Dissecting the Genetic Architecture of Aphanomyces Root Rot Resistance in Lentil by QTL Mapping and Genome-Wide Association Study

Abstract

Lentil (Lens culinaris Medikus) is an important source of protein for people in developing countries. Aphanomyces root rot (ARR) has emerged as one of the most devastating diseases affecting lentil production. In this study, we applied two complementary quantitative trait loci (QTL) analysis approaches to unravel the genetic architecture underlying this complex trait. A recombinant inbred line (RIL) population and an association mapping population were genotyped using genotyping by sequencing (GBS) to discover novel single nucleotide polymorphisms (SNPs). QTL mapping identified 19 QTL associated with ARR resistance, while association mapping detected 38 QTL and highlighted accumulation of favorable haplotypes in most of the resistant accessions. Seven QTL clusters were discovered on six chromosomes, and 15 putative genes were identified within the QTL clusters. To validate QTL mapping and genome-wide association study (GWAS) results, expression analysis of five selected genes was conducted on partially resistant and susceptible accessions. Three of the genes were differentially expressed at early stages of infection, two of which may be associated with ARR resistance. Our findings provide valuable insight into the genetic control of ARR, and genetic and genomic resources developed here can be used to accelerate development of lentil cultivars with high levels of partial resistance to ARR.

Genomics‐assisted lentil breeding: Current status and future strategies

“…The recombinant inbred line (RIL) populations have been developed from three biparental crosses ([CDC Redberry × ILL7502], [ILL8006 × CDC Milestone], and [PI320937 × Eston]) for quality traits and used to construct linkage maps and identify the QTLs for Fe, Mn, and Se uptake (Aldemir et al, 2017; Ates et al, 2016; Ates, Aldemir, Alsaleh, et al, 2018; Ates, Aldemir, Yagmur, et al, 2018). A mapping population composed of 189 RILs has been developed from a cross between partial resistant and susceptible breeding lines for genetic dissection of Aphanomyces root rot resistance in lentil (Ma et al, 2020). Intraspecific mapping populations in general have low genetic diversity, and only a limited number of markers can be incorporated to genetic maps (Bohra et al, 2012).…”

“…These markers were assigned on seven LGs with a total genetic distance of 809.4 cM with an average marker density of 3.05 cM (Mane et al, 2020). Further reduction in the cost of sequencing has led to the development of a greater number of high‐density linkage maps based only on SNP markers in lentil (Aldemir et al, 2017; Bhadauria, Ramsay, et al, 2017; Gujarai‐Verma et al, 2014; Ma et al, 2020; Polanco et al, 2019; Sudheesh, Rodda, et al, 2016; Temel et al, 2014). A high‐density consensus map of lentil comprising 9793 SNP markers covering a total of 977.47‐cM distance was developed from three mapping populations.…”

Generalized Linear Model with Elastic Net Regularization and Convolutional Neural Network for Evaluating Aphanomyces Root Rot Severity in Lentil

“…The third experiment was conducted in November 2018 and consisted of 334 lentil accessions from the LSP grown in a randomized complete block design with ten replicates. In all experiments, plants were grown in a greenhouse with a day temperature of 25°C, night temperature of 23°C, and photoperiod of 16 h. Details for inoculum preparation and inoculation of plant material are described in our previous studies [ 20 , 21 ]. The procedure for RGB image capture is also described in our previous work [ 20 ].…”

Intelligent Characterization of Lentil Genetic Resources: Evolutionary History, Genetic Diversity of Germplasm, and the Need for Well‐Represented Collections

“…Pavan et al (2019) found that genetic clusters of Mediterranean lentils are related to geographic patterns and suggested post-domestication spreading routes. More recently, GBS was used to conduct an AM analysis to identify genes related to Aphanomyces root rot resistance in lentil (Ma et al, 2020). Although GBS is a cost-effective alternative for studies of neutral genetic variation, its extensive implementation in lentil is limited because it does not provide sufficient marker density and depth to confidently identify variants under selection in such large and complex genomes.…”