Table_3_High-density genetic mapping identified QTLs for anaerobic germination tolerance in rice.xlsx

The tolerance of rice anaerobic germination (AG) is the main limiting factor for direct seeding application, yet the genetics mechanism is still in its infancy. In the study, recombinant inbred lines population of TD70 Japonica cultivar and Kasalath Indica cultivar, was employed to construct a high-density genetic map by whole genome re-sequencing. As a result, a genetic map containing 12,328 bin-markers was constructed and a total of 50 QTLs were then detected for CL(coleoptile length), CD (coleoptile diameter), CSA (coleoptile surface area) and CV (coleoptile volume) related traits in the two stages of anaerobic treatment using complete interval mapping method (inclusive composite interval mapping, ICIM). Among the four traits associated with coleoptile, coleoptile volume had the largest number of QTLs (17), followed by coleoptile diameter (16), and coleoptile length had 5 QTLs. These QTLs could explain phenotypic contribution rates ranging from 0.34% to 11.17% and LOD values ranging from 2.52 to 11.57. Combined with transcriptome analysis, 31 candidate genes were identified. Furthermore, 12 stable QTLs were used to detect the aggregation effect analysis. Besides, It was found that individuals with more aggregation synergistic alleles had higher phenotypic values in different environments. Totally, high-density genetic map, QTL mapping and aggregation effect analysis of different loci related to the anaerobic germination of rice seeds were conducted to lay a foundation for the fine mapping of related genes in subsequent assisted breeding.

水稻厌氧发芽（AG）的耐受度是直接播种应用的主要限制因素，然而其遗传机制尚处于初级阶段。在本研究中，利用TD70日本品种和Kasalath印度品种的重组自交系群体，通过全基因组重测序构建了高密度遗传图谱。据此，构建了一个包含12,328个二分标记的遗传图谱，并采用完整区间作图法（包括复合区间作图，ICIM）检测到50个与CL（鞘翅长度）、CD（鞘翅直径）、CSA（鞘翅表面积）和CV（鞘翅体积）相关的QTL。在四个与鞘翅相关的性状中，鞘翅体积具有最多的QTL（17个），其次是鞘翅直径（16个），而鞘翅长度具有5个QTL。这些QTL可以解释从0.34%到11.17%的表型贡献率以及从2.52到11.57的LOD值。结合转录组分析，共鉴定出31个候选基因。此外，利用12个稳定的QTL进行了聚合效应分析。同时，发现具有更多聚合协同等位基因的个体在不同环境中具有更高的表型值。总之，通过对与水稻种子厌氧发芽相关的不同位点的遗传图谱、QTL作图和聚合效应分析，为后续辅助育种中相关基因的精细定位奠定了基础。