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 13573 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 1246 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 2704 (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 (qPH16) 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.

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

School of Life Sciences,Liaoning Normal University,Dalian 116081,P.R.China;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;School of Plant and Environmental Sciences,Virginia Polytechnic Institute and State University,Blacksburg,VA 24060,USA

农业科学学报（英文）

[1]LIU Chen;TIAN Yu;LIU Zhang-xiong;GU Yong-zhe;ZHANG Bo;LI Ying-hui;NA Jie;QIU Li-juan-.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.))[J].农业科学学报（英文）,2022(07):1903-1912

agronomical,Zhongpin,Zhonghuang,Chr11,Chr18,pericentromeric,qPH16

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