利用东乡普通野生稻染色体片段置换系定位产量相关性状QTL

以东乡普通野生稻和日本晴为亲本构建的染色体片段置换系为研究材料, 2019年分别在北京、山东临沂和江西南昌对分蘖数、穗粒数和粒形等11个产量相关性状进行多环境鉴定,结合染色体片段置换系基因型数据定位水稻产量相关性状QTL。3个环境共检测到68个QTL,包括株高4个、穗长5个、分蘖数2个、一次枝梗数7个、一次枝梗粒数8个、二次枝梗数8个、二次枝梗粒数10个、每穗粒数6个、千粒重7个、粒长8个和粒宽3个; LOD值介于2.50～12.66之间,贡献率变幅为4.67%～27.79%,15个QTL的贡献率大于15%;24个QTL与已报道位点/基因位置重叠,44个QTL为新发现位点; 6个QTL在2个环境能被检测到, 1个QTL qTGW2能在3个环境检测到,且是还未报道的新位点。最后,利用BSA法验证了qPH7、qPBPP8-2和qGW10三个QTL的可靠性。本研究将为后续产量相关性状基因克隆以及进一步解析其遗传基础和分子调控机制奠定基础。     

基于陆地棉背景的海岛棉染色体片段导入系产量性状QTL定位

棉花产量分为籽棉产量和皮棉产量,其中高皮棉产量总是育种的首要目标。皮棉产量由单株铃数、衣分、单铃重等因素组成。其中衣分在各因素中的遗传率最高,同时也是产量育种中重要的选择指标。育种中利用分离群体对单株铃数、铃重等产量性状选择受环境影响较大。利用染色体片段导入系进行铃数、铃重等产量性状的定位,定向改良产量性状,是棉花分子设计育种的有效方法。本研究利用陆地棉TM-1为轮回亲本和海岛棉海7124为非轮回亲本构建了一套陆地棉背景的染色体片段导入系,并在7个环境的田间试验下,鉴定了它们的产量表现,定位了28个与单株铃数、铃重、衣分和籽指相关的QTL。其中,在Dt亚组染色体上鉴定出的产量性状QTL多于在At亚组染色体上鉴定出的。28个QTL中,加性效应为正的16个,加性效应为负的12个,表明海岛棉不同的导入片段效应不同,有的片段可以提高陆地棉产量,有的则降低陆地棉产量。在6个环境下,导入系IL008(特征标记NAU2573和NAU3576)的衣分均显著高于轮回亲本TM-1,因此IL008可以应用于棉花分子育种,定向改良陆地棉的衣分。     

利用染色体片段代换系定位陆地棉株高QTL

以陆地棉中棉所36为轮回亲本和海岛棉海1为供体亲本, 构建染色体片段代换系。为了能检测到稳定的株高QTL,将三个代换系群体(BC₅F₃, BC₅F_3:4和BC₅F_3:5)在5个环境中种植,2009年和2010年分别在河南安阳种植BC₅F₃单株、BC₅F_3:4株行, 2011年分别在河南安阳、辽宁辽阳和新疆石河子种植BC₅F_3:4株系。结果表明,在不同群体环境中株高的超亲比例为53.43%~88.97%。从早期构建的总图距为5088.28 cM, 含有2280个SSR标记位点,覆盖26条染色体的遗传连锁图谱中筛选标记,对408个单株进行的SSR鉴定,结果检测到16个株高QTL,分布在10条染色体上。单个QTL解释的表型变异为7.35%~13.17%。有7个QTL在2个以上环境被检测到。与标记MUSS563紧密连锁的qPH-15-19在一个环境中被检测到,在前人的研究中也有报道。这些结果为进一步精细定位QTL、基因克隆、分子辅助选择等研究奠定基础。     

