Cross transferability of finger millet and maize genomic SSR markers for genetic diversity and population structure analysis of barnyard millet

Abstract

The genomic information available in barnyard millet is very scarce though it is a rich source of highly digestible proteins and dietary fibre with good amounts of soluble and insoluble fractions. In the present investigation, 64 maize and finger millet genomic SSRs were used for cross transferability analysis among barnyard millet cultivated and wild species for identification of polymorphic markers, syntenic regions, genetic diversity and population structure analysis. Out of the 64 SSRs, only 39 (61%) were amplified across the barnyard millet genotypes. The PIC values of all the polymorphic loci for 24 barnyard millet genotypes varied from 0.25 to 0.73 at an average of 0.35. Based on the values of different parameters i.e., PIC values (andgt;0.7), gene diversity (andgt;0.6), inbreeding coefficient (andgt;0.27), the SSR loci bnlg2323 and bnlg2123 were observed to be highly polymorphic. Polymorphism comparison of maize and finger millet SSRs revealed that maize microsatellites were highly transferable, more polymorphic and were able to distinguish barnyard millet genotypes clearly. Results of population structure and genetic diversity analysis were similar in differentiating the barnyard millet genotypes into two groups. The structure analysis showed that all genotypes were pure lines (no admixture) while two (IEC514, and IEC409) had mixture of alleles from other genotypes of population which is depicted from the SSRs used in the study. The present study enriched the barnyard millet genetic resources by identifying suitable polymorphic markers of maize and finger millet for diversity analysis, cultivar identification and marker assisted breeding programmes.

Barnyard Millet for Food and Nutritional Security: Current Status and Future Research Direction

“…Babu and Chauhan (2017) also found homology of some barnyard millet ESTs against the chromosomal regions of 2, 5, 6, 8, 9, and 12 of rice, the waxy gene of maize, granule-bound starch synthase I (GBSSI-S) gene of Panicum repens, Setaria italica, Panicum miliaceum, and super oxide dismutase (SOD) gene of Colletotrichum eremochloae. On the other hand, Babu et al (2018a;2018b) compared rice, maize, and finger millet gSSRs for cross species amplification in barnyard millet and reported that maize and finger millet SSRs exhibited higher PIC values, efficient cross species amplification, and polymorphism percentage than rice SSRs. However, the comparative genetic mapping between rice and barnyard millet showed several putative syntenic regions across the genome that regulated the traits including seed dormancy, plant height, panicle length, spikelet characters, leaf senescence, seed weight/yield-related traits, shattering character, root traits, blast resistance, brown plant hopper (BPH) resistance, and amylose content (Babu et al, 2018b).…”