Identification of genomic regions and the isoamylase gene for reduced grain chalkiness in rice

PloS One
Wenqian SunSibin Yu

Abstract

Grain chalkiness is an important grain quality related to starch granules in the endosperm. A high percentage of grain chalkiness is a major problem because it diminishes grain quality in rice. Here, we report quantitative trait loci identification for grain chalkiness using high-throughput single nucleotide polymorphism genotyping of a chromosomal segment substitution line population in which each line carried one or a few introduced japonica cultivar Nipponbare segments in the genetic background of the indica cultivar ZS97. Ten quantitative trait loci regions were commonly identified for the percentage of grain chalkiness and the degree of endosperm chalkiness. The allelic effects at nine of these quantitative trait loci reduced grain chalkiness. Furthermore, a quantitative trait locus (qPGC8-2) on chromosome 8 was validated in a chromosomal segment substitution line-derived segregation population, and had a stable effect on chalkiness in a multiple-environment evaluation of the near-isogenic lines. Residing on the qPGC8-2 region, the isoamylase gene (ISA1) was preferentially expressed in the endosperm and revealed some nucleotide polymorphisms between two varieties, Nipponbare and ZS97. Transgenic lines with suppression of I...Continue Reading

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Citations

Dec 9, 2017·TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik·Xinxin TangSibin Yu
Jan 10, 2020·TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik·Sibin YuQifa Zhang
Feb 23, 2020·International Journal of Molecular Sciences·Shaowen YuanSibin Yu
Mar 17, 2017·TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik·Xianjin QiuZhikang Li

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Methods Mentioned

BETA
three-line hybrid
genotyping
chip
transgenic
PCR

Software Mentioned

R package “ ridge
R
lmg
Statistica
relaimpo

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