A high‐density linkage map of finger millet provides QTL for blast resistance and other agronomic traits

Abstract

Finger millet [Eleusine coracana (L.) Gaertn.] is a critical subsistence crop in eastern Africa and southern Asia but has few genomic resources and modern breeding programs. To aid in the understanding of finger millet genomic organization and genes underlying disease resistance and agronomically important traits, we generated a F2:3 population from a cross between E. coracana (L.) Gaertn. subsp. coracana accession ACC 100007 and E. coracana (L.) Gaertn. subsp. africana , accession GBK 030647. Phenotypic data on morphology, yield, and blast (Magnaporthe oryzae) resistance traits were taken on a subset of the F2:3 population in a Kenyan field trial. The F2:3 population was genotyped via genotyping‐by‐sequencing (GBS) and the UGbS‐Flex pipeline was used for sequence alignment, nucleotide polymorphism calling, and genetic map construction. An 18‐linkage‐group genetic map consisting of 5,422 markers was generated that enabled comparative genomic analyses with rice (Oryza sativa L.), foxtail millet [Setaria italica (L.) P. Beauv.], and sorghum [Sorghum bicolor (L.) Moench]. Notably, we identified conserved acrocentric homoeologous chromosomes (4A and 4B in finger millet) across all species. Significant quantitative trait loci (QTL) were discovered for flowering date, plant height, panicle number, and blast incidence and severity. Sixteen putative candidate genes that may underlie trait variation were identified. Seven LEUCINE‐RICH REPEAT‐CONTAINING PROTEIN genes, with homology to nucleotide‐binding site leucine‐rich repeat (NBS‐LRR) disease resistance proteins, were found on three chromosomes under blast resistance QTL. This high‐marker‐density genetic map provides an important tool for plant breeding programs and identifies genomic regions and genes of critical interest for agronomic traits and blast resistance.

Finger millet: a hero in the making to combat food insecurity

“…Because of the difficulty in generating crosses, trait mapping in biparental populations has been very limited. Pendergast et al ( 2021 ) mapped QTL for flowering date, plant height, panicle number, and blast incidence and severity in F 2 -derived F 3 progeny from a cross between the cultivated line ACC100007 and an unidentified wild accession. Genotyping was conducted using 5422 SNP markers derived from genotyping-by-sequencing (GBS) (Qi et al 2018 ).…”

Revitalization of small millets for nutritional and food security by advanced genetics and genomics approaches

“…Linkage maps with SNP markers were also later developed in proso millet by Rajput et al (2016) . A high-density linkage map with SNPs for finger millet was recently developed by Pendergast et al (2022) . Subsequently, molecular markers such as AFLP, RAPD, CAP, miRNA, EST, ISSR, SRAP, DEG, and SNP in proso millet were implied for genotyping the diversity, while EST, RAPD, and AFLP were used to analyze the calcium dynamics in finger millet ( Habiyaremye et al, 2017 ).…”

Identification of QTL Associated with Agro-Morphological and Phosphorus Content Traits in Finger Millet under Differential Phosphorus Supply via Linkage Mapping

“…Several linkage-mapping studies have been conducted in other cereals to dissect the genetic mechanisms that control different traits using RILs [24,28,29,32,35]. Very recently, eight QTL for blast-resistance traits (leaf blast severity and panicle blast incidence at maturity) and agronomic traits (flowering date, pH, and panicle number) were identified in finger millet through linkage mapping [48]. This is the only available study on linkage mapping in finger millet.…”