应用剩余杂合体衍生的近等基因系分解水稻产量性状QTL

以杂合区间为RM587-RM402的水稻剩余杂合体（RHL）衍生群体为材料,应用SSR标记检测,筛选到杂合区间分别为RM587-RM225、RM204-RM6119和RM6119-RM402的3个单株,进一步检测其F2群体,分别获得母本纯合型材料10株、父本纯合型材料10株和杂合型材料20株。种植这3套近等基因系材料,考查单株产量及其构成因子每株穗数、每穗实粒数和千粒重。经应用目标区间内等位基因效应分析和交迭重组染色体片段代换系分析,分解出3个控制每穗实粒数的QTL和2个控制单株产量的QTL,这些QTL分别位于物理距离为0.66 ~ 2.49 Mb的区间中,全部表现为加性作用为主,增效等位基因除qNFGP6 1来自父本密阳46外,其余均来自母本珍汕97B。提出了构建新型遗传材料,提高水稻QTL精细定位效率的策略。     

Quantitative Trait Loci for Yield Traits Located Between Hd3a and Hd1 on the Short Arm of Chromosome 6 in Rice

QTLs for heading date located in the region between Hd3a and Hd1 were detected using an F2:3 population developed from a residual heterozygous line (RHL) identified from the recombinant inbred lines of the indica rice cross Zhenshan 97B/Milyang 46. Linkage in coupling phase between the heading date QTLs and QTLs for yield traits detected in a previous study was found. Four more F2:3 populations were each developed from an RHL, which were homozygous at Hd3a and Hd1 but heterozygous in a portion of the intervals flanked by Hd3a and Hd1. QTLs for grain yield per plant, number of panicles per plant, number of grains per panicle and 1000-grain weight were detected in the heterozygous region. Five sets of near-isogenic lines (NILs) with overlapping heterogenous segments covering the interval RM6119-RM6779 were developed and used to validate and delimitate the QTLs. A QTL having a consistent effect for the number of grains per panicle was located within the interval RM19615-RM19652 that corresponded to a 514.4 kb region on chromosome 6. The same region might have pleiotropic effects on the other three yield traits analyzed, but the effects varied greatly among different populations and across different environments. This study suggests that it is possible to develop a population with little variation on heading date and to identify QTLs for yield traits that might not be associated with heading date by using information of the physical positions of DNA markers and cloned genes.     

Dissection of QTLs for Yield Traits Using Near Isogenic Lines Derived from Residual Heterozygous Lines in Rice

Three residual heterozygous lines (RHLs) carrying heterozygous segments in the intervals RM587-RM225, RM204-RM6119 and RM6119-RM402 on the short arm of rice chromosome 6, respectively, were selected from a rice population derived from an RHL for the interval RM587-RM402. Ten maternal homozygotes, 10 paternal homozygotes and 20 heterozygotes were selected from each of the F2 populations derived from the three RHLs. The three sets of near isogenic lines (NILs) were grown to detect the grain yield per plant, n...     

水稻第1染色体短臂粒长和粒宽QTL的精细定位

以第1染色体短臂RM1-RM3746和RM151-RM243区间内呈杂合、背景基本纯合的2个水稻剩余杂合体（RHL）衍生两个F6群体,将控制水稻粒长和粒宽的2个粒形QTL（qGL 1和qGW 1）定位于RM3746-RM243区间内。在此基础上,应用SSR标记检测,从其中1个群体中筛选到杂合区间分别为RM151-RM10404、RM10398-RM5359、RM10435-RM259和RM10381-RM243的4个单株,应用SSR标记进一步检测4套F2群体,从每套F2群体中分别筛选到母本珍汕97B和父本密阳46纯合型材料各10株,自交获得4套近等基因系材料并考查其粒长和粒宽。利用交迭重组染色体片段代换系分析法,将控制粒长和粒宽的QTL （qGL 1和qGW 1）界定于437.5 kb的RM10390-RM1344区间和392.9 kb的RM10376-RM10398区间,增效等位基因均来自母本珍汕97B,表明qGL 1和qGW 1是紧密连锁的不同座位。     

Fine-Mapping of qTGW1.2a,a Quantitative Trait Locus for 1000-Grain Weight in Rice