利用海岛棉染色体片段导入系定位衣分和籽指QTL

以染色体片段导入系IL-15-5和IL-15-5-1构建的F2和F2:3分离群体,利用SSR标记对数量性状衣分和籽指QTL进行了定位。应用复合区间作图法分析两个组合的774个F2单株和F2:3家系衣分和籽指,检测到2个衣分的QTL,1个籽指的QTL。衣分QTLqLP-15-1在两世代中都被检测到,位于相同的分子标记置信区间JESPR152～NAU3040,置信的遗传距离分别为5.40cM和3.20cM;qLP-15-2只在F2:3中被检测到,位于分子标记NAU5302～NAU2901之间,置信的遗传距离为0.08cM。籽指QTLqSI-15-1在F2和F2:3中都被检测到,分别位于分子标记NAU2814～NAU3040和JESPR152～NAU3040,置信的遗传距离分别为6.70cM和5.70cM。利用染色体片段导入系能准确地定位产量组分的QTL,为棉花产量的分子设计育种奠定基础。     

染色体单片段代换系的构建及应用于QTL精细定位

染色体片段代换系(Chromosome Segment Substitution Lines,CSSLs),又称为代换系(Substitution lines,SLs)或导入系(Introgression lines,ILs)。只含一个代换片段的代换系,即单片段代换系(Single Segment Substitution Lines,SSSLs)是理想的代换系。单片段代换系只有代换片段与受体亲本不同,其它遗传背景与受体亲本完全一致,对代换区段中的QTL进行分析时遗传背景干扰很小,有利于QTL的分析,不少学者利用单片段代换系材料对许多QTL进行了鉴定和精细定位,并克隆了一些重要性状的QTL。本文介绍了染色体单片段代换系构建的原理和利用微卫星标记(SSR）进行单片段代换系鉴定的方法,讨论了代换系构建过程中值得注意的问题,并对用染色体单片段代换系进行QTL精细定位做了展望。     

利用染色体片段代换系定位水稻叶片形态性状QTL

水稻叶片形态是理想株型的重要组成部分,控制叶片形态基因的挖掘对于塑造水稻理想株型,实现水稻超高产目标具有重要意义。本研究利用广陆矮4号为受体亲本,日本晴为供体亲本构建的一套染色体片段代换系,对水稻上三叶(倒一叶、倒二叶和倒三叶)形态性状与单株籽粒产量进行了相关性分析,并开展了相关QTL定位。结果表明,除剑叶宽外,水稻上三叶的叶长、叶宽都与单株产量呈极显著正相关。同时,通过单因素方差分析和Dunnett’s多重比较,在两年间重复检测到20个控制叶形的QTL,其中叶长QTL 13个(8个表现正向效应,5个表现负向效应);叶宽QTL 7个(4个表现正向效应,3个表现负向效应)。这些QTL的鉴定为水稻叶形性状的分子改良提供了重要遗传信息。     

利用染色体片段置换系定位低温影响水稻萌芽期根长和芽长QTL

根和芽的正常生长和发育对保障水稻产量有重要作用。为探究在低温条件下影响幼芽期根长和芽长的QTL,以9311（受体）和日本晴（供体）染色体片段置换系群体为材料,将萌发种子置于15℃低温处理7d,然后在25℃下恢复生长7d,连续测量根长和芽长,以25℃下根长和芽长作为对照,定位低温条件下影响根长和芽长的QTL。15℃条件下,定位到9个根长QTL,贡献率为8.65%~24.35%,其中qRL15T7.2和qRL15T10.3在根生长不同时期被重复检测到;定位到9个影响芽长的QTL,贡献率为1.73%~28.89%,其中qBL15T6、qBL15T7、qBL15T9和qBL15T10被重复检测到。25℃条件下,定位到9个根长QTL,贡献率为1.73%~28.89%,qRL25T7、qRL25T9.3、qRL25T10和qRL25T12在根生长不同时期被重复检测到;定位到5个影响芽长QTL,贡献率为0.58%~38.26%,qBL25T3.3在芽生长不同时期被重复检测到。其中,第2、7、9和10号染色体上4个Bin标记区域存在既控制根长又控制芽长的QTL。通过比较发现,15℃下定位到的根长或芽长QTL与25℃定位到的根长或芽长QTL均不相同,表明低温条件下控制水稻幼芽期根和芽生长的遗传机制可能与正常温度下不同。     

