臺灣水稻種原遺傳歧異度與種子休眠相關外表型之調查

Investigation of Genetic Diversity and Traits Related to Seed Dormancy in Rice Collections in Taiwan

葉人豪(Jen-Hau Yeh)

指導教授 ： 陳凱儀

共同指導教授 ： 蔡政安

國立臺灣大學/生物資源暨農學院/農藝學研究所/碩士(2014年)

https://doi.org/10.6342/NTU.2014.01348

摘要

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。

關鍵字

RAD定序法 ； 穗上發芽 ； 種子休眠性 ； 族群結構 ； 全基因組關聯性分析

並列摘要

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.

並列關鍵字

RAD sequencing ； pre-harvest sprouting ； seed dormancy ； population structure ； GWAS

參考文獻

謝明修，吳東鴻，陳凱儀。(2014) 使用限制酶位點標定之核酸定序法進行稉稻雜交組合之穗上發芽數量性狀基因座的遺傳定位。作物、環境與生物資訊 11:11-25。

陳榮坤，蔡孟勳，陳凱儀。(2013) 臺灣稉型水稻品種隨機型SNP分子標誌資料庫的建構。臺南區農業改良場研究彙報 61:15-28。

Altmann A, Weber P, Bader D, Preuss M, Binder EB, Muller-Myhsok B. (2012) A beginners guide to SNP calling from high-throughput DNA-sequencing data. Hum an Genetics 131(10):1541-54.

Bradbury PJ, Zhang Z, Kroon DE, Casstevens TM, Ramdoss Y, Buckler ES. (2007) TASSEL: Software forassociation mapping of complex traits in diverse samples. Bioinformatics 23:2633-2635.

Cai HW, Morishima H. (2000) Genomic regions affecting seed shattering and seed dormancy in rice. Theoretical and Applied Genetics 100:840-846.