增加穗粒数的水稻染色体代换系Z747鉴定及相关性状QTL定位

增加穗粒数对水稻高产品种培育至关重要。其遗传基础复杂,由多基因控制。水稻染色体片段代换系可以将多基因控制的复杂性状分解,因而是理想的遗传研究材料。本研究通过高代回交和自交结合分子标记辅助选择方法,鉴定了一个以日本晴为受体、西恢18为供体亲本的、含有15个代换片段的增加穗粒数的水稻染色体片段代换系Z747,平均代换长度为4.49 Mb。与受体日本晴相比, Z747的每穗总粒数、一次枝梗数、二次枝梗数、穗长和粒长显著增加,粒宽显著变窄、结实率显著降低,但结实率仍为81%。进一步以日本晴和Z747杂交构建的次级F2群体鉴定出46个相关性状的QTL,分布于水稻1号、2号、3号、5号、6号、9号、11号和12号染色体上。其中qGPP12、qPH-3-1、qPH-3-2等12个QTL可能与已克隆的基因等位, qSPP9等34个可能是新鉴定的QTL。Z747的每穗总粒数由2个具有增加粒数效应的QTL (qSPP3和qSPP5)和1个具有减少粒数效应的QTL (qSPP9)控制。研究结果对主效QTL的精细定位和克隆、以及有利基因的单片段代换系培育有重要意义。     

基于染色体片段置换系对水稻粒形及千粒重QTL检测与稳定性分析

粒形及千粒重是水稻产量的重要影响因素,通过挖掘这些性状的优异基因,对水稻超高产育种具有重要意义。本研究利用1套以籼稻恢复系昌恢121为背景亲本,粳稻越光为供体亲本构建的染色体片段代换系为材料,在3个环境下对水稻粒形及千粒重进行QTL检测及稳定性分析,共检测到59个QTL,分布于1号、2号、3号、4号、5号、6号、7号、10号、11号和12号染色体上,贡献率为0.77%～36.26%,其中发现10个QTL多效位点。值得关注的是qGW2-1、qGW2-2、qGW3-1、qGW3-2、qGL3和qGL12这6个QTL能在3个环境中重复检测到,其中qGW3-1为新鉴定的QTL位点。这些结果为进一步开展水稻粒形基因的精细定位、克隆和分子辅助育种奠定了一定的理论基础。     

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。     

Detection of QTLs to reduce cadmium content in rice grains using LAC23/Koshihikari chromosome segment substitution lines

To advance the identification of quantitative trait loci (QTLs) to reduce Cd content in rice (Oryza sativa L.) grains and breed low-Cd cultivars, we developed a novel population consisting of 46 chromosome segment substitution lines (CSSLs) in which donor segments of LAC23, a cultivar reported to have a low grain Cd content, were substituted into the Koshihikari genetic background. The parental cultivars and 32 CSSLs (the minimum set required for whole-genome coverage) were grown in two fields with different natural levels of soil Cd. QTL mapping by single-marker analysis using ANOVA indicated that eight chromosomal regions were associated with grain Cd content and detected a major QTL (qlGCd3) with a high F-test value in both fields (F = 9.19 and 5.60) on the long arm of chromosome 3. The LAC23 allele at qlGCd3 was associated with reduced grain Cd levels and appeared to reduce Cd transport from the shoots to the grains. Fine substitution mapping delimited qlGCd3 to a 3.5-Mbp region. Our results suggest that the low-Cd trait of LAC23 is controlled by multiple QTLs, and qlGCd3 is a promising candidate QTL to reduce the Cd level of rice grain.     

Development and evaluation of chromosome segment substitution lines (CSSLs) carrying chromosome segments derived from Oryza rufipogon in the genetic background of Oryza sativa L.

