Genetic analysis and QTL mapping of the seed hardness trait in a black common bean (Phaseolus vulgaris) recombinant inbred line (RIL) population

K S Sandhu,Anfu Hou,F M You,R L Conner,P M Balasubramanian

doi:10.1007/s11032-018-0789-y

K S Sandhu, Anfu Hou + Show 3 more

Open Access

https://doi.org/10.1007/s11032-018-0789-y

Copy DOI

Journal: Molecular Breeding	Publication Date: Feb 23, 2018
Citations: 31	License type: open-access

Affiliation: Agriculture and Agri-Food Canada

Abstract

Seed hardness trait has a profound impact on cooking time and canning quality in dry beans. This study aims to identify the unknown genetic factors and associated molecular markers to better understand and tag this trait. An F2:7 recombinant inbred line (RIL) population was derived from a cross between the hard and soft seeded black bean parents (H68-4 and BK04-001). Eighty-five RILs and the parental lines were grown at two locations in southern Manitoba during years 2014–2016. Seed samples were harvested manually at maturity to test for seed hardness traits. The hydration capacity and stone seed count were estimated by soaking the seeds overnight at room temperature following AACC method 56-35.01. Seed samples from 2016 tests were also cooked to determine effect of seed hardness on cooking quality. For mapping of genomic regions contributing to the traits, the RIL population was genotyped using the genotype by sequencing (GBS) approach. The QTL mapping revealed that in addition to the major QTL on chromosome 7 at a genomic location previously reported to affect seed-hydration, two novel QTL with significant effects were also detected on chromosomes 1 and 2. In addition, a major QTL affecting the visual appeal of cooked bean was mapped on chromosome 4. This multi-year-site study shows that despite large environmental effects, seed hardness is an oligo-genic and highly heritable trait, which is inherited independently of the cooking quality scored as visual appeal of cooked beans. The identification of the QTLs and development of SNP markers associated with seed hardness can be applied for common bean variety improvement and genetic exploitation of these traits.

Highlights

Legumes contribute an average of 2.5 and 7.5% of total protein intake in developed and developing countries, respectively
Transgressive segregation was observed for all the traits, indicating that the parents were genetically diverse for these traits (Table 1)
There was an inverse relationship between these two traits, they were complementary to each other as hydration capacity (HC) measurement took into account all seeds, including fully and partially hydrated while stone seed percentage (SSP) was only based on completely un-hydrated seeds (Supplementary Fig. 1)

Summary

Introduction

Legumes contribute an average of 2.5 and 7.5% of total protein intake in developed and developing countries, respectively. In sub-Saharan Africa, Latin America, and the Caribbean, dry beans (Phaseolus vulgaris L.) are the major legumes produced and consumed. In 2006–2008, worldwide dry bean production reached 15 million ha with a harvest of 10.65 million t (Akibode and Meridia 2011). In Canada, dry bean is an important rotation and cash crop, planted on 119,000 ha in 2016. Canada is the world’s fifth-largest exporter of dry bean with an annual production of 229,000 t in 2014 (Statistics Canada 2016). With greater emphasis on sustainable agriculture and dietary diversification, the importance of dry bean cultivation is likely to increase. The effect of climate change on crop productivity could favor dry bean production in the northern hemisphere, including Canada (Ramirez-Cabral et al 2016)

Objectives

Methods

Results

Conclusion