基于染色体片段置换系群体检测水稻株型性状QTL

株型是由多个形态和生理性状集成的复合性状,它与水稻产量密切相关。挖掘优异株型等位基因或QTL,对水稻超高产育种具有重要意义。本研究利用籼稻昌恢121和粳稻Koshihikari构建的208个染色体片段置换系(chromosome segment substitution lines, CSSLs),在3个环境下,对控制株高、剑叶形态和分蘖数的QTL进行检测,共鉴定到35个株型性状QTL,分布于11条染色体上(除9号染色体以外),解释表型变异2.00%～22.86%。值得关注的是qPH-1-1、qFLW-6和qFLA-3均能在3个环境下被检测到,其中qFLW-6为1个新鉴定到的剑叶宽QTL。对qPH-1-1和qFLA-3位点进行鉴定,验证了这2个位点等位基因的加性效应和环境稳定性。本研究为株型性状QTL的进一步精细定位、克隆及分子辅助聚合育种奠定了基础。     

利用陆地棉置换系进行海岛棉主要性状基因的染色体定位

 利用海岛棉染色体置换陆地棉一对染色体或染色体臂的置换系,进行主要农艺性状、抗黄萎病性和纤维品质基因染色体定位。结果表明,海岛棉1号染色体可以增加株高;16、17、18、4号染色体携带降低铃数基因;22Lo、22Sh、16、11Sh、26Lo号染色体可以提高衣分;大部分染色体降低铃重。16、26Lo染色体可以增强抗黄萎病性。对纤维品质性状分析表明,14Sh、26Lo号染色体可以提高纤维长度;14Sh、15Sh号染色体可以提高强度;4号染色体可以降低麦克隆值;22Sh、16、22Lo、11Sh号染色体可以提高伸长率。推测这些染色体上可能具有对应性状的基因。     

水稻高秆染色体片段代换系Z1377的鉴定及重要农艺性状QTL定位

株高是水稻重要的农艺性状, 往往与产量相关性状密切关联, 在水稻育种中有重要利用价值。本研究以日本晴为受体、缙恢35为供体亲本, 经表型和分子标记双重选择, 鉴定了一个水稻高秆染色体片段代换系Z1377。Z1377共含有18个代换片段, 平均代换长度为2.95 Mb。与日本晴相比, Z1377的株高、倒一节间至倒四节间长、穗长、一次枝梗数、二次枝梗数、粒长、每穗实粒数、总粒数显著增加; 粒宽显著变细, 有效穗数、结实率显著减少, 但仍达86.75%。用日本晴与Z1377杂交构建的次级F₂群体共检测到16个相关QTL, 分布于第2、第3、第4、第5、第6、第7和第9染色体。其中有8个可能与已克隆基因等位, 如GW2、EUI1、ZFP185等, 另8个如qPH3等尚未见报道。Z1377的株高由一个主效QTL (qPH3)和一个微效QTL (qPH5)控制, 其中qPH3的贡献率达28.59%。而且, 在F₂群体中, 高秆和矮秆基本呈现双峰分布, 经卡平方测验, 符合3∶1分离比, 表明高秆对矮秆显性, 并主要由qPH3负责。这将为该主效基因的精细定位和克隆奠定基础, 同时为进一步选育含2~3个代换片段的中高优良染色体片段代换系并应用于育种奠定基础。     

Mapping QTL of Fiber Yield and Quality Traits in F2 Populations of Chromosome Segment Substitution Lines from Gossypium hirsutum × Gossypium barbadense

