Sequencing of bulks of segregants allows dissection of genetic control of amylose content in rice

Plant Biotechnology Journal
Peterson WambuguRobert Henry

Abstract

Amylose content (AC) is a key quality trait in rice. A cross between Oryza glaberrima (African rice) and Oryza sativa (Asian rice) segregating for AC was analysed by sequencing bulks of individuals with high and low AC. SNP associated with the granule bound starch synthase (GBSS1) locus on chromosome 6 were polymorphic between the bulks. In particular, a G/A SNP that would result in an Asp to Asn mutation was identified. This amino acid substitution may be responsible for differences in GBSS activity as it is adjacent to a disulphide linkage conserved in all grass GBSS proteins. Other polymorphisms in genomic regions closely surrounding this variation may be the result of linkage drag. In addition to the variant in the starch biosynthesis gene, SNP on chromosomes 1 and 11 linked to AC was also identified. SNP was found in the genes encoding the NAC and CCAAT-HAP5 transcription factors that have previously been linked to starch biosynthesis. This study has demonstrated that the approach of sequencing bulks was able to identify genes on different chromosomes associated with this complex trait.

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Citations

Feb 23, 2019·International Journal of Molecular Sciences·Sajid FiazFahad Ali
Apr 2, 2020·Frontiers in Genetics·Edwige Gaby Nkouaya MbanjoNese Sreenivasulu
Jan 26, 2020·TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik·Huaiyong LuoHuifang Jiang
Dec 24, 2018·Trends in Plant Science·Khanh Le NguyenPascal Gantet

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Methods Mentioned

BETA
genotyping
electrophoresis
Assay

Software Mentioned

CLC Genomic Workbench
GBSS
CLC
PlantPAN
CandiSNP
RiceFREND
MAS
CLC genomics Workbench

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