Construction of a high-density interspecific (Lens culinaris x L. odemensis) genetic map based on functional markers for mapping morphological and agronomical traits, and QTLs affecting resistance to Ascochyta in lentil.

Carlos Polanco,Pedro García,Richard Fratini,Ana Isabel González,Luis Enrique Sáenz De Miera,Francisco Javier Vences,Marcelino Pérez De La Vega,Francisca Vaquero,Roberto Papa

doi:10.1371/journal.pone.0214409

Abstract

Usage of high-throughput sequencing approaches allow for the generation and characterization of reference transcriptome datasets that support gene-based marker discovery, which in turn can be used to build genetic maps among other purposes. We have obtained a transcriptome assembly including 49,453 genes for the lentil (Lens culinaris Medik.) cultivar Alpo using RNAseq methodology. This transcriptome was used as reference to obtain 6,306 quality polymorphic markers (SNPs and short indels) analyzing genotype data from a RIL population at F7 generation derived from the interspecific cross between L. culinaris cv. Alpo and L. odemensis accession ILWL235. L. odemensis is a wild species included in the secondary gene pool and can be used as a source for gene introgression in lentil breeding programs. Marker data were used to construct the first genetic interspecific map between these two species. This linkage map has been used to precisely identify regions of the CDC-Redberry lentil draft genome in which the candidate genes for some qualitative traits (seed coat spotting pattern, flower color, and stem pigmentation) could be located. The genome regions corresponding to a significant single quantitative trait locus (QTL) controlling “time to flowering” located in chromosome 6 and three QTLs regulating seed size and positioned in chromosomes 1 and 5 (two QTLs) were also identified. Significant QTLs for Ascochyta blight resistance in lentil were mapped to chromosome 6 in the genome region or close to it where QTLs for Ascochyta blight resistance have previously been reported.

Highlights

In agriculture, the main goal of hybridization between crops and their wild relatives is the introgression of adaptive traits from the wild relatives into the cultivated forms as part of breeding programs [1]
We present here the first genetic interspecific map between L. culinaris and L. odemensis, from the primary and the secondary gene pools [33] respectively, based on 6,306 SNPs and short indels
High-throughput sequencing approaches, such as the RNAseq used in the present work, allow to generate and to characterize reference transcriptome datasets that support gene-based marker discovery useful and robust to undertake linkage mapping, trait dissection, or genetic diversity studies

Summary

Introduction

The main goal of hybridization between crops and their wild relatives (widecrosses) is the introgression of adaptive traits from the wild relatives into the cultivated forms as part of breeding programs [1]. Interspecific (Lens culinaris x L. odemensis) genetic map based on functional markers. The lentil draft genome assembly v1.2 can be accessed through the JBrowse or BLAST function at http://knowpulse.usask.ca

Methods

Results

Conclusion