Genome Wide Association mapping of grain and straw biomass traits in the rice Bengal and Assam Aus Panel (BAAP)

Growing demand for staple crops like rice will need to be achieved predominately through agricultural intensification and more efficient use of inputs. To meet this demand it is essential that the genetic diversity within rice is fully utilised. The aus subpopulation is considered an underappreciated resource within that diversity. A new rice panel, the Bengal and Assam Aus Panel (BAAP) of 266 aus accessions was generated with ~2 million informative SNPs obtained using skim sequencing at ~4x depth. The BAAP was grown in the field in Bangladesh in the ‘boro’ season under both continuously flooded and Alternate Wetting and Drying (AWD) irrigation during 2013 and 2014 in Mymensingh and during 2014 in Madhupur. Heading date, grain mass, straw biomass and harvest index were measured. The majority (94%) of BAAP accessions flowered within a relatively small window of 10 days. The AWD irrigation treatment generally caused an increase in grain mass, but no significant genotype by treatment interactions were detected for this trait. Shoot biomass was the only trait that showed evidence of genotype by treatment interaction. The average LD (Linkage Disequilibrium) decay across the genome was 243 Kbp. Genome wide association mapping revealed 115 quantitative trait loci (QTLs). There was little evidence of QTLs specific to the irrigation treatment, and only a few QTLs co-localised with known genes. However, some QTLs were detected across multiple sites and years. These QTLs should be targets for breeding, and include a region around 2.2 Mbp on chromosome 1, a large region in the middle of chromosome 7 and two regions on chromosome 11 (~10 Mbp and ~29 Mbp). The BAAP appears to be a valuable addition to the growing collection of GWA mapping populations of rice.

水稻等主粮作物的需求增长，主要需通过农业集约化与投入品高效利用来满足。为达成这一需求，充分挖掘水稻的遗传多样性至关重要，其中aus亚群（aus subpopulation）被认为是该多样性资源中尚未得到充分重视的一类材料。本研究构建了一套全新的水稻种质面板——孟加拉-阿萨姆aus种质面板（Bengal and Assam Aus Panel, BAAP），包含266份aus种质材料；该面板通过约4×深度的skim测序（skim sequencing）获得了约200万个有效单核苷酸多态性（Single Nucleotide Polymorphism, SNP）标记。2013至2014年在孟加拉国迈门辛（Mymensingh），以及2014年在马杜布尔（Madupur）的‘boro’稻季，研究团队于田间设置持续淹水与干湿交替灌溉（Alternate Wetting and Drying, AWD）两种处理，种植BAAP面板材料，并对抽穗期、粒重、秸秆生物量及收获指数四项性状进行了表型鉴定。结果显示，BAAP中94%的种质材料的开花期集中在10天左右的窄幅区间内。干湿交替灌溉处理总体上提升了粒重，但未在该性状上检测到显著的基因型×处理互作效应；地上部生物量是唯一表现出基因型×处理互作效应的性状。全基因组平均连锁不平衡（Linkage Disequilibrium, LD）衰减距离为243千碱基对（Kbp）。全基因组关联定位共检测到115个数量性状位点（quantitative trait locus, QTL），几乎未发现灌溉处理特异性的QTL，且仅有少量QTL与已知功能基因共定位。不过，部分QTL可在多个试验地点与年份中被重复检测到。这些可重复的QTL可作为水稻育种的目标位点，包括第1染色体约2.2兆碱基对（Mbp）处的区域、第7染色体中部的大片段区域，以及第11染色体上的两处区域（约10 Mbp与29 Mbp处）。总体而言，BAAP为日益壮大的水稻全基因组关联定位群体库增添了极具价值的新成员。