In this study, F₂ populations from two chromosome segment substitution lines MBI7455 and MBI7358, were quantified using SSR to evaluate the parents' genotype and detect QTL related to fiber quality plus yield traits of cotton. Results show that the recurrent parent (CCRI45) hosted 96.70% and 95.60% of chromosome segment substitution in MBI7455 with 12 chromosome segments and in MBI7358 with 16 chromosome substitution segments of Gossypium barbadense, respectively. In the F₂ population, the average rate of chromosome substitution of the recurrent parent (CCRI45) was 96.44%, and the average segments of chromosome substitution of Gossypium barbadense was 13.42, with an average segments of homozygous donor chromosome value of 3.90. Analysis showed 19 fiber quality-related QTL with a phenotypic variance of between 2.52%-13.11% and seven yield traits-related QTL with a range of 2.93%-11.40% phenotypic variance, resulting in a total of 26 QTL. The CSSLs could be used to detect QTL for fiber yield and quality traits, which offer an important foundation for the cotton molecular-assisted breeding.     

Evaluation of Chromosome Segment Substitution Lines Related to Fiber Yield and Quality Traits from Gossypium hirsutum×Gossypium barbadense

Three generations of chromosome segment substitution lines lines (BC₄F₃, BC₄F_3:4, and BC₄F_3:5, Anyang, Korla) were used to evaluate phenotypic traits related to fiber yield and quality. The average performance of the traits in the population was near to the control, CCRI45, in the four populations. Seventy-eight percent of the lines showed longer and stronger fibers than the recurrent parent, and 22.59%～53.61% of lines had bigger bolls and higher lint percentages than the recurrent parent. Correlation analysis showed that the yield and fiber quality traits were positively correlated among the four populations. These results indicated that most of the genetic background in the substitution lines has been restored to the recurrent parent with abundant genetic variations. In addition, most of substitution lines had good yield and fiber quality. This study provided a large amount of basic research materials for cotton quantity genetics, gene pyramiding, and gene function analysis, and provided parent materials and new strains that can directly applied for cotton breeding.     

Improving Fiber Quality Traits of Xinluzao 45 Using Gossypium barbadense Chromosome Segment Substitution Lines

Gossypium barbadense chromosome segment substitution lines could be used as an important germplasm resource for improving fiber quality traits of upland cotton. In this study, we used TM-1 background substitution lines CSSL-122, the Xinjiang upland cotton Xinluzao 45 and hybrid, backcross progeny BC₂F₁ populations comprising 120 individual plants as test materials. Nineteen SSR markers located in Gossypium barbadense chromosomes land inked with fiber length and strength were used to screen out obvious polymorphic primers between the parents. We then traced and detected chromosome segments of Gossypium barbadense in the BC₂F₁ populations. Simultaneously, we compared fiber quality traits of positive plants that contained Gossypium barbadense chromosome segments with non-positive plants in the BC₂F₁ populations. The results showed that two markers, NAU2987 and BNL3145, which were linked with fiber length, could accurately identify the positive plants. In addition, compared with non-positive plants, the increased fiber length and strength of the positive plants were very significant (P < 0.01). Our research suggested that alien Gossypium barbadense chromosome segments significantly improved the fiber quality traits of Xinluzao 45. Thus, the Gossypium barbadense chromosome segment substitution lines will provide a vital theoretical basis and practical reference for improving Upland Cotton fiber quality traits.     

A Preliminary Study of Mapping Genes Underlying Complex Traits Based on Chromosome Segment Substitution Lines

Complex traits are the features whose properties are determined by multiple factors, which can be genetic or environmental. Most of economically important characteristics of plants and animals belong to this special category. Hence, identification of genes underlying complex traits is theoretical and applied important. However, the conventional mapping populations with complex genetic background pose major challenge to distinguish the single QTL responsible for phenotypic variation. Paterson et al. （1990） pioneered the research on fine mapping of QTL by substitution mapping method. Nadeau et al. （2000） discussed the construction, applications and advantages of chromosome segment substitution （CSS） lines for dissecting complex traits. Indeed, CSS lines with the controlled genetic noise from genome background are ideal material for studying individual QTL as a Mendelian factor. In flee, CSS lines have been created for QTL fine mapping and further functional research （Ebitani et al., 2005; Xi et al., 2006）.     

