Association mapping in rice: basic concepts and perspectives for molecular breeding

Holden Verdeprado,Prakash Lakshmanan,Hasina Begum,Bertrand C.Y. Collard,Joshua N. Cobb,Tobias Kretzschmar,Priya Joyce,Chitra Raghavan

doi:10.1080/1343943x.2018.1483205

Abstract

ABSTRACTIn the last decade, association mapping (AM) has become a well-established method to detect genes and quantitative trait loci (QTLs) associated with agronomically important traits. The identification of a large number of single nucleotide polymorphisms (SNPs) from genome sequencing and concurrent development of high-throughput genotyping platforms has led to AM being widely used for a range of crops. These technologies have been used in rice (Oryza sativa) to explore the abundant diversity and there is enormous potential to identify novel QTLs for traits of interest. Due to the availability of cost-effective high-throughput SNP genotyping methods and rapid developments in rice genomics, it is inevitable that these AM approaches will become more popular in the future, especially in the context of genome-wide association studies (GWASs). In this paper, we review the fundamental concepts, critical considerations and limitations of AM focusing on rice, and reiterate the importance of accurate phenotypic data. We also include a section about connecting GWAS to molecular breeding, covering practical consideration for breeders, which is required to use GWAS results in actual rice molecular breeding programs and which has not received adequate attention in the scientific literature.

Highlights

The development of quantitative trait loci (QTL) mapping methods to identify genes or QTLs controlling quantitative traits was a landmark achievement in plant genetics research in the late 1980s (Doerge, 2002; Mohan et al, 1997; Semagn, Bjornstad, & Xu, 2010)
association mapping (AM) has become an increasingly popular approach in crop genetics to understand the architecture of quantitative traits and to identify QTLs controlling important traits
By combining genome-wide association studies (GWASs) with functional genomics, it is inevitable that the growing use of AM in rice will lead to the identification of new QTLs and candidate genes in the future (Yano et al, 2016)

Summary

Introduction

The development of quantitative trait loci (QTL) mapping methods to identify genes or QTLs controlling quantitative traits was a landmark achievement in plant genetics research in the late 1980s (Doerge, 2002; Mohan et al, 1997; Semagn, Bjornstad, & Xu, 2010). Since literally thousands of research papers have reported the identification of genes or QTLs for important traits across a diverse range of plant species. This wealth of genetic information was built on the foundation of decades of research in crop molecular genetics and genomics. DNA (or molecular) markers have enabled selection of major genes or QTLs for critical or important traits in a process called marker-assisted selection (MAS), which has revolutionized plant breeding. Insertion-deletion (Indel) markers are prevalent and can be screened using high-throughput genotyping platforms (Misra et al, 2017; Yonemaru et al, 2015) These platforms are cost-efficient, can handle large sample sizes and provide fast data turn-around time. The availability of genome sequences and genomic resources continues to provide a wealth of SNP and Indel markers which will undoubtedly be the marker type of choice for decades to come (McCouch et al, 2010)

VERDEPRADO ET AL

Analysis methods for AM

Conclusion and future perspective

Findings

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