Gene/QTL discovery for Anthracnose in common bean (Phaseolus vulgaris L.) from North-western Himalayas.

Neeraj Choudhary,Mohd Ashraf Bhat,Rajeev K Varshney,Vanya Bawa,Mahendar Thudi,Bikram Singh,Rajneesh Paliwal,Moni Gupta,Parvaze A Sofi,Reyazul Rouf Mir,Javid Iqbal Mir

doi:10.1371/journal.pone.0191700

Abstract

Common bean (Phaseolus vulgaris L.) is one of the most important grain legume crops in the world. The beans grown in north-western Himalayas possess huge diversity for seed color, shape and size but are mostly susceptible to Anthracnose disease caused by seed born fungus Colletotrichum lindemuthianum. Dozens of QTLs/genes have been already identified for this disease in common bean world-wide. However, this is the first report of gene/QTL discovery for Anthracnose using bean germplasm from north-western Himalayas of state Jammu & Kashmir, India. A core set of 96 bean lines comprising 54 indigenous local landraces from 11 hot-spots and 42 exotic lines from 10 different countries were phenotyped at two locations (SKUAST-Jammu and Bhaderwah, Jammu) for Anthracnose resistance. The core set was also genotyped with genome-wide (91) random and trait linked SSR markers. The study of marker-trait associations (MTAs) led to the identification of 10 QTLs/genes for Anthracnose resistance. Among the 10 QTLs/genes identified, two MTAs are stable (BM45 & BM211), two MTAs (PVctt1 & BM211) are major explaining more than 20% phenotypic variation for Anthracnose and one MTA (BM211) is both stable and major. Six (06) genomic regions are reported for the first time, while as four (04) genomic regions validated the already known QTL/gene regions/clusters for Anthracnose. The major, stable and validated markers reported during the present study associated with Anthracnose resistance will prove useful in common bean molecular breeding programs aimed at enhancing Anthracnose resistance of local bean landraces grown in north-western Himalayas of state Jammu and Kashmir.

Highlights

Common bean (Phaseolus vulgaris L.; 2n = 2x = 22) known as kidney bean, French bean, dry bean, field bean etc. is one of the most precious and highly relished pulse crop used for direct human consumption globally
QTLs/genes are known for this disease but there is hardly any report available about the identification of QTLs/genes for anthracnose identified from Himalayan beans genetic background
The major and stable marker-trait associations (MTAs) identified during the present study will prove useful for marker-assisted breeding (MAB) programs aimed at enhancing anthracnose resistance of Himalayan beans

Summary

Introduction

Anthracnose is a seed-borne disease in common bean caused by Collectotricum lindemuthianum This pathogen possesses high degree of pathogenic variability throughout the world including India. The prevalence of anthracnose disease has posed a serious threat for bean production in common bean growing areas of Himalayan state of Jammu & Kashmir, India. QTLs/genes are known for this disease but there is hardly any report available about the identification of QTLs/genes for anthracnose identified from Himalayan beans genetic background. For tackling this disease efficiently in this Himalayan region, we have collected/procured a set of 428 common bean lines from different hot-spots in state Jammu and Kashmir and from National Gene bank (NBPGR, New Delhi, India). The major and stable MTAs identified during the present study will prove useful for marker-assisted breeding (MAB) programs aimed at enhancing anthracnose resistance of Himalayan beans

Materials and methods

Results and discussion

Method