SNP-Based Linkage Mapping for Validation of QTLs for Resistance to Ascochyta Blight in Lentil

Abstract

Lentil (Lens culinaris Medik.) is a self-pollinating, diploid, annual, cool-season, food legume crop that is cultivated throughout the world. Ascochyta blight (AB), caused by Ascochyta lentis Vassilievsky, is an economically important and widespread disease of lentil. Development of cultivars with high levels of durable resistance provides an environmentally acceptable and economically feasible method for AB control. A detailed understanding of the genetic basis of AB resistance is hence highly desirable, in order to obtain insight into the number and influence of resistance genes. Genetic linkage maps based on single nucleotide polymorphisms (SNP) and simple sequence repeat (SSR) markers have been developed from three recombinant inbred line (RIL) populations. The IH × NF map contained 460 loci across 1461.6 cM, while the IH × DIG map contained 329 loci across 1302.5 cM and the third map, NF × DIG contained 330 loci across 1914.1 cM. Data from these maps were combined with a map from a previously published study through use of bridging markers to generate a consensus linkage map containing 689 loci distributed across seven linkage groups (LGs), with a cumulative length of 2429.61 cM at an average density of one marker per 3.5 cM. Trait dissection of AB resistance was performed for the RIL populations, identifying totals of two and three quantitative trait loci (QTLs) explaining 52 and 69% of phenotypic variation for resistance to infection in the IH × DIG and IH × NF populations, respectively. Presence of common markers in the vicinity of the AB_IH1- and AB_IH2.1/AB_IH2.2-containing regions on both maps supports the inference that a common genomic region is responsible for conferring resistance and is associated with the resistant parent, Indianhead. The third QTL was derived from Northfield. Evaluation of markers associated with AB resistance across a diverse lentil germplasm panel revealed that the identity of alleles associated with AB_IH1 predicted the phenotypic responses with high levels of accuracy (~86%), and therefore have the potential to be widely adopted in lentil breeding programs. The availability of RIL-based maps, a consensus map, and validated markers linked to AB resistance provide important resources for lentil improvement.

Molecular Breeding for Ascochyta Blight Resistance in Lentil: Current Progress and Future Directions

“…Due to differing nomenclature systems for linkage groups (LGs) and a dearth of common marker loci between genetic maps, common QTL locations between studies are difficult to establish. Nonetheless, AB_NF1 on LG6 in the study of Sudheesh et al (2016) is comparable in position to QTL5 on LG1 of Rubeena et al (2006) and QTL1 on LG1 of Gupta et al (2012), based on a common SSR locus location. QTLs have also been correlated with known resistance determinants such the dominant Ral2 and AbR 1 and recessive ral2 genes (Ford et al, 1999; Chowdhury et al, 2001; Tar'an et al, 2003b).…”

“…They have been extensively used to construct densely populated intraspecific genetic linkage maps, and to identify QTLs (Sharpe et al, 2013; Kaur et al, 2014a; Sudheesh et al, 2016). The information from multiple population-specific genetic maps can be integrated to produce high-density consensus structures utilizing the sequence-linked genetic markers which enables the identification of bridging loci between maps (Sudheesh et al, 2015a,b).…”

“…Several generations of marker technology have been used, from low-fidelity and non-locus-specific systems such as RAPDs, AFLPs, and ISSRs (Ford et al, 1999; Chowdhury et al, 2001; Tar'an et al, 2003b; Rubeena et al, 2006; Tullu et al, 2006) to high-fidelity, locus-specific and frequently gene-associated systems such as RFLPs, SSRs, and SNPs (Gupta et al, 2012; Sudheesh et al, 2016). Cultivar Northfield (ILL5588) has been a common parent in the majority of the published studies.…”

“…Molecular genetic marker studies have identified three trait-linked markers relevant to Australian breeding germplasm (Sudheesh et al, 2016). One of these markers, AB_IH1 (see Table 1), is linked to a key resistance gene, which predicted field AB resistance in more than 85% of diverse validation panel, composed both Australian and international germplasm.…”

“…Genetic linkage maps of lentil have been constructed based on a range of molecular genetic marker types such as randomly amplified polymorphic DNAs (RAPDs), amplified fragment length polymorphisms (AFLPs), sequence characterized amplified regions (SCARs), resistance gene analogs (RGAs), simple sequence repeats (SSRs), inter-simple sequence repeats (ISSRs), and single nucleotide polymorphism (SNPs) (Eujayl et al, 1998; Rubeena et al, 2003; Tullu et al, 2006; Sharpe et al, 2013; Kaur et al, 2014a; Verma et al, 2015). Through the use of these maps, a number of genomic regions controlling AB resistance have been identified (Ford et al, 1999; Rubeena et al, 2006; Sudheesh et al, 2016). …”