QTL-Seq Identified a Major QTL for Grain Length and Weight in Rice Using Near Isogenic F2 Population
QTL-Seq Identified a Major QTL for Grain Length and Weight in Rice Using Near Isogenic F2 Population
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DOI：
10.1016/j.rsci.2018.04.001
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发表时间：
2018-05-01
期刊：
影响因子：
4.8
通讯作者：
Ying Jiezheng
中科院分区：
文献类型：
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作者：
Qin Yaobin;Cheng Peng;Ying Jiezheng
数量性状基因座（qtl）的定位和分离对揭示种子发育和作物育种的分子机制具有重要意义。为了确定控制籽粒大小和重量的qtl，我们从重组自交系（RIL） F-7代的残杂合植株中开发了一个近等基因系F-2 （NIL-F-2）群体。完成对亲本30倍以上的全基因组重测序，大颗粒和小颗粒两个DNA块，共生成58.94 Gb的干净核苷酸数据。共鉴定出父母间455 262个单核苷酸多态性（snp），并进行批量QTL-seq。在第5染色体15 ~ 20 Mb处发现了一个与粒长和粒重密切相关的候选snp区域。我们确定候选区域的主要QTL为qTGW5.3。然后，通过在F-2群体中建立简单的序列重复和插入/删除标记，利用基于pcr的传统QTL定位方法进一步验证qTGW5.3。此外，重组和子代测试将qTGW5.3的候选区域划分为1.13 Mb，两侧是HX5009 （15.15 Mb）和HX5003 （16.28 Mb）。从F-2群体中选择一组NILs来评价qTGW5.3的遗传效应。H12-29等位基因对粒长、粒宽和千粒重的QTL效应显著，分别为1.14 mm、-0.11 mm和3.11 g，解释了99.64%、95.51%和97.32%的表型变异。
Mapping and isolation of quantitative trait loci (QTLs) or genes controlling grain size or weight is very important to uncover the molecular mechanisms of seed development and crop breeding. To identify the QTLs controlling grain size and weight, we developed a near isogenic line F-2 (NIL-F-2) population, which was derived from a residual heterozygous plant in an F-7 generation of recombinant inbred line (RIL). With the completion of more than 30x whole genome re-sequencing of the parents, two DNA bulks for large and small grains, a total of 58.94 Gb clean nucleotide data were generated. A total of 455 262 single nucleotide polymorphisms (SNPs) between the parents were identified to perform bulked QTL-seq. A candidate genomic region containing SNPs strongly associated with grain length and weight was identified from 15 to 20 Mb on chromosome 5. We designated the major QTL in the candidate region as qTGW5.3. Then, qTGW5.3 was further validated with PCR-based conventional QTL mapping method through developing simple sequence repeat and Insertion/Deletion markers in the F-2 population. Furthermore, recombinants and the progeny tests delimited the candidate region of qTGW5.3 to 1.13 Mb, flanked by HX5009 (15.15 Mb) and HX5003 (16.28 Mb). A set of NILs, selected from the F-2 population, was developed to evaluate the genetic effect of qTGW5.3. Significant QTL effects were detected on grain length, grain width and 1000-grain weight of H12-29 allele with 1.14 mm, -0.11 mm and 3.11 g, which explained 99.64%, 95.51% and 97.32% of the phenotypic variations, respectively.