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 ISA1 by RNA interference produced grains with 20% more chalkiness than the control. The results support that the gene may underlie qPGC8-2 for grain chalkiness. The multiple-environment trials of the near-isogenic lines also show that combination of the favorable alleles such as the ISA1 gene for low chalkiness and the GS3 gene for long grains considerably improved grain quality of ZS97, which proves useful for grain quality improvement in rice breeding programs.
Highlights
Rice (Oryza sativa L.) is one of the most important staple crops, providing food for nearly half of the world’s population
A large-effect QTL qPGC5–1 on chromosome 5 was mapped to Bin 263 of a 1.5-Mb region that contains the cloned gene Chalk5 [10]. qPGC8–2 in Bin 393 holds the starch-debranching enzyme gene ISA1
QPGC8–2, with a stable effect on percentage of grains with chalkiness (PGC) and degree of endosperm chalkiness (DEC), is interesting because it partially overlaps with a QTL region of grain chalkiness that was previously detected in numerous studies across different genetic populations [3,4,5,6,7, 35]
Summary
Rice (Oryza sativa L.) is one of the most important staple crops, providing food for nearly half of the world’s population. The improvement of grain quality and yield potential is a priority if rice production is to meet the demands of an ever-growing global population. Grain quality encompasses physical appearance and cooking, eating, and nutritional properties. Favorable Alleles Reduced Grain Chalkiness in Rice the key factors determining grain quality are physical appearances related to grain shape and chalkiness. High chalkiness is directly associated with inferior cooking and eating qualities, and it generally causes grains to break during the milling process, leading to a decrease in the amount of acceptable and marketable rice. Rice grain characteristic preferences vary among consumer groups in different countries, slender and translucent kernels without chalkiness are preferred by the majority of rice consumers [2]. Improving rice varieties to have low or no chalkiness is a main objective in rice breeding programs
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