Application of Genomics Approaches for the Improvement in Ascochyta Blight Resistance in Chickpea

Shimna Sudheesh,Sukhjiwan Kaur,Hossein V Kahrood,Nicole Dron,Noel O I Cogan,Kristy Hobson,Shivraj Braich

doi:10.3390/agronomy11101937

Abstract

Advancements in high-throughput genotyping and sequencing technologies are enabling the development of a vast range of genomic tools and resources for a new revolution in plant breeding. Several genotyping-by-sequencing (GBS) methods including capture-based, genome complexity reduction and sequencing of cDNA (GBS-t) are available for application in trait dissection, association mapping, and genomic selection (GS) in crop plants. The aims of this study were to identify genomic regions conferring resistance to Ascochyta blight (AB) introgressed from the wild Cicer echinospernum into the domesticated C. arietinum, through a conventional recombinant inbred population genotyped using a variety of GBS methods. Evaluation of GBS methods revealed that capture-based approaches are robust and reproducible while GBS-t is rapid and flexible. A genetic linkage map consisting of 5886 polymorphic loci spanning 717.26 cM was generated. Using field phenotyping data from two years, a single genomic region on LG4 was identified with quantitative trait loci (QTL) mapping. Both GBS methods reported in this study are well suited for applications in genomics assisted plant breeding. Linked markers for AB resistance, identified in the current study, provide an important resource for the deployment into chickpea breeding programs for marker-assisted selection (MAS).

Highlights

Chickpea (Cicer arietinum L.) is the third most important grain legume crop after soybean and pea, grown worldwide on c. 17.8 Mha with an annual production of 17.2 million tonnes [1]
Selecting the best suited method depends on the genome size of the crop, population structure, availability of prior genomic information, reproducibility, ease of application, and the relative scale of the industry
These results indicate that capture-based approach is more robust, reproducible, and scalable as compared to GBS-t

Summary

Introduction

Chickpea (Cicer arietinum L.) is the third most important grain legume crop after soybean and pea, grown worldwide on c. 17.8 Mha with an annual production of 17.2 million tonnes [1]. Chickpea productivity can reach up to 6 t/ha; exposure to biotic and abiotic stresses can reduce the average yield to

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