Thousand-grain weight(TGW) is a key component of grain yield in rice. This study was conducted to validate and fine-map qTGW1.2a, a quantitative trait locus for grain weight and grain size previously located in a 933.6-kb region on the long arm of rice chromosome 1. Firstly, three residual heterozygotes(RHs) were selected from a BC_2F_(11) population of the indica rice cross Zhenshan 97(ZS97)///ZS97//ZS97/Milyang 46. The heterozygous segments in these RHs were arranged successively in physical positions, forming one set of sequential residual heterozygotes(SeqRHs). In each of the populations derived, non-recombinant homozygotes were identified to produce near isogenic lines(NILs)comprising the two homozygous genotypes. The NILs were tested for grain weight, grain length and grain width. QTL analyses for the three traits were performed. Then, the updated QTL location was followed for a new run of SeqRHs identification-NIL development-QTL mapping. Altogether, 11 NIL populations derived from four sets of SeqRHs were developed and used. qTGW1.2a was finally delimitated into a77.5-kb region containing 13 annotated genes. In the six populations segregating this QTL, which were in four generations and were tested across four years, the allelic direction of qTGW1.2a remained consistent and the genetic effects were stable. For TGW, the additive effects ranged from 0.23 to 0.38 g and the proportions of phenotypic variance explained ranged from 26.15% to 41.65%. These results provide a good foundation for the cloning and functional analysis of qTGW1.2a.     

利用剩余杂合体衍生的近等基因系精细定位水稻粒长微效QTL qGL1.1

【目的】本研究旨在对前期在水稻第1染色体长臂521.8 kb的区间内定位到的q TGW1.1b进行精细定位。【方法】从qTGW1.1和qTGW1.2所在区间分别呈杂合的2个BC2F9单株配组衍生的F4群体中,筛选到Wn28826-RM1231区间内杂合片段呈梯系排列的3个单株,构建了3套F5:6近等基因系。2017年种植于浙江杭州,考查千粒重、粒长和粒宽。利用SAS软件的GLM程序进行双因素方差分析,对qTGW1.1b的效应进行了验证。在此基础上,筛选出杂合片段更小且呈交迭排列的6个剩余杂合体,发展了6套F8:9近等基因系,2018年种植于海南陵水。对每套近等基因系中双亲基因型株系的表型差异进行双因素方差分析。【结果】qTGW1.1b在2个试验中对粒长和千粒重均呈极显著差异,效应方向一致且大小稳定。密阳46等位基因能分别增加粒长0.027 mm和提高千粒重0.17 g,贡献率分别达到27.12%和19.09%。【结论】鉴于qTGW1.1b在前后试验中对粒长影响最为显著,而对粒宽作用不显著,故将qTGW1.1b重新命名为qGL1.1。通过比较各套近等基因系的分离区间的基因组位置,最终将qGL1.1定位于Wn29077和Wn29154之间约76.8 kb的区间内。     

粳稻垩白性状的QTL检测

 利用大粒粳稻DL115与小粒粳稻XL005杂交获得的F2群体200个单株为作图群体,采用复合区间作图方法,利用SSR标记对稻米垩白性状进行了数量性状基因座(QTL)检测。研究结果表明,稻米垩白粒率、垩白大小和垩白度在F3株系均呈连续分布,表现为由多基因控制的数量性状。检测到与稻米垩白性状相关的QTL 8个,分别位于第3（5个）、第5（2个）和第6（1个）染色体上,包括与垩白粒率有关的QTL 3个,与垩白大小相关的QTL 2个,与垩白度有关的QTL 3个。其中位于第3染色体RM6832-RM411、RM15456-RM6832和RM6266-RM15456区间的qPGWC3、qACE3b和qDEC3b,分别解释垩白粒率、垩白大小和垩白度表型变异的43.89%、18.83%和19.57%,为主效QTL。上述3个主效QTL所在染色体上的位置与前人研究结果均不一致,认为是新的QTL。所检测到的8个QTL中,除qPGWC6的增效等位基因来自无垩白亲本XL005外,其他7个QTL的增效等位基因均来自垩白性状值较大的亲本DL115。垩白粒率和垩白大小基因作用表现为部分显性,垩白度基因作用表现为加性。     

