结合QTL-seq和连锁分析发掘水稻中胚轴伸长相关QTL

Combining QTL-seq and linkage analysis to identify the QTL of mesocotyl elongation in rice(Oryza sativa L.)

中胚轴长度(mesocotyl length, ML)是影响旱直播水稻出苗和早期幼苗活力的重要性状。发掘中胚轴伸长相关位点,解析其遗传机制,选育长中胚轴品种是促进旱直播技术推广最为经济和有效的方式。本研究以长中胚轴品种‘Changai’和短中胚轴品种‘IR 145’为亲本构建的F_2遗传分离群体为材料,构建长池和短池并开展深度重测序(50×)。利用Δ(SNP-index)和G-value两种方法在3号染色体29.56~33.28 Mb处鉴定到1个中胚轴伸长相关位点qML3。在候选区域开发KASP标记,对184个F_2株系开展连锁分析,将候选区间缩小到28.89~31.03Mb。结合基因注释、连锁分析和基因表达分析结果,推测LOC_Os03g52450、LOC_Os03g56060、LOC_Os03g58290、LOC_Os03g58300、LOC_Os03g58320、LOC_Os03g56050和LOC_Os03g57640为候选基因。这些基因分别与植物激素的调控和细胞分裂相关机制有关。本研究发掘了一个水稻中胚轴伸长相关位点,对选育长中胚轴品种有一定帮助。

Mesocotyl length is an important trait,which affects seedling establishment and early seedling vigor after dry direct seeding.Identifying the loci related to mesocotyl elongation,analyzing the genetic mechanism and selecting varieties with long mesocotyl is the most economic and effective way to promote the popularization of dry direct seeding technology.In this study,an F2 population constructed with‘Changai’(an extremely long mesocotyl variety)and‘IR 145’(an extremely short mesocotyl variety)was used to construct long and short DNA pool,which were re-sequenced at 50×level.Two methods,ΔSNP–index and G–value,were used to identify the quantitative trait loci(QTL)for mesocotyl elongation.A QTL named as q ML3,located in the region of 29.56–33.28 Mb on chromosome 3 were detected.After linkage analysis of 184 F2 lines with the newly developed KASP markers based on this locus,the region was narrowed down to 28.89–31.03 Mb.Combining the results of gene annotation,linkage analysis,and gene expression analysis,LOCOs03g52450,LOCOs03g56060,LOCOs03g58290,LOCOs03g58300,LOCOs03g58320,LOCOs03g56050,and LOCOs03g57640 were speculated to be candidate genes in this region.These genes were involved in the regulation of plant hormones as well as the mechanism of cell division.This study uncovers a locus related to rice mesocotyl elongation and is helpful for the breeding of long mesocotyl varieties.