QTL mapping of pearl millet rust resistance using an integrated DArT- and SSR-based linkage map

Abstract

Rust, caused by the fungus Puccinia substriata var. indica, is one of the most important production constraints of pearl millet worldwide, leading to grain yield losses of up to 76 % as well as major losses in fodder yield and quality. Here, we report the development of a linkage map integrating Diversity Arrays Technology (DArT) markers and simple sequence repeat (SSR) markers, using this to identify quantitative trait loci (QTLs) for pearl millet rust resistance. Genotyping data from 256 DArT and 70 SSR markers on 168 F 7 recombinant inbred lines from cross 81B-P6 9 ICMP 451-P8 were used to construct a linkage map comprised of 286 loci (229 DArT and 57 SSR markers) spanning a total length of 740.3 cM (Haldane) with an average adjacent marker distance of 2.7 cM. Linkage group 7 (LG7) (153.5 cM) was the longest and LG6 the shortest (45.0 cM). The map was used to identify a major QTL for rust resistance with an LOD score of 27 on LG1, which explained 58 % of the observed phenotypic variation. In addition, two putative modifiers of small effect were detected, one each on LG4 and LG7. The novel rust resistance QTL identified on LG1 is thought to confer a durable slow-rusting phenotype, which is still effective in India more than 20 years after it was first deployed in the previously popular single-cross hybrid MH 179 (ICMH 451). The flanking markers reported here provide a framework for marker-assisted selection and possible future map-based cloning of this resistance gene.

Mapping quantitative trait loci (QTLs) associated with resistance to major pathotype-isolates of pearl millet downy mildew pathogen

“…The availability of densely-saturated genetic molecular maps those are feasible by microsatellites, DArT, SNPs and other marker system pipelines will offer breeders and geneticists with an enviable tool to identifying different genomic regions of interest, which in turn will enhance the efficiency of marker-assisted breeding (Ambawat et al 2016). QTL mapping is a prerequisite for the identification of molecular markers associated with tolerance/resistance to abiotic/biotic stresses and agronomically important traits (Kumar et al 2018).…”

“…Note: The marker name and genetic distance (cM) are listed on right and left sides, respectively on a few linkage groups Rajaram et al 2013). Such discordance in terms of marker order among diverse genetic maps is not unexpected, as genetic mapping reflects merely a gesture of the relative positions and genetic distances of markers to each other (Sourdille et al 2004;Ambawat et al 2016). Under the present investigation, segregation distortion was observed for 39.7% of the total marker loci assessed, which is similar to earlier research reports (Supriya et al 2011).…”

Genome-Wide Association Studies and Genomic Selection in Pearl Millet: Advances and Prospects

“…An identified SCAR marker was eventually validated using diverse pearl millet genotypes belonging to Asia and Africa, and the outcomes demonstrate that the marker was linked to downy mildew disease-resistant genotypes only (Jogaiah et al, 2014). The development of a linkage map was reported to integrate 256 DArT markers and 70 SSR markers and used to identify QTLs on LG1 with LOD score of 27 for rust resistance in 168 F 7 pearl millet RILs derived from cross 81B-P6 × ICMP 451-P8 (Ambawat et al, 2016). Using a total of 106 pearl millet RILs (F6) derived from ICMB 841-P3 × 863B-P2 cross and 305 (96 SSRs and 208 DArT) markers, a linkage map was generated to map QTLs for grain iron and zinc content (Kumar et al, 2016).…”

Genomics-assisted breeding in minor and pseudo-cereals

“…Studies involving the QTL mapping of other minor and pseudo-cereals, however, are relatively limited and mostly include studies in rye (Erath et al 2016, Miedaner et al 2018, Myśków et al 2018, Wang et al 2015, oat (Admassu-Yimer et al 2019, Babiker et al 2015, Pellizzaro et al 2016, Schneider et al 2015, Sunstrum et al 2018, Zimmer et al 2018, and millet. Of the various types of millet, pearl millet (Ambawat et al 2016, Aparna et al 2015, Kumar et al 2016b, 2018, Pucher et al 2018, Punnuri et al 2016, Taunk et al 2018 and foxtail millet (Fang et al 2016, Mauro-Herrera and Doust 2016, Ni et al 2017, Odonkor et al 2018, Wang et al 2017a, 2017b have received the majority of research attention, although one study also focused on proso millet (Rajput et al 2016). Notably, very few QTL mapping studies have focused on pseudocereals.…”