The wild relatives of rice (Oryza sativa L.) are useful sources of alleles that have evolved to adapt in diverse environments around the world. Oryza rufipogon, the known progenitor of the cultivated rice, harbors genes that have been lost in cultivated varieties through domestication or evolution. This makes O. rufipogon an ideal source of value-added traits that can be utilized to improve the existing rice cultivars. To explore the potential of the rice progenitor as a genetic resource for improving O. sativa, 33 chromosome segment substitution lines (CSSLs) of O. rufipogon (W0106) in the background of the elite japonica cultivar Koshihikari were developed and evaluated for several agronomic traits. Over 90% of the entire genome was introgressed from the donor parent into the CSSLs. A total of 99 putative QTLs were detected, of which 15 were identified as major effective QTLs that have significantly large effects on the traits examined. Among the 15 major effective QTLs, a QTL on chromosome 10 showed a remarkable positive effect on the number of grains per panicle. Comparison of the putative QTLs identified in this study and previous studies indicated a wide genetic diversity between O. rufipogon accessions.     

Detection and characterization of epistasis between QTLs on plant height in rice using single segment substitution lines

Hua-jing-xian 74 and its 12 single segment substitution lines (SSSLs) in rice were used as crossing parents to construct a half diallel crossing population. A total number of 91 materials were grown under three planting densities. By analysis of average plant height (PH) over all environments 10 SSSLs were detected with significant additives and 6 SSSLs with significant dominances. These SSSLs were further tested under different densities respectively, indicating that some of single locus effects were sensitive to densities and the conditions under the density of 16.7 cm × 16.7 cm maybe inhibited the expressing of these PH QTLs. Qualitative and quantitative analyses of each four participating genotypes indicated that digenic interactions among these QTLs were prevalent. Of 66 tested interactions, about 42.4% were epistatic (P < 5%). Although some QTLs hadn’t single locus effects, they were possible to form digenic interactions. A significant finding was that the detected epistases were mostly negative. Additionally, these epistases were also found being sensitive to planting densities, the conditions under the density of 10 cm × 16.7 cm perhaps promoted the expressing of epistatic interactions among PH QTLs.     

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。     

优良水稻染色体片段代换系Z746的鉴定及重要农艺性状QTL定位及其验证

粒型、株高及穗部组成性状与产量形成密切相关,是水稻重要农艺性状,但遗传基础复杂。染色体片段代换系是用于复杂性状遗传研究的良好材料。本研究鉴定了一个以日本晴为受体、西恢18为供体亲本的水稻优良染色体片段代换系Z746。Z746携带来自西恢18的7个代换片段,平均代换长度为3.99 Mb,其株高、粒长和穗部性状均与受体存在显著差异。进一步通过日本晴与Z746杂交构建的次级F2群体共检测到36个相关QTL,分布于2号、3号、4号、6号和11号染色体。其中5个可能与已克隆基因等位,如qPH3-1等, 8个可被多次检出,表明这些是遗传稳定的主效QTL。Z746的粒长主要由4个QTL(qGL3、qGL4、qGL2、qGL6)控制,其中qGL3和qGL4对粒长变异的贡献率分别为60.28%和27.47%。株高由5个QTL控制,穗长由4个QTL控制,每穗粒数由2个QTL控制,千粒重由2个QTL控制。然后以MAS在F3共选出8个单片段代换系,并以此在F4进行了相关QTL验证,共有24个QTL可被8个单片段代换系(SSSL)检出,重复检出率为66.7%,表明这些QTL遗传稳定。本研究为目的 QTL的进一步...     

Quantitative trait loci mapping for flag leaf traits in rice using a chromosome segment substitution line population

To study the genetic basis of rice flag leaf morphology, quantitative genetic analysis was conducted in a population of 37 chromosome segment substitution lines (CSSLs) of indica elite variety ‘Habataki’ in the background of japonica cultivar ‘Sasanishiki’ across three different environments. The CSSLs showed normal distribution with transgressive segregation, indicating that these four traits are controlled by polygenes. Moreover, analyses of variance showed that these traits were highly influenced by the growing environment, which are typical for polygenic quantitative traits. Seven quantitative trait loci (QTLs) on four chromosomes were detected in total: four for flag leaf width, one for flag leaf area and two for flag leaf angle. Two key QTLs, qFLW4 and qFLAG5 controlling flag leaf width and angle, respectively, were identified in all three environments. These QTLs could provide useful information for marker‐assisted selection in improving the performance of plant architecture with regard to leaf angle and area. Moreover, developed CSSLs with these QTLs information are also useful research materials to reveal the importance of leaf morphology in relation to grain yield.     

