NGS-based Mapping of a Gene for Rice Grain length

• Main Authors: Yu-Ming Hsu, 許育鳴
• Other Authors: 邢禹依
• Format: Others
• Language: zh-TW
• Published: 2013
• Online Access: http://ndltd.ncl.edu.tw/handle/61336777982885189244

碩士 === 國立臺灣大學 === 農藝學研究所 === 101 === With rapid population growth and climate changes, sufficient food production is a major challenge. Rice is one of major crops in the world, and the major goal is to increase grain yield. Rice grain length is an important component of grain yield, so we examined the T-DNA mutant line TALL,with agronomically important long grain length and tall height. The mutant line does not have the recessive phenotype cosegregated with its T-DNA insertion, so we used bulked segregant analysis (BSA) with next-generation sequencing (NGS) to isolate the gene controlling the important traits. We crossed Tall163 and an elite rice cultivar, TK9, showing normal grain length, and generated an F2 population of 1000 individuals. After phenotyping, we divided 62 long-grain and 20 normal-grain plants into 5 samples:2 bulked samples of 20 and 40 long-grain plants and 1 of 20 normal-grain plants, and 2 samples of 1 long-grain plant each. The 4 long-grain samples had a non-recombinant region close to the centromere region of chromosome 3 and showed the same genotype as TALL. By combining the2 mutant bulked samples into a sample of 60 long-grain plants and comparing with the 2 mutant bulked samplesof 20 and 40 mutant plants, the location of the candidate gene could be narrowed down to a 2.5-Mb region. Annotating each position in the candidate region with putative SNP frequency of 1 revealed 172 missense mutations and 108 silent mutations.Futhermore, the only mutationwith an early stop codon was caused by a C-A mutation in position 17365441, which is the published gene, GS3. The mutant genotype and position were verified with previous studies, so GS3may be the candidate gene. With few F2 plants and a short time, we identified the candidate gene by NGS-based BSA, which may be useful in identifying other agronomical traits.TALLshows more than 5200 homozygous SNPs in the candidate region of chromosome 3, possibly caused by somaclonal variations, as compared with its parent line TNG67, but further studies are needed to identify the mechanism of the somaclonal variations.