Comparative Genomics and Association Mapping Approaches for Blast Resistant Genes in Finger Millet Using SSRs

Abstract

The major limiting factor for production and productivity of finger millet crop is blast disease caused by Magnaporthe grisea. Since, the genome sequence information available in finger millet crop is scarce, comparative genomics plays a very important role in identification of genes/QTLs linked to the blast resistance genes using SSR markers. In the present study, a total of 58 genic SSRs were developed for use in genetic analysis of a global collection of 190 finger millet genotypes. The 58 SSRs yielded ninety five scorable alleles and the polymorphism information content varied from 0.186 to 0.677 at an average of 0.385. The gene diversity was in the range of 0.208 to 0.726 with an average of 0.487. Association mapping for blast resistance was done using 104 SSR markers which identified four QTLs for finger blast and one QTL for neck blast resistance. The genomic marker RM262 and genic marker FMBLEST32 were linked to finger blast disease at a P value of 0.007 and explained phenotypic variance (R2) of 10% and 8% respectively. The genomic marker UGEP81 was associated to finger blast at a P value of 0.009 and explained 7.5% of R2. The QTLs for neck blast was associated with the genomic SSR marker UGEP18 at a P value of 0.01, which explained 11% of R2. Three QTLs for blast resistance were found common by using both GLM and MLM approaches. The resistant alleles were found to be present mostly in the exotic genotypes. Among the genotypes of NW Himalayan region of India, VHC3997, VHC3996 and VHC3930 were found highly resistant, which may be effectively used as parents for developing blast resistant cultivars in the NW Himalayan region of India. The markers linked to the QTLs for blast resistance in the present study can be further used for cloning of the full length gene, fine mapping and their further use in the marker assisted breeding programmes for introgression of blast resistant alleles into locally adapted cultivars.

Gene Discovery and Advances in Finger Millet [Eleusine coracana (L.) Gaertn.] Genomics—An Important Nutri-Cereal of Future

“…Only 20 primers showed polymorphism, and 13 primers were identified as having a PIC value above 0.5. Later, Kalyana Babu et al (2014b) used two search criteria for identification of EST-SSRs. In the first criterion, the minimum number of repeats was 6 for dinucleotide, 4 for trinucleotide, and three for tetra, penta and hexa-nucleotides.…”

“…Kalyana Babu et al (2014a) identified four markers UGEP 81, UGEP 77, UGEP 90, and FM 9 tightly linked to QTLs of basal tiller number, days to flowering, flag leaf blade width and plant height, respectively. For blast resistance, 104 SSR markers identified four QTLs for finger blast and one QTL for neck blast resistance (Kalyana Babu et al, 2014b). The rice genomic marker RM 262 and genic marker FMBLEST32 were linked to finger blast disease resistance at a P -value of 0.007 and explained a low phenotypic variance of 10 and 8% respectively (Table 2).…”

“…The genomic marker UGEP81 was associated to finger blast resistance at a P -value of 0.009 and explained 7.5% of phenotypic variance. The QTLs for neck blast was associated with the genomic SSR marker UGEP18 at a P -value of 0.01 which explained 11% of phenotypic variance (Table 2; Kalyana Babu et al, 2014b). Some loci UGEP56, UGEP8, UGEP65, and UGEP31 had multi trait associations (Bharathi, 2011).…”

“…A similar strategy to improve finger millet seed calcium content was also reported independently that focused on orthologs of calcium-binding proteins (CBPs) with extensive characterization of a seed dominant calmodulin (Kumar et al, 2014a, 2015b). A parallel strategy has been suggested for disease resistance in finger millet based on the initial isolation of disease resistance receptors (Reddy et al, 2011; Kalyana Babu et al, 2014b). …”

Genetic and Genomic Resources of Small Millets

“…To develop molecular markers for MAS and breeding in finger millet for fungal blast disease resistance, Panwar et al (2011) have reported developing EST-based resistance gene analogue (RGA) markers. A comparative genomics approach was used to establish association of SSR markers to finger millet blast disease resistant QTL (Babu et al, 2014). Isolation of candidate genes and gene families, such as RGAs Weng et al, 2009), SiNAC (Puranik et al, 2011a), Dof1 (Gupta et al, 2012), and calcium sensor CaM gene (Nath et al, 2010), from finger millet and foxtail millet in the past few years has provided opportunities to develop functional markers for MAS and breeding for nutritional quality improvement and blast disease resistance.…”