mQTL-seq and classical mapping implicates the role of an AT-HOOK MOTIF CONTAINING NUCLEAR LOCALIZED (AHL ) family gene in Ascochyta blight resistance of chickpea

Abstract

Ascochyta blight (AB) caused by the fungal pathogen Ascochyta rabiei is a serious foliar disease of chickpea (Cicer arietinum L.). Despite many genetic studies on chickpea-Ascochyta interaction, genome-wide scan of chickpea for the identification of AB-associated quantitative trait loci (QTLs) and their gene(s) has not been accomplished. To elucidate narrow QTLs for AB resistance, here, we report the use of multiple QTL-sequencing approach on 2 sets of extreme AB phenotype bulks derived from Cicer intraspecific and interspecific crosses. Two major QTLs, qABR4.1 and qABR4.2, and a minor QTL, qABR4.3, were identified on assembled chickpea pseudomolecule 4. We narrowed qABR4.1 to a "robust region" at 4.568-4.618 Mb through mapping on a larger intraspecific cross-derived population and comparative analysis. Among 4 genes, the CaAHL18 gene showed higher expression under Ascochyta stress in AB resistant parent suggesting that it is the candidate gene under "robust qABR4.1." Dual-luciferase assay with CaAHL18 polymorphic cis-regulatory sequences showed that allelic variation is associated with higher expression. Thus, our findings on chickpea-Ascochyta interaction have narrowed down AB resistance associated QTLs on chickpea physical map. The narrowed QTLs and gene-associated markers will help in biotechnological and breeding programs for chickpea improvement.

Genome-wide SNP discovery for development of high-density genetic map and QTL mapping of ascochyta blight resistance in chickpea (Cicer arietinum L.)

“…This QTL region has been narrowed down to 4.3–4.5 Mb genomic region using NGS-based BSA sequencing. A candidate gene Ca-AKL18 (AT‐HOOK MOTIF CONTAINING NUCLEAR LOCALIZED 18) gene was identified within this region (Kumar et al 2018 ). The Ca-AKL18 showed structural variation in the promoter region and had higher expression under ascochyta blight infection in the moderately resistant parent FLIP84‐92C, suggesting that this gene is the most probable candidate involved in resistance to ascochyta blight in chickpea (Kumar et al 2018 ).…”

“…A candidate gene Ca-AKL18 (AT‐HOOK MOTIF CONTAINING NUCLEAR LOCALIZED 18) gene was identified within this region (Kumar et al 2018 ). The Ca-AKL18 showed structural variation in the promoter region and had higher expression under ascochyta blight infection in the moderately resistant parent FLIP84‐92C, suggesting that this gene is the most probable candidate involved in resistance to ascochyta blight in chickpea (Kumar et al 2018 ). Although the QTL interval of qAB4.1 overlapped with the QTL interval of QTL AR1 , fine mapping of this region by Kumar et al ( 2018 ) and Madrid et al ( 2012 ) suggested that the qAB4.1 identified in cultivar Amit (genomic region 6.0–8.6 Mb) could be different than the fine-mapped QTL region of FLIP84-92C.…”

“…Another QTL on chromosome 4 identified in the present study (qAB4.2) located at 21.5–26.7 Mb genomic region overlapped with QTL AR2 flanked by TA146-TA72 physically located at 24.4–43.6 Mb (Iruela et al 2006 ), QTL2 flanked by TA146-TA2 physically located at 24.4–41.9 Mb (Taran et al 2007 ), ab_QTL1 flanked by TA146-TA72 markers physically located at 24.4–43.6 Mb (Stephens et al 2014 ), AB-Q-SR-4-2 flanked by CaM2049-H4G11 markers and physically located at 31.8–41.7 Mb (Sabbavarapu et al 2013 ), qABR4.2 located at 26.2–31.77 Mb (Kumar et al 2018 ) and qAB4.1, qAB4.2 and qAB4.3 (24.4–31.0 Mb) (Deokar et al 2018 ). An ethylene receptor (ER2) a member of the ethylene signalling pathway was found overlapping (26.6 Mb) with the qAB4.2 identified in the present study.…”

Is Chickpea a Potential Substitute for Soybean? Phenolic Bioactives and Potential Health Benefits

“…Most of the genetic studies of chickpea have focused on the identification of genetic regions using different methodologies associated to improving agronomic traits, such as increasing seed yield and the yield of components [95,96,97,98,99,100,101,102,103]. In addition, a genetic approach has been used to develop drought/heat tolerance [70,104,105,106,107,108], as well as disease resistance, for example, Ascochyta blight [109,110]. Solid and broad genetic studies on chickpeas are emerging and paving the way for breeding approaches targeting phenolic compounds in general [111,112,113].…”

Pair-wise Comparison Analysis for Multiple Pool-seq: an efficient method identified anthocyanin biosynthesis genes in rice pericarp

“…Das et al(Das et al, 2016) crossed a less pod number variety ILWC 46 with two more pod number varieties Pusa 1103 and Pusa 256 respectively to obtain the F2 population for mQTL-seq, and then narrowed the candidate region through taking the intersection of the two candidate intervals. Kumar et al (Kumar et al, 2018) identified three genes related to Ascochyta blight resistance of chickpea based on mQTL-seq technology. The application of QTL-seq to some large genome, such as barley, is challenging, so Hisano et al (Hisano et al, 2017)identified the monogenic Mendelian locus and associated QTLs using Exome QTL-seq.…”