Background

Seed-set density is an important agronomic trait in rice. However, its genetic mechanism is complex. Chromosome segment substitution lines (CSSLs) are ideal materials for studying complex traits.

Results

A rice CSSL, Z749, with a dense and erect panicle phenotype, was identified among progeny of the recipient parent Nipponbare and the donor parent Xihui 18. Z749 carried seven substitution segments (average length 2.12 Mb). Compared with Nipponbare, Z749 showed significant increases in the numbers of primary (NPB) and secondary branches (NSB), number of spikelets (SPP) and grains per panicle (GPP), seed-set density (SSD), and decrease in panicle length (PL). A secondary F₂ population derived from a cross between Nipponbare and Z749 was used to map quantitative trait loci (QTLs) for associated traits. Fifteen QTLs distributed on chromosomes 5, 7, 8, and 10 were detected. The QTL qPL7 might be an allele of OsFAD8 and the remaining 14 QTLs (e.g., qSSD5 and qSSD10 etc.) might be novel. Fourteen QTLs were verified using five single-segment substitution lines (SSSLs). The seed-set density of Z749 was controlled predominantly by one major QTL (qSSD10) and two minor QTLs (qSSD5 and qSSD8). The QTLs qSSD10, qSSD5, and qSSD8 were fine-mapped to intervals of 1.05, 1.46, and 1.53 Mb on chromosomes 10, 5, and 8, respectively. Analysis of QTL additive effects indicated that qSSD5, qSSD8, and qSSD10 from Xihui18 increased seed-set density of Z749 by 14.10, 11.38, and 5.11 spikelets per 10 cm panicle, respectively. Analysis of QTL epistatic effects revealed that pyramiding of qSSD5 and qSSD8, qSSD5 and qSSD10, qSSD8 and qSSD10, and qSSD5, qSSD8 and qSSD10 produced novel genotypes with increased seed-set density.

Conclusions

Inheritance of seed-set density in Z749 was controlled predominantly by one major QTL (qSSD10) and two minor QTLs (qSSD5 and qSSD8). Then, they were fine-mapped to intervals of 1.05, 1.46, and 1.53 Mb on chromosomes 10, 5, 8, respectively. Two MAPK genes (OsMPK9 and OsMPK17) and one gene (candidate gene 6) involved in auxin metabolism might be candidate genes for qSSD5, and OsSAUR32 might be the candidate gene for qSSD8. Pyramiding of qSSD5, qSSD8, and qSSD10 enhanced seed-set density.

中文翻译：

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基于密直穗水稻CSSL-Z749和5个SSSL、3个DSSL和1个TSSL的关联性状QTL的鉴定、金字塔和候选基因

背景

结实密度是水稻重要的农艺性状。但其遗传机制复杂。染色体片段置换系 (CSSL) 是研究复杂性状的理想材料。

结果

在受体亲本 Nipponbare 和供体亲本 Xihui 18 的后代中鉴定出具有密集且直立的穗表型的水稻 CSSL，Z749。Z749 携带七个替代片段（平均长度 2.12 Mb）。与日本晴相比，Z749 的主枝数 (NPB) 和次生枝数 (NSB)、小穗数 (SPP) 和每穗粒数 (GPP)、结实密度 (SSD) 显着增加，穗长减少(PL)。来自日本晴和 Z749 杂交的次级 F ₂群体用于绘制相关性状的数量性状基因座 (QTL)。检测到分布在 5、7、8 和 10 号染色体上的 15 个 QTL。QTL qPL7可能是OsFAD8和其余 14 个 QTL（例如，qSSD5和qSSD10等）可能很新颖。使用 5 个单段置换系 (SSSL) 验证了 14 个 QTL。Z749 的种子集密度主要由一个主要 QTL ( qSSD10 ) 和两个次要 QTL ( qSSD5和qSSD8 ) 控制。QTLs qSSD10、qSSD5和qSSD8分别精确映射到10、5和 8 号染色体上1.05、1.46和 1.53 Mb 的间隔。QTL加性效应分析表明，qSSD5、qSSD8和qSSD10从 Xihui18 开始，Z749 的结实密度分别增加了 14.10、11.38 和 5.11 个小穗/10 cm 穗。QTL 上位效应分析表明，qSSD5和qSSD8、qSSD5和qSSD10、qSSD8和qSSD10以及qSSD5、qSSD8和qSSD10 的金字塔化产生了种子集密度增加的新基因型。

结论

Z749 中种子集密度的遗传主要由一个主要 QTL ( qSSD10 ) 和两个次要 QTL ( qSSD5和qSSD8 ) 控制。然后，它们分别被精细定位到 10、5、8 号染色体上 1.05、1.46 和 1.53 Mb 的间隔。涉及生长素代谢的两个MAPK基因（OsMPK9和OsMPK17）和一个基因（候选基因6）可能是qSSD5的候选基因，而OsSAUR32可能是qSSD8的候选基因。金字塔的qSSD5，qSSD8和qSSD10增强的种子集密度。