Exploiting the Genomic Diversity of Rice (Oryza sativa L.): SNP-Typing in 11 Early-Backcross Introgression-Breeding Populations.

Jauhar Ali,Delin Li,Jose E Hernandez,Jianlong Xu,Zhikang Li,Muhammad Arif,Patrick S Schnable,Corinne M Marfori-Nazarea,Umair M Aslam,Varunseelan Murugaiyan,Rida Tariq

doi:10.3389/fpls.2018.00849

Abstract

This study demonstrates genotyping-by-sequencing-based single-nucleotide polymorphism (SNP)-typing in 11 early-backcross introgression populations of rice (at BC1F5), comprising a set of 564 diverse introgression lines and 12 parents. Sequencing using 10 Ion Proton runs generated a total of ∼943.4 million raw reads, out of which ∼881.6 million reads remained after trimming for low-quality bases. After alignment, 794,297 polymorphic SNPs were identified, and filtering resulted in LMD50 SNPs (low missing data, with each SNP, genotyped in at least 50% of the samples) for each sub-population. Every data point was supported by actual sequencing data without any imputation, eliminating imputation-induced errors in SNP calling. Genotyping substantiated the impacts of novel breeding strategy revealing: (a) the donor introgression patterns in ILs were characteristic with variable introgression frequency in different genomic regions, attributed mainly to stringent selection under abiotic stress and (b) considerably lower heterozygosity was observed in ILs. Functional annotation revealed 426 non-synonymous deleterious SNPs present in 102 loci with a range of 1–4 SNPs per locus and 120 novel SNPs. SNP-typing this diversity panel will further assist in the development of markers supporting genomic applications in molecular breeding programs.

Highlights

Rice is considered as one of the world’s most important staple foods and is the key to food security especially under the threats of climate change in the coming decades
Cost-effective next-generation sequencing has been successfully employed for whole genome sequencing, gene expression, and single-nucleotide polymorphism (SNP) discovery (Xu et al, 2011; Harper et al, 2012; Li et al, 2014; The 3,000 Rice Genomes Project, 2014)
The tGBS R analysis was used for SNP-typing a rice diversity panel comprising 12 parents and 564 introgression lines (ILs)

Summary

Introduction

Rice is considered as one of the world’s most important staple foods and is the key to food security especially under the threats of climate change in the coming decades. The predicament caused by climate change and a burgeoning population is leading to increased food insecurity and poverty. Breeding improved rice cultivars using cutting-edge biotechnological tools and delivering them efficiently within shorter time frames is the fundamental solution to this. Cost-effective next-generation sequencing has been successfully employed for whole genome sequencing, gene expression, and single-nucleotide polymorphism (SNP) discovery (Xu et al, 2011; Harper et al, 2012; Li et al, 2014; The 3,000 Rice Genomes Project, 2014). Several approaches and methods are already developed for SNP discovery and genotyping in several crop species (Elshire et al, 2011; Wang et al, 2012)

Methods

Results

Conclusion