Construction of chromosomal segment substitution lines and genetic dissection of introgressed segments associated with yield determination in the parents of a super‐hybrid rice

Heterosis is a phenomenon whereby hybrids of inbred lines produce favourable phenotypes that exceed those of their parents. Traits of interest are higher yield and stronger stress tolerance. The two‐line super‐hybrid rice ‘Liangyoupei9’ (LYP9) shows superiority to both its elite inbred line ‘93‐11’ and ‘Pei'ai64s’ (‘PA64s’) parents and conventional hybrids. However, the genetic basis of its hybrid vigour, especially yield determination, remains elusive. In the present study, a set of 156 chromosome segment substitution lines (CSSLs) carrying overlapping segments from ‘PA64s’ in a genetic background of ‘93‐11’ were constructed and planted in six environments. Three major agronomic traits, viz. panicle length (PL), heading date (HD) and plant height (PH), and five yield‐related traits, viz. grain weight per panicle (GWP), number of grains per panicle (GPP), 1000‐grain weight (TGW), seed set (SS) and number of panicles of per plant (PPP), were evaluated over 3 years. Quantitative trait loci (QTL) analysis was conducted using a likelihood ratio test based on stepwise regression. Forty‐six putative QTL distributed on 11 chromosomes were detected in more than one year. Remarkably, GWP of four CSSLs carrying positive yield QTL outperformed the recurrent parent ‘93‐11’ by more than 15%, in at least two environments. These results indicate that CSSLs are effective in identifying yield‐associated traits, and lines harbouring such QTL will be rich in resources for future molecular breeding programmes.     

QTL mapping for agronomic and fibre traits using two interspecific chromosome substitution lines of Upland cotton

CS‐B14Sh and CS‐B22Sh are cotton interspecific chromosome substitution (CS)‐B lines, in which a pair of short arms of chromosome 14 and chromosome 22 were introgressed from Gossypium barbadense doubled‐haploid line 3‐79 with the background of Gossypium hirsutum line TM‐1, respectively. These two CS‐B lines were crossed with TM‐1, and segregating progenies (F₂ and F_2:3, respectively) were obtained. Phenotypic data of lint yield, yield‐related traits and fibre‐quality traits were collected from two trials. In the cross CS‐B14SH X TM‐1, QTL for boll weight (BW), lint percentage (LP), fibre upper half mean length (UHML), micronaire reading (MIC), and fibre breaking tensile strength (STR) were repeatedly detected. Alleles from 3‐79 decreased BW and MIC, but increased UHML and STR. In the cross CS‐B22Sh X TM‐1, QTL for BW, LP, UHML, MIC, STR, fibre elongation (EL),seed weight(SW), node of first fruiting branch (NFB) and fibre uniformity index (UI) were repeatedly detected, and alleles from 3‐79 decreased UHML, UI and STR, but increased NFB, SW, MIC and EL. QTL clusters were found in both populations.     

Detection of additive and additive×environment interaction effects of QTLs for yield‐component traits of rice using single‐segment substitution lines (SSSLs)

Additive effects (A) and additive‐by‐environment interactions (A×E) for five rice yield components were analysed using 20 SSSLs under mixed linear model methodology. Thirty‐one QTLs were detected. Different yield components have different QTL‐by‐environment (Q×E) interaction patterns. No A×E interaction effects were detected for the four QTLs for panicle number (PN). Four QTLs detected for spikelets per panicle (SPP) had A×E interactions. Five of seven QTLs detected for grains per panicle (GPP), two of 10 QTLs detected for 1000‐grains weight (GWT) and three of six QTLs detected for seed set ratio (SSR) showed significant A×E interaction. Most of these QTLs were distributed in clusters across the genome. The complexity of linkage and pleiotropy of these QTLs plus environmental effect may result in the diversity of the yield phenotype in the SSSLs. Only S19 exhibited a significant increase in yield with a predicted gain by 281.58 kg ha^?1. The results may be useful to design a better breeding strategy that takes advantage of QTL‐by‐environment interaction effects in each of the SSSLs.     

