotton fiber length (Fig. 2, Fig. 3), and lint (Fig. 4).
表1 筛选共有区间信息Table 1 Screening common interval information
注:共有的峰值图所对应的D02染色体上的起始位置,长度等信息,最小的QTL起始位置为17241605bp, 终止位置为20388962bp,大小为3.15MB。Note: The starting position, length and other information on the D02 chromosome corresponding to the common peak map, the smallest QTL start position is 17241605bp, the end position is 20388962bp, and the size is 3.15MB.
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