QTL Mapping for Yield and Fiber Quality Traits in Double-Cross Population of Chromosome Segment Introgression Lines from Gossypium hirsutum×Gossypium barbadense

[Objective] The aim of this study was to map quantitative traits loci (QTLs) for yield and fiber quality traits in chromosome segment introgression lines (CSILs) from Gossypium hirsutum×Gossypium barbadense. [Method] Four CSILs, MBI 7115, MBI 7412, MBI 7153 and MBI 7346, which were obtained by advanced backcrossing and continuous inbreeding from upland cotton variety CCRI 45 and sea-island cotton variety Hai 1, were used to construct double-cross segregating populations F1 and F1:2 through the following crosses: [(MBI 7115×MBI 7412)×(MBI 7153×MBI 7346)]. Simple sequence repeat (SSR) molecular markers were used to evaluate the genotyes of parents. The F1 and F1:2 populations were used to map QTLs for yield and fiber quality-related traits. [Result] The recovery rates of the recurrent parent CCRI 45 in the four CSILs were all above 97%. Forty-one QTLs, which were distributed across 11 chromosomes, were detected using the two segregating populations. There were 30 QTLs controlling fiber quality with phenotypic variations ranging from 1.11% to 11.80% and 11 QTLs controlling yield-related traits with 1.09%–13.57% phenotypic variations. [Conclusion] Five QTLs for fiber quality were consistently detected in two populations and they were all newly discovered QTLs. This study provides an important theoretical basis for fine mapping of these QTLs and molecular marker-assisted breeding for excellent fiber quality.     

基于染色体单片段代换系的水稻粒形QTL定位

水稻的粒形是影响水稻产量和品质的重要因子之一, 是由多基因控制的数量性状。染色体单片段代换系由于减少了个体间遗传背景的干扰, 已经成为鉴定复杂性状QTL的新型遗传材料。本研究以广陆矮4号为受体,日本晴为供体的119个染色体单片段代换系群体为试验材料,通过单因素方差分析和Dunnett’s多重比较,测验单片段代换系与受体亲本之间粒形的差异,鉴定了代换片段上粒形相关的QTL。以P≤0.001为阈值, 共检测到39个粒形相关的QTL。其中,粒长相关的19个,其加性效应值为0.18~1.06 mm,加性效应百分率为2.40%~14.13%;粒宽相关的14个,其加性效应值为0.09~0.31 mm,加性效应百分率为2.71%~9.15%;粒厚相关的6个,其加性效应值为0.05~0.10 mm,加性效应百分率为2.14%~4.46%。这些QTL的鉴定,为进一步精细定位并克隆相应QTL和高产、优质水稻新品种的分子标记辅助选择奠定了基础。     

利用9311来源的粳型染色体片段代换系定位控制稻米糊化温度的微效QTL

糊化温度(gelatinization temperature, GT)是评价稻米蒸煮与食味品质的重要因素之一, 除受一主效基因控制外, 还受多个微效基因的影响。本研究利用粳稻品种日本晴和籼稻品种9311作为受体和供体来源的一套染色体片段代换系为研究对象, 于2010-2011年连续2年分别于2个环境内种植, 测定各株系稻米的糊化温度(碱消值), 利用t测验与轮回亲本比较。结合高通量重测序技术鉴定各代换系的基因型, 以一年两地检出的极显著差异位点作为一个QTL, 共检测到4个控制GT的微效QTL, 即qGT2-1、qGT7-1、qGT8-1和qGT12-1, 分别位于第2、7、8和12号染色体上。加性效应分析结果显示, 4个QTL的效应值均为负值, 表明来自籼稻品种9311的这4个片段对碱消值的效应均为负效应。其中qGT7-1和qGT12-12个QTL在2年4个环境均被检测到, 遗传效应的趋势也一致, 加性效应贡献率为11.31%~28.95%。以受体亲本碱消值差异最大的代换系N53株系及亲本为材料, 对稻米淀粉精细结构进行分析, 推测支链淀粉中短链含量的减少可能会引起GT的升高。上述结果为进一步精细定位和克隆相应QTL及开展稻米品质改良的分子育种奠定了基础。