Mining QTL and genes for root traits and biochemical parameters under vegetative drought in South Indian genotypes of finger millet (Eleusine coracana (L.) Gaertn) by association mapping and in silico comparative genomics

Abstract

Abstract Finger millet (Elusine coracana) in an important nutria-rich cereal crop. A total of 42 Indian genotypes were used to identify quantitative trait loci (QTL) associated with root traits (root length and root weight) and biochemical parameters (activities of catalase (CAT), ascorbate peroxidase (APX), glutathione reductase (GR), peroxidase (POD), and superoxide dismutase (SOD) enzymes) under drought condition in finger millet. The highest root length (126.40 cm), fresh weight (32.67 gm) and CAT activity (873.13 μM min−1g−1 FW) were observed in TRY-01 genotype under drought condition. Furthermore, the highest APX enzyme activity was observed in GPU-28, INDOF-08, ML-365, THRV-PP, PR-202, and INDOF-07 genotypes. In the present study, five (qtlSSR-06, qtlUGEP-13, qtlUGEP-18, qtlUGEP-104 and qtlUGEP-106) and two (qtlUGEP-07 and qtlUGEP-16) QTL were associated with root length and root weight respectively. Six QTL were associated with biochemical traits such as APX (qtlSSR-06 and qtlUGEP-16), CAT (qtlUGEP-07 and qtlUGEP-16), GR (qtlUGEP-18, qtlUGEP-95, and qtlUGEP-101), SOD (qtlSSR-06 and qtlUGEP-16), and POD (qtlSSR-06 and qtlUGEP-16) activities. An In-silico comparative genomic analysis was performed with genomes of various Poaceae family members to find the QTL associated with any candidate gene. The qtlUGEP-07 was associated with five candidate genes in the different Poaceae family members. Similarly, the qtlUGEP-13 was corresponding to two candidate genes of Panicum hallii. Furthermore, qtlUGEP-16 and qtlUGEP-95 were also associated with candidate genes in foxtail millet and maize. This study will help improve finger millet genotypes under both biotic and abiotic stress conditions.