水稻第6染色体短臂株高及产量性状QTL的分解

针对第6染色体短臂上一个对产量性状遗传具有重要作用的区间RM587-RM19715,从珍汕97B/密阳46重组自交系群体中筛选到1个剩余杂合体,自交衍生获得一个由195个个体组成的F2群体,检测控制株高和产量性状的QTL。经分析,在目标区间的上部和下部分别检测到1个QTL簇,分别对除单株穗数以外的产量性状因子具显著作用,单个QTL对群体性状表型变异的贡献率为5.0%~55.5%。将第6染色体上的产量性状QTL分解到更小的区间中,为产量性状QTL的精细定位和克隆打下了基础。     

籼稻C84和粳稻春江16B重组自交系遗传图谱构建及籽粒性状QTL定位与验证

【目的】本研究旨在挖掘水稻粒型新基因、探索其分子机理,解析籽粒发育调控遗传网络奠定基础,并为通过分子标记聚合有利基因开展超级稻分子设计育种提供理论依据。【方法】以植株和籽粒形态差异较大的晚粳稻品种春江16B(CJ16B）和广亲和中籼稻背景恢复系C84为亲本构建含有188个家系的重组自交系为作图群体,利用158对在双亲中存在多态性差异的分子标记,构建了遗传连锁图谱,总遗传距离为1428.40cM,平均标记间距为9.04cM。在构建遗传图谱的基础上,完成RIL188个株系籽粒的粒长、粒宽、粒厚、长宽比和千粒重等5个性状考查并进行QTL定位。【结果】在海南陵水和浙江杭州两地共检测到籽粒相关主效QTL30个,包括籽粒QTL新座位18个,解释遗传变异3.51%~17.25%。其中粒长、粒宽、粒厚和长宽比QTL位点分别为9个、5个、5个和6个,千粒重QTL位点5个。经基因座位比对,发现有5个QTL区间与已克隆的调控籽粒形态相关基因座位相近,我们通过对双亲目标基因的测序并根据差异位点设计dCAPs分子标记进行验证。【结论】该RIL群体及其遗传图谱可用于水稻重要农艺性状主效QTL基因的定位和克隆,新定位的18个粒型QTL可以为水稻籽粒发育调控网络提供补充和资料积累。     

水稻胚芽鞘长度与抗旱性的关系及QTL定位

对由水稻品种珍汕97B和旱稻品种IRAT109构建的重组自交系195个株系的胚芽鞘长度及抗旱系数的研究表明,水分胁迫下水稻重组自交系群体的胚芽鞘长度与抗旱系数的相关系数为0.2206**。应用由213个SSR标记构建的遗传连锁图对控制胚芽鞘长度和抗旱系数的QTL进行了定位。检测到胚芽鞘长度和抗旱系数的主效QTL各为13个和5个,单个QTL对表型的贡献率为2.28%～22.65%;在第9染色体上两者的QTL出现在相同的分子标记区间（RM160-RM215）。检测到胚芽鞘长度和抗旱系数的互作位点分别为17对和3对,影响胚芽鞘长度的互作位点联合贡献率为5835%;影响抗旱系数的互作位点联合贡献率为11.93%。控制胚芽鞘长度和抗旱系数的QTL分别与其他研究中控制根系性状（深根干质量、根深、根长、根数等）的QTL位于相同的标记区间。     

水稻单穗重和千粒重的QTL定位

用基于混合线性模型的统计方法对一套来源于亲本IR64/Azucena的加倍单倍体群体在两个生产季节的水稻单穗重和千粒重进行了分析,各检测到15个QTL分别控制这两个性状,其中有6个QTL同时与这两个性状有关。所有QTL分布在除第11、12染色体以外的其余10条染色体的相应标记区间内。在控制千粒重的QTL中,12个QTL有加性效应,6对QTL带有加加上位性效应,它们不受环境条件的影响。在控制单穗重的QTL中,7个QTL具有加性效应,但其中4个QTL的表达随环境而异;6对QTL具有加加上位性,但其中1对对环境敏感。qTGW2的加性效应对千粒重的贡献率超过10%;3个QTL（qGW1、qGW7和 qGW8 1）在早季环境的加性效应对单穗重的贡献率亦都大于10%,但对环境敏感。     

