Association analysis of markers derived from starch biosynthesis related genes with starch physicochemical properties in the USDA rice mini-core collection

Kehu Li, Jinsong Bao, Harold Corke, Mei Sun*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

16 Scopus citations

Abstract

Rice eating and cooking quality is largely determined by starch physicochemical properties. The diverse accessions in the USDA rice mini-core collection (URMC) facilitate extensive association analysis of starch physicochemical properties with molecular markers specific to starch biosynthesis related genes. To identify significant trait-marker associations that can be utilized in rice breeding programs for improved starch quality, we conducted two association analyses between 26 molecular markers derived from starch biosynthesis related genes and 18 parameters measured of starch physicochemical properties in two sets of the mini-core accessions successfully grown in two environments in China. Many significant trait-marker associations (P < 0.001) were detected in both association analyses. Five markers of Waxy gene, including the (CT)n repeats, the G/T SNP of intron 1, the 23 bp sequence duplication (InDel) of exon 2, the A/C SNP of exon 6, and the C/T SNP of exon 10, were found to be primarily associated with starch traits related to apparent amylose content (AAC), and two markers targeting the 4,329-4,330 bp GC/TT SNPs and 4,198 bp G/A SNP of SSIIa gene were mainly associated with traits related to gelatinization temperature (GT). Two new haplotypes were found in the mini-core collection based on the combinations of the 23 bp InDel and three SNPs (G/T of intron 1, A/C of exon 6, and C/T of exon 10) of Waxy gene. Furthermore, our analyses indicated that the (CT)n polymorphisms of Waxy gene had a non-negligible effect on AAC related traits, as evidenced by significant variation in AAC related traits among rice accessions with the same Waxy SNPs but different (CT)n repeats. As the five Waxy markers and the two SSIIa markers showed consistent major effects on starch quality traits across studies, these markers should have priority for utilization in marker-assisted breeding.

Original languageEnglish
Article number424
JournalFrontiers in Plant Science
Volume8
DOIs
StatePublished - 3 Apr 2017
Externally publishedYes

Keywords

  • Marker-trait association
  • Rice
  • Starch biosynthesis
  • Starch physicochemical properties
  • USDA rice mini-core collection
  • Waxy gene haplotype

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