Construction of high‐throughput genotyped chromosome segment substitution lines in rice (Oryza sativa L.) and QTL mapping for heading date

Chromosome segment substitution lines (CSSLs) provide ideal materials for quantitative trait loci (QTLs) mapping and genetic dissection of complex traits. In this study, we developed a set of CSSL population consisting of 175 lines, which were derived between the recipient ‘Guangluai 4’ and the donor ‘Nipponbare’. Based on 260 molecular markers, we firstly constructed a physical map of core 97 lines. Then, these 97 lines were further genotyped based on resequencing data, and a resequencing‐based physical map was constructed. Compared with the molecular marker‐based physical map, the resequencing‐based physical map of 97 lines contained 367 substituted segments with 252 newly discovered segments. The total size of the 367 substituted segments was 1,074 Mb, which was 2.81 times the size of rice genome. Using the 97 CSSLs as materials, we identified nine QTLs for heading date and three of them were firstly reported. All the QTLs had positive additive effects, ranging from 9.50 to 16.50 days. These CSSLs may greatly help forge a new resource for functional genomics studies and molecular breeding in rice.     

QTL epistatic analysis for yield components with single‐segment substitution lines in rice

Epistasis is an important genetic component in determining the phenotype of complex quantitative trait. In this article, 12 single‐locus heterozygotes and 66 double‐locus heterozygotes were developed and then were applied to assay QTL epistasis for four yield‐associated traits under two planting densities. Of 264 (66 × 4) tested interactions, 130 (49.2%) were significant at the p < .05 level. QTL with the same effect directions had higher probabilities of interactions. The negative epistasis at least included one positive effect QTL but the positive epistasis one negative QTL. The detected epistasis was sensitive to planting density. Epistasis also exhibited pleiotropic effects.     

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.     

Genetic analysis of agronomic and fibre traits using four interspecific chromosome substitution lines in cotton

Backcrossed chromosome substitution lines (CS‐B) have been developed with a homologous pair of chromosomes or chromosome arms of Gossypium barbadense (3‐79) germplasm substituted for the homologous Gossypium hirsutum(TM‐1) chromosomes or chromosome segments. We report on agronomic and fibre trait performance of four backcrossed chromosome or chromosome arm substitution lines including chromosomes 01, 11sh (chromosome 11 short arm), 12 sh and 26 Lo (chromosome 26 long arm). Data for agronomic and fibre traits were collected from replicated field experiments at two different locations in 2 years, and analysed under an additive dominance genetic model. CS‐B 12sh had higher, while CS‐B 01 and CS‐B 26Lo had lower boll weight than TM‐1. The presence of significant negative additive effects for micronaire with CS‐B 01 and significant positive additive effects for elongation and fibre strength with CS‐B 11sh suggested the substituted chromosome arms of 3‐79 in these CS‐B lines were more likely carrying genes causing these effects. Results revealed that several CS‐B lines had significant homozygous and heterozygous dominance effects for different agronomic and fibre traits suggesting that specific CS‐B lines may be useful for improving agronomic and fibre traits in hybrid cottons. These CS‐B lines also provide novel genetic resources for improving upland cotton germplasm.     

Identification and application of major quantitative trait loci for panicle length in rice (Oryza sativa) through single‐segment substitution lines

Panicle length (PL), an important yield‐related trait, strongly affects yield components, such as grain number, grain density and rice quality. More than 200 panicle length quantitative trait loci (PL QTLs) are identified, but only a small number are applied in rice breeding. In this study, we performed QTL analysis for PL using 42 single‐segment substitution lines (SSSLs) derived from nine donors in the genetic background of HJX74. Fourteen QTLs and five heterosis QTLs (HQTLs) for PL were recognised. Three QTLs and four HQTLs acted positively, and the other eleven QTLs and one HQTL acted negatively. By scanning the single heterozygous background region of the F₂ population with large‐genetic‐effect SSSLs, we mapped PL loci qPL6‐2 and qPL7‐1 to different locations on chromosomes 6 and 7, respectively, in three consecutive years of independent trials. The genetic effects of these QTLs were further assessed. qPL6‐2 demonstrated the most positive additive effect (QTL), whereas qPL7‐1 achieved the most positive dominant effect (HQTL) for PL. These results indicated that the pyramiding of PL QTLs might increase grain yield and facilitate the application of the beneficial allele in hybrid rice breeding.     

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.     

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。