特大粒水稻材料粒型性状的QTL检测

 利用特大粒粳稻TD70（2011年千粒重达80 g）和籼稻品种Kasalath杂交,经单粒传法获得的240个重组自交系（RIL）为作图群体,分别于2010年和2011年对粒长、粒宽、粒厚性状进行鉴定,用完备区间作图法,以均匀分布于12条染色体的141个SSR标记对粒型性状进行QTL检测。共检测到粒型性状的 QTL 18 个,分布于第2、3、5、7、9和12染色体上。其中,控制粒长的QTL 5个,控制粒宽的QTL 6个,控制粒厚的QTL 7个。两年间均能检测到的QTL有7个,分别为粒长QTL qGL3.1,粒宽QTL qGW2.1、qGW2.2、qGW5.1、qGW5.2,粒厚QTL qGT2.3、qGT3.1;其平均贡献率分别为56.19%、4.42%、29.41%、10.37%、7.61%、21.19%和17.06%。第2染色体RM1347-RM5699区间是粒长、粒宽、粒厚的共同标记区间。第3染色体RM6080-RM6832区间为粒长qGL3.1、粒厚qGT3.1共同标记区间。18 个QTL的增效等位基因均来源于大粒亲本TD70,且增效作用显著。定位的大部分位点包含已报道的精细定位和克隆的主要粒型基因;除第2染色体的qGW2.1（qGT2.1）、qGW2.3、qGL2.2和第12染色体的qGT12等位点已有粒型性状相关报道外,定位的qGT22,qGW9 和qGT9可能是新的QTL。     

RFT1与Hd1所在区间对水稻抽穗期、株高和千粒重的作用

 抽穗期是决定水稻品种适应地区和季节的关键性状。水稻抽穗期QTL对产量性状和（或）株高具多效作用是个普遍现象, 但是, 除了Ghd7和DTH8（Ghd8）, 其他水稻抽穗期基因的多效性尚需进一步验证。本研究针对抽穗期基因RFT1 Hd3a所处区间和Hd1所处区间, 以珍汕97B为轮回亲本、密阳46为供体亲本, 构建了遗传背景基本一致的2个BC2F5分离群体;采用Windows QTL Cartographer 2.5进行抽穗期、株高及千粒重的QTL分析, 并根据RFT1 Hd3a下游17 kb处的连锁标记Si2944及Hd1的基因标记Si9337的基因型, 将每个群体中的纯合基因型材料分成4组, 比较其表型差异。结果表明, 这2个区间对抽穗期、株高及千粒重均呈显著作用, 它们之间不呈显著互作, 且Hd1所处区间对3个性状的作用均强于RFT1 Hd3a所处区间。     

Genome-Wide Association Analysis and Allelic Mining of Grain Shape-Related Traits in Rice

Excavating single nucleotide polymorphisms(SNPs) significantly associated with rice grain shape and predicting candidate genes through genome-wide association study(GWAS) can provide a theoretical basis for discovery and utilization of excellent genetic resources in rice. Based on 16 352 SNPs, 161 natural indica rice varieties with various grain sizes in southern China were used for GWAS of grain shape-related traits, referring to grain length(GL), grain width(GW), 1000-grain weight(TGW), and grain length/width(GLW). Phenotypic statistics showed that coefficient of variation values for these four traits GL, GW, TGW and GLW were 9.92%, 9.09%, 20.20% and 16.38%, respectively. Each trait showed a normal distribution, and there was a certain correlation between these traits. Through general linear model correlation analysis, a total of 38 significant loci were identified, and a range of 100 kb upstream and downstream of the significant loci was identified as the candidate interval. On chromosome 3, GS3 and q GL3 were found to regulate GL. On chromosome 6, TGW6 and GW6 a were found to regulate TGW. Also, some QTLs related to grain shape were found on chromosomes 5 and 9. Besides that, using sequenced 3 K-germplasm resources, we found that there are 22 overlapped varieties between these two natural populations. Twenty-six SNPs and fourteen haplotypes were identified in five regions of GS3 genes. The detection of multiple candidate genes/QTLs within the candidate interval is beneficial for further excavation of superior rice genetic resources.     

水稻粒重粒形QTL的定位及qTGW1.2/qGL1.2的验证

[目的]粒重粒形对水稻的产量和品质均有重要的影响.本研究通过开展水稻粒重粒形QTL的初步定位,并对新鉴定的第1染色体长臂qTGW1.2/qGL1.2区间进行验证,旨在进一步揭示水稻粒重粒形的遗传调控机制.[方法]以大粒的FM9为父本,小粒的EFT为母本,配组衍生遗传群体,先后获得包含277个株系的F2:3群体和211个...     

