Identification of Genomic Regions and the Isoamylase Gene for Reduced Grain Chalkiness in Rice

PLOS ONE, Dec 2019

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.

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Identification of Genomic Regions and the Isoamylase Gene for Reduced Grain Chalkiness in Rice

March Identification of Genomic Regions and the Isoamylase Gene for Reduced Grain Chalkiness in Rice Wenqian Sun 0 1 2 Qiaoling Zhou 0 1 2 Yue Yao 0 1 2 Xianjin Qiu 0 1 2 Kun Xie 0 1 2 Sibin Yu 0 1 2 0 1 National Key Laboratory of Crop Genetic Improvement , Wuhan , China , 2 College of Plant Science and Technology, Huazhong Agricultural University , Wuhan , China 1 Funding: This work was supported by the National Natural Science Foundation of China (Grant No.31261140369, 31271695), the Ministry of Science and Technology (Grant No.2013CB127006), and the Bill & Melinda Gates Foundation. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript 2 Academic Editor: Chengdao Li, Department of Agriculture and Food Western Australia , AUSTRALIA 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 highthroughput 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 multipleenvironment 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. - Competing Interests: The authors have declared that no competing interests exist. Rice (Oryza sativa L.) is one of the most important staple crops, providing food for nearly half of the worlds 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. Among these, the key factors determining grain quality are physical appearances related to grain shape and chalkiness. Grain shape or size is characterized by grain length, width, and length-to-width ratio. Chalkiness is usually measured by the percentage of grains with chalkiness (PGC) and the area of opaque parts in the endosperm [1]. 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. Although 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]. Hence, improving rice varieties to have low or no chalkiness is a main objective in rice breeding programs. Grain chalkiness is a complex trait controlled by multiple genetic factors and influenced by the environment. Numerous quantitative trait loci (QTLs) have been identified for grain chalkiness in various rice mapping populations over the past two decades (http://www. gramene.org). Of these, several major QTLs such as on chromosomes 1, 5, 7, 8, and 9 are stably expressed across multiple environments or various populations [37]. Two QTLs for grain chalkiness have been mapped to a small region on chromosomes 7 and 8 [8, 9], respectively. However, the genes responsible for these QTLs have not been determined. Recently, a major QTL for grain chalkiness located on chromosome 5 has been cloned as Chalk5, which encodes a vacuolar H+-translocating pyrophosphatase in rice endosperm [10]. The elevated activity of Chalk5 increases the small vesicle-like structures, coupled with an abnormal decrease in protein body number and size, causing the formation of air spaces among starch granules and resulting in chalky grains. Grain chalkiness has been reported to be associated with content and structural alteration of starch, which is composed of a (...truncated)


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Wenqian Sun, Qiaoling Zhou, Yue Yao, Xianjin Qiu, Kun Xie, Sibin Yu. Identification of Genomic Regions and the Isoamylase Gene for Reduced Grain Chalkiness in Rice, PLOS ONE, 2015, Volume 10, Issue 3, DOI: 10.1371/journal.pone.0122013