Sar Puranjoy, Gupta Sonal, Behera Motilal, Chakraborty Koushik, Ngangkham Umakanta, Verma Bibhash Chandra, Banerjee Amrita, Hanjagi Prashantkumar S, Bhaduri Debarati, Shil Sandip, Kumar Jitendra, Mandal Nimai Prasad, Kole Paresh Chandra, Purugganan Michael D, Roy Somnath
Central Rainfed Upland Rice Research Station, ICAR-National Rice Research Institute, Hazaribag, Jharkhand, 825 301, India.
Center for Genomics and Systems Biology, New York University, New York, NY, USA.
Rice (N Y). 2024 Mar 25;17(1):20. doi: 10.1186/s12284-024-00700-4.
The aus (Oryza sativa L.) varietal group comprises of aus, boro, ashina and rayada seasonal and/or field ecotypes, and exhibits unique stress tolerance traits, making it valuable for rice breeding. Despite its importance, the agro-morphological diversity and genetic control of yield traits in aus rice remain poorly understood. To address this knowledge gap, we investigated the genetic structure of 181 aus accessions using 399,115 SNP markers and evaluated them for 11 morpho-agronomic traits. Through genome-wide association studies (GWAS), we aimed to identify key loci controlling yield and plant architectural traits.Our population genetic analysis unveiled six subpopulations with strong geographical patterns. Subpopulation-specific differences were observed in most phenotypic traits. Principal component analysis (PCA) of agronomic traits showed that principal component 1 (PC1) was primarily associated with panicle traits, plant height, and heading date, while PC2 and PC3 were linked to primary grain yield traits. GWAS using PC1 identified OsSAC1 on Chromosome 7 as a significant gene influencing multiple agronomic traits. PC2-based GWAS highlighted the importance of OsGLT1 and OsPUP4/ Big Grain 3 in determining grain yield. Haplotype analysis of these genes in the 3,000 Rice Genome Panel revealed distinct genetic variations in aus rice.In summary, this study offers valuable insights into the genetic structure and phenotypic diversity of aus rice accessions. We have identified significant loci associated with essential agronomic traits, with GLT1, PUP4, and SAC1 genes emerging as key players in yield determination.
稻（Oryza sativa L.）品种群包括aus、boro、ashina和rayada季节型和/或田间生态型，具有独特的耐胁迫特性，对水稻育种具有重要价值。尽管其具有重要性，但aus水稻的农艺形态多样性和产量性状的遗传控制仍知之甚少。为填补这一知识空白，我们使用399,115个单核苷酸多态性（SNP）标记对181份aus种质进行了遗传结构研究，并对它们的11个形态农艺性状进行了评估。通过全基因组关联研究（GWAS），我们旨在鉴定控制产量和株型性状的关键基因座。我们的群体遗传分析揭示了六个具有强烈地理模式的亚群。在大多数表型性状中观察到亚群特异性差异。农艺性状的主成分分析（PCA）表明，主成分1（PC1）主要与穗部性状、株高和抽穗期相关，而PC2和PC3与初级产量性状相关。使用PC1进行的GWAS在第7号染色体上鉴定出OsSAC1是影响多个农艺性状的重要基因。基于PC2的GWAS突出了OsGLT1和OsPUP4/大粒3在决定产量方面的重要性。在3000份水稻基因组面板中对这些基因的单倍型分析揭示了aus水稻中不同的遗传变异。总之，本研究为aus水稻种质的遗传结构和表型多样性提供了有价值的见解。我们已经鉴定出与重要农艺性状相关的显著基因座，其中GLT1、PUP4和SAC1基因成为产量决定的关键因素。
