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

Sun W, Zhou Q, Yao Y, Qiu X, Xie K, Yu S - PLoS ONE (2015)

Bottom Line: 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.The results support that the gene may underlie qPGC8-2 for grain chalkiness.

View Article: PubMed Central - PubMed

Affiliation: National Key Laboratory of Crop Genetic Improvement, Wuhan, China; College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China.

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.

No MeSH data available.


Related in: MedlinePlus

Validation of qPGC8–2.(a) The schematic bins on chromosome 8 defined by SNP genotyping of the CSSL population, where one bin contains an introduced qPGC8–2 (ISA1). (b) Grain chalkiness in the three genotypic classes in a CSSL-derived segregation population. Means and standard deviations of grain chalkiness for the three genotypes by the gene marker DE2 are given inside the panel.
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pone.0122013.g003: Validation of qPGC8–2.(a) The schematic bins on chromosome 8 defined by SNP genotyping of the CSSL population, where one bin contains an introduced qPGC8–2 (ISA1). (b) Grain chalkiness in the three genotypic classes in a CSSL-derived segregation population. Means and standard deviations of grain chalkiness for the three genotypes by the gene marker DE2 are given inside the panel.

Mentions: QTL analysis of the CSSL population with 518 bin markers identified 17 and 12 QTLs for PGC and DEC, respectively. The detail information on location and effect of the identified QTLs is presented in S3 Dataset. Ten common QTL regions were detected for both PGC and DEC and distributed on chromosomes 1, 2, 5, 8, and 10 (Fig. 2, Table 1). All of these QTLs but one (Bin 109) had the same direction of allelic effect that reduced grain chalkiness. The QTL qPGC3–1 located on Bin 167 (26.8–28.9 Mb) of chromosome 3 showed the strongest effect on PGC, explaining 7.4% of the variation. The QTL with the largest effect on DEC was mapped to Bin 441 on chromosome 10. The qPGC8–2 on Bin 393 (24.7–26.1 Mb) of chromosome 8 showed a medium effect on PGC, explaining 3.3% of the variation (Fig. 3a). Notably, using the bin mapping, qPGC1–2 was located in a 500-kb region containing a starch biosynthesis gene SSIV. A large-effect QTL qPGC5–1 was mapped to Bin 263 of a 1.5-Mb region containing Chalk5, a recently cloned rice gene with a significant role in chalkiness formation.


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

Sun W, Zhou Q, Yao Y, Qiu X, Xie K, Yu S - PLoS ONE (2015)

Validation of qPGC8–2.(a) The schematic bins on chromosome 8 defined by SNP genotyping of the CSSL population, where one bin contains an introduced qPGC8–2 (ISA1). (b) Grain chalkiness in the three genotypic classes in a CSSL-derived segregation population. Means and standard deviations of grain chalkiness for the three genotypes by the gene marker DE2 are given inside the panel.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4366167&req=5

pone.0122013.g003: Validation of qPGC8–2.(a) The schematic bins on chromosome 8 defined by SNP genotyping of the CSSL population, where one bin contains an introduced qPGC8–2 (ISA1). (b) Grain chalkiness in the three genotypic classes in a CSSL-derived segregation population. Means and standard deviations of grain chalkiness for the three genotypes by the gene marker DE2 are given inside the panel.
Mentions: QTL analysis of the CSSL population with 518 bin markers identified 17 and 12 QTLs for PGC and DEC, respectively. The detail information on location and effect of the identified QTLs is presented in S3 Dataset. Ten common QTL regions were detected for both PGC and DEC and distributed on chromosomes 1, 2, 5, 8, and 10 (Fig. 2, Table 1). All of these QTLs but one (Bin 109) had the same direction of allelic effect that reduced grain chalkiness. The QTL qPGC3–1 located on Bin 167 (26.8–28.9 Mb) of chromosome 3 showed the strongest effect on PGC, explaining 7.4% of the variation. The QTL with the largest effect on DEC was mapped to Bin 441 on chromosome 10. The qPGC8–2 on Bin 393 (24.7–26.1 Mb) of chromosome 8 showed a medium effect on PGC, explaining 3.3% of the variation (Fig. 3a). Notably, using the bin mapping, qPGC1–2 was located in a 500-kb region containing a starch biosynthesis gene SSIV. A large-effect QTL qPGC5–1 was mapped to Bin 263 of a 1.5-Mb region containing Chalk5, a recently cloned rice gene with a significant role in chalkiness formation.

Bottom Line: 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.The results support that the gene may underlie qPGC8-2 for grain chalkiness.

View Article: PubMed Central - PubMed

Affiliation: National Key Laboratory of Crop Genetic Improvement, Wuhan, China; College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China.

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.

No MeSH data available.


Related in: MedlinePlus