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. 2018 Jan;16(1):100-110.
doi: 10.1111/pbi.12752. Epub 2017 Jul 11.

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

Peterson Wambugu  1 , Marie-Noelle Ndjiondjop  2 , Agnelo Furtado  1 , Robert Henry  1
Affiliations

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

Peterson Wambugu et al. Plant Biotechnol J. 2018 Jan.

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.

Keywords: allele frequency; amylose content; bulk segregant analysis; genetic linkage; genetic markers; whole genome sequencing.

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Conflict of interest statement

The authors declare no conflict of interest.

Figures

Figure 1
Figure 1
Frequency distribution of amylose content (AC) in 100 individuals and parental genotypes of a BC2F8 population of an interspecific cross between Oryza glaberrima and Oryza sativa (CG14 X WAB 56–104). AC was determined using the Megazyme kit as a % of total starch by weight.
Figure 2
Figure 2
Plot of chromosomal positions and allele frequency of putative candidate nonsynonymous SNPs located on chromosome 6. The indicated allele frequencies are from the high amylose bulk. Almost all the putative candidate genes where these SNPs are located, cluster with GBSS1 suggesting an apparent close linkage with this locus. The putative candidate genes cluster within a region of about 2.1 Mbp which is equivalent to about 10 cM. The SNPs were plotted using CandiSNP (Etherington et al., 2014).
Figure 3
Figure 3
Schematic diagram of bulk segregant analysis experimental set‐up and data analysis pipeline.
See this image and copyright information in PMC

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