臺灣水稻種原遺傳歧異度與種子休眠相關外表型之調查

Abstract

限制酶位點標定 (Restriction-site associated DNA, RAD) 定序法為針對基因體中限制酶切位鄰近序列進行定序，使得開發大量 SNP 分子標記與樣本基因型定型 (genotyping) 得以一次完成的定序法。本篇研究針對蒐集自臺灣各農業改良場所的 425 個水稻種原，使用 RAD 定序技術進行各個種原的基因型定型工作，獲得這425 個水稻種原 14,377 個單一核苷酸多型性分子標記的基因型資料，並據此評估參試水稻種原之族群結構。同時於臺大農場試驗田 102 年二期作栽培這些水稻種原，調查其種子休眠性與穗上發芽率，並使用全基因組關聯性分析法 (Genome-Wide Association Study, GWAS)，結合基因型與外表型資料進行數量性狀基因座的遺傳定位。試驗結果顯示，參試水稻種原的遺傳組成源自三群不同的先祖: 秈稻、熱帶稉稻、與溫帶稉稻，而溫帶稉稻又可分為早期品種與現代品種。KHY4625、B6490 以及 NKY 982117 三個稉稻品系具備低穗上發芽率及低種子休眠性，為耐穗上發芽育種計畫的理想親本。此外，至少有一個與稉稻穗上發芽性顯著相關之數量性狀基因座被定位在第 1 對染色體前端。

RAD (Restriction-site associated DNA) sequencing is a cost-efficient genotyping technique capabable of discovering substaintial genome-wide SNP markers and determining their genotypes simultaneously for selected DNA samples. In current study, 425 rice (Oryza Sativa L.) accessions mainly collected from agricultural experimental stations in Taiwan were genotyped using the RAD sequencing technique. Genotypic data from 14,377 SNP markers of 425 rice accessions were used to investigate genetic diversity and population structure. Seed dormancy and pre-harvest sprouting were measured for the same rice collections at NTU farm in the second season in 2013. In combination of the aforementioned genetic and phenotypic data, QTL mapping were conducted using GWAS (genome-wide association study). The result showed that the genetic compositions of these 425 rice collections were derived from three ancenstral groups: indica rice, temperate japonica rice, and tropical japonica rice. For rice collections possessing genetic background mainly from temperate japonica rice, their genetic components could be further divided into two groups, one for old varieties and the other for modern varieties. In addition, three japonica varieties KHY4625, B6490, and NKY 982117 were characterized for low pre-harvest sprouting rate and low seed dormancy, and are ideal parental lines to breed rice varieties with such characteristics. Futhermore, at least one significant QTL associated with pre-harvest sprouting were detected at the distal end of chromosome 1 in japonica subspicies.