2 research outputs found
Development of a new AgriSeq 4K mid-density SNP genotyping panel and its utility in pearl millet breeding
Pearl millet is a crucial nutrient-rich staple food in Asia and Africa and adapted
to the climate of semi-arid topics. Since the genomic resources in pearl millet
are very limited, we have developed a brand-new mid-density 4K SNP panel
and demonstrated its utility in genetic studies. A set of 4K SNPs were mined
from 925 whole-genome sequences through a comprehensive in-silico
pipeline. Three hundred and seventy-three genetically diverse pearl millet
inbreds were genotyped using the newly-developed 4K SNPs through the
AgriSeq Targeted Genotyping by Sequencing technology. The 4K SNPs were
uniformly distributed across the pearl millet genome and showed considerable
polymorphism information content (0.23), genetic diversity (0.29), expected
heterozygosity (0.29), and observed heterozygosity (0.03). The SNP panel
successfully differentiated the accessions into two major groups, namely B
and R lines, through genetic diversity, PCA, and structure models as per their
pedigree. The linkage disequilibrium (LD) analysis showed Chr3 had higher LD
regions while Chr1 and Chr2 had more low LD regions. The genetic divergence
between the B- and R-line populations was 13%, and within the sub-population
variability was 87%. In this experiment, we have mined 4K SNPs and optimized
the genotyping protocol through AgriSeq technology for routine use, which is cost-effective, fast, and highly reproducible. The newly developed 4K middensity
SNP panel will be useful in genomics and molecular breeding
experiments such as assessing the genetic diversity, trait mapping, backcross
breeding, and genomic selection in pearl millet
Identification of Candidate Genes Regulating Drought Tolerance in Pearl Millet
Pearl millet is an important crop of the arid and semi-arid ecologies to sustain food and fodder production. The greater tolerance to drought stress attracts us to examine its cellular and molecular mechanisms via functional genomics