Identification and characterization of long-InDels through whole genome resequencing to facilitate fine-mapping of a QTL for plant height in soybean(Glycine max L.Merr.)  

作　　者：LIU Chen TIAN Yu LIU Zhang-xiong GU Yong-zhe ZHANG Bo LI Ying-hui NA Jie QIU Li-juan 

机构地区：[1]School of Life Sciences,Liaoning Normal University,Dalian 116081,P.R.China [2]National Key Facility for Gene Resources and Genetic Improvement/Key Laboratory of Crop Germplasm Utilization,Ministry of Agriculture and Rural Affairs/Institute of Crop Sciences,Chinese Academy of Agricultural Science,Beijing 100081,P.R.China [3]School of Plant and Environmental Sciences,Virginia Polytechnic Institute and State University,Blacksburg,VA 24060,USA

出　　处：《Journal of Integrative Agriculture》2022年第7期1903-1912,共10页农业科学学报（英文版）

基　　金：supported by the National Key R&D Program of China(2016YFD0100201 and 2020YFE0202300);the Agricultural Science and Technology Innovation Program(ASTIP)of the Chinese Academy of Agricultural Sciences。

摘　　要：With the development of sequencing technology, insertions-deletions(InDels) have been increasingly reported to be involved in the genetic determination of agronomical traits. However, most studies have focused on the identification and application of short-InDels(1–15 bp) for genetic analysis. The objective of this study was to deeply deploy long-InDels(>15 bp) for the genetic analysis of important agronomic traits in soybean. A total of 13 573 polymorphic long-InDels were identified between parents Zhongpin 03-5373(ZP) and Zhonghuang 13(ZH), which were unevenly distributed on 20 chromosomes of soybean, varying from 321 in Chr11 to 1 246 in Chr18. Consistent with the distribution pattern of annotated genes, the average density of long-InDels in arm regions was significantly higher than that in pericentromeric regions at the P=0.01 level. A total of 2 704(19.9% of total) long-InDels were located in genic regions, including 319 large-effect long-InDels, which resulted in truncated or elongated protein sequences. A previously identified QTL(qP H16) underlying plant height was further analyzed, and it was found that 26 out of 35(74.3%) long-InDel markers located in the qPH16 region showed clear polymorphisms between parents ZP and ZH. Seven markers, including three long-InDels and four previously reported SNP markers, were used to genotype 242 recombinant inbred lines derived from ZP×ZH. As a result, the qPH16 locus was narrowed from a 960-kb region to a 477.55-kb region, containing 65 annotated genes. Therefore, these long-InDels are a complementary genetic resource of SNPs and short-InDels for plant height and can facilitate genetic studies and molecular assisted selection breeding in soybean.

关 键 词：SOYBEAN plant height whole genome re-sequencing long-InDels QTL 

分 类 号：S565.1[农业科学—作物学]