DEP1、Gn1a和qSW5组合应用调控水稻穗部性状

doi:10.3864/j.issn.0578-1752.2023.07.002

摘要/Abstract

摘要：

【目的】水稻是重要的粮食作物，为全球超过一半的人口提供主食。穗部性状是影响水稻产量的主要因素，挖掘调控穗部性状的优异基因组合，为提高水稻产量提供聚合育种策略。【方法】以弯穗型籼稻品种R99和直立穗型粳稻品种SN265构建的151个重组自交系为试材，应用Illumina测序平台对重组自交系和双亲进行全基因组重测序。结合表型数据与遗传图谱，对每穗粒数、一次枝梗着粒数、二次枝梗着粒数和粒型进行QTL分析，筛选QTL区间内的候选基因，应用基于三代测序组装的SN265和R99高质量基因组进行候选基因预测和序列比对，在重组自交系中筛选产量性状表现最好的基因组合，并在SN265遗传背景下应用CRISPR基因编辑技术对目标位点进行基因编辑。【结果】 R99每穗粒数和二次枝梗着粒数显著多于SN265，SN265的一次枝梗着粒数显著高于R99，R99粒型细长，SN265粒型短圆。每个重组自交系平均测序深度为6.25×，R99和SN265的测序深度分别为30×和32×。获得1 456 445个高质量的SNP，利用划bin策略进行图谱构建，得到一个包含3 569个bins，平均长度为58.17 kb的遗传图。QTL分析在第9染色体检测到一个同时调控每穗粒数、一次枝梗着粒数和二次枝梗着粒数的QTL，在第1染色体鉴定到一个调控每穗粒数和二次枝梗着粒数的QTL，在第5染色体鉴定到一个调控粒型的QTL。候选基因预测和序列比对发现第9染色体的DEP1同时调控水稻一次和二次枝梗着粒数，第1染色体的Gn1a主要调控水稻二次枝梗着粒数，第5染色体的qSW5主要调控粒型。在151个重组自交系中，对DEP1、Gn1a和qSW5的不同组合进行分类并调查产量构成因素，发现Gn1a^R99/DEP1^SN265/qSW5^SN265等位基因组合产量表现最好，Gn1a^SN265/DEP1^R99/qSW5^R99产量表现最差。对SN265的Gn1a位点进行分子设计育种，获得2个独立的CRISPR基因编辑株系，通过调查其产量构成因素，发现基因编辑植株穗长显著变长，每穗粒数显著增加，进而显著增加单株产量。【结论】揭示了DEP1、Gn1a和qSW5对每穗粒数和粒型的影响，明确了Gn1a^SN265/DEP1^R99/qSW5^R99为重组自交系中最佳基因组合，通过改良SN265的Gn1a位点进一步提高了其单株产量。

关键词: 水稻, 高密度遗传图谱, 每穗粒数, 粒型, 基因编辑

Abstract:

【Objective】 Rice is an important food crop, providing staple food for more than half of the world’s population. Panicle traits are the main factors affecting rice yield. Discover the elite haplotype of the panicle regulation gene, and provide important germplasm and gene resources for pyramiding breeding. 【Method】 In this study, recombinant inbred lines (RILs) derived from a cross between SN265 and R99 were re-sequenced through high-throughput sequencing. QTL analysis and candidate gene identification were conducted on the grain number on the primary branch, the grain number on the secondary branch, and the grain shape. The sequences of candidate genes were compared using the long-read sequence assemblies of SN265 and R99. The combination of candidate genes that can maximize grain yield was selected among RILs. Finally, the super rice variety SN265 was improved using CRISPR/Cas9 gene editing technology. 【Result】 The R99 had significantly more grain number per panicle and grain number on the secondary branch, whereas SN265 had significantly more grain number on the primary branch. The grain of R99 is slender, and the grain of SN265 is short and round. The RILs were sequenced with approximately 6.25-fold depth. For parent lines, 30.0-fold depth and 32.0-fold depth data were generated for R99 and SN265, respectively. Subsequently, a bin map was constructed by 1456445 high-quality SNPs. The genetic map containing 3 569 recombinant blocks, with an average length of 58.17 kb. The QTL analysis detected a QTL on Chr.9 for grain number per panicle and grain number on both primary and secondary branch, a QTL on Chr.1 for grain number per panicle and grain number on the secondary branch, a QTL on Chr.5 for grain shape. The candidate gene prediction and sequence comparison showed that DEP1 regulated the grain number on both primary and secondary branches of rice, Gn1a mainly regulated the grain number on secondary branches of rice, and qSW5 mainly regulated the grain shape. The yield of the combination of Gn1a^R99/DEP1^SN265/qSW5^SN265 alleles showed an advantage in yield performance among the RILs. We further conducted a molecular design breeding to SN265 by knocking out the Gn1a locus using CRISPR/Ca9 gene editing technology, and the grain number per panicle of the transgenic plants increased significantly compared to that of SN265. 【Conclusion】 This study used RILs derived from a XI/GJ cross and high-throughput sequencing technology to conduct QTL analysis of rice panicle traits, revealed the effects of DEP1, Gn1a, and qSW5 on grain number per panicle and grain shape, and clarified that Gn1a^SN265/ DEP1^R99/qSW5^R99 was the best gene combination in RILs. The yield per plant was further improved by knocking out the Gn1a locus of SN265. This study provided important germplasm and gene resources for pyramiding breeding with elite alleles.

Key words: rice, high density genetic map, grain number, grain shape, gene editing

温一博, 陈淑婷, 徐正进, 孙健, 徐铨. DEP1、Gn1a和qSW5组合应用调控水稻穗部性状[J]. 中国农业科学, 2023, 56(7): 1218-1227.

WEN YiBo, CHEN ShuTing, XU ZhengJin, SUN Jian, XU Quan. Combination of DEP1, Gn1a, and qSW5 Regulates the Panicle Architecture in Rice[J]. Scientia Agricultura Sinica, 2023, 56(7): 1218-1227.

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