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.)

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

Research output: Contribution to journalArticlepeer-review

Abstract

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 (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.

Original languageEnglish
Pages (from-to)1903-1912
Number of pages10
JournalJournal of Integrative Agriculture
Volume21
Issue number7
DOIs
StatePublished - Jul 2022
Externally publishedYes

Bibliographical note

Publisher Copyright:
© 2022 CAAS. Publishing services by Elsevier B.V

Keywords

  • long-InDels
  • plant height
  • QTL
  • soybean
  • whole genome re-sequencing

ASJC Scopus subject areas

  • Food Science
  • Biochemistry
  • Ecology
  • Food Animals
  • Animal Science and Zoology
  • Agronomy and Crop Science
  • Plant Science

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