QTL mapping of grain quality traits in rice

Grain quality improvement is one of the most important goals in a rice breeding program. An indica variety with small grain size was crossed to a japonica variety with large grain size to construct a set of recombinant inbred lines (RILs) which was used to identify quantitative trait loci (QTLs) controlling eight grain quality traits. Based on a linkage map of 185 SSR markers, a total of 16 QTLs were mapped on six chromosomes. A pleiotropic main effect QTL (M-QTL) flanked by RM3204 and RM16 on chromosome 3 influences the grain length (GL), length width ratio (LWR) and head rice ratio (HRR), explaining the phenotypic variation of 46.0, 36.1 and 29.7%, respectively. A total of 18 epistatic QTLs were identified for all the traits except MRR, distributed on all the chromosomes except chromosome 10. Two M-QTLs for GL and one M-QTL for GW were involved in epistatic QTL. No significant interaction between M-QTL or epistatic QTL and environment was detected except AC having significant M-QTL by environment interaction with minor effect. GL and LWR have a significant negative relation with HRR which might make it difficult to develop long grain with higher HRR in the rice breeding practice.     

野生稻增产QTL导入9311之近等基因系的构建

以超级杂交中稻恢复系9311为受体和轮回亲本,马来西亚普通野生稻(O.rufipogon)为增产QTL yld1.1和yld2.1的供体进行杂交和连续回交,各世代采用分子标记辅助选择,至BC6F1后自交,得到BC6F2群体,通过分子标记检测,获得分别携带野生稻增产QTL yld1.1、yld2.1及同时携带yld1.1和yld2.1的3套近等基因系.对同时携带yld1.1和yld2.1的近等基因系进行遗传背景分析,发现其与受体9311的遗传组成有93.9%一致.田间试验表明,野生稻增产QTL近等基因系的产量均高于受体,说明将野生稻增产QTL转移至杂交稻恢复系中,能提高其产量水平,且2个QTL的增产效果大于单个QTL的效果.     

Dissection of QTLs for Hull Silicon Content on the Short Arm of Rice Chromosome 6

The QTL qHUS6 for hull silicon content in rice was previously located on the short arm of rice chromosome 6.By using an F2:3 population segregating in the RM587-RM19784 region harboring qHUS6 in an isogenic background,two QTLs for hull silicon content were detected,of which qHUS6-1 was located in the distal region and qHUS6-2 in the region proximal to the centromere.Three rice plants carrying small heterozygous segments in the target region were selected,of which two covered the qHUS6-1 region and the other...     

水稻第6染色体短臂谷壳硅含量QTL的分解

报道了水稻谷壳硅含量QTLqHUS6的分解研究。针对前期定位的qHUS-6区域,应用在第6染色体短臂RM587-RM19784区间分离、背景基本纯合的F2:3群体,将qHUS-6分解为2个QTL;其中,qHUS-6-1位于目标区间的上部,qHUS-6-2位于下部。同时,筛选出在目标区间内携带更小杂合片段的3个单株。其中,2株覆盖qHUS-6-1区间,各自交产生了1个F2:3群体,应用这2个群体将qHUS-6-1定位于RM510和RM19417之间约147.0kb的区间内;另1株覆盖qHUS-6-2区间,自交产生了1个F2:3群体,从中挑选出在qHUS-6-2区间具有不同基因型组成的5套F3株系,将qHUS-6-2分解为qHUS-6-2a和qHUS-6-2b,分别位于RM19706-RM19795和RM314-RM19665区间。     

水稻抽穗期基因的精细定位、克隆和生物学功能分析

介绍了水稻抽穗期QTL研究的进展,在相同亲本日本晴/Kasalath衍生的不同类型的多个群体中,共检测到15个QTL;应用高世代回交后代,精细定位了其中8个QTL;将在初步定位时同一区间检测到的1个控制种子休眠期QTL(Sdr1)和1个抽穗期QTL (Hd8),分解为两个紧密连锁的基因;将经过精细定位表明可能具有双重功能的单个孟德尔因子Hd3,分解为两个功能不同的紧密连锁的基因Hd3a和Hd3b;根据QTL近等基因系的光周期反应以及这些座位间上位性互作的研究,明确了其中6个QTL的生物学功能;应用图位法克隆了其中3个QTL,研究了它们的表达和调控,并与拟南芥的同源基因进行比较。为水稻其他数量性状以及其他作物数量性状的遗传学研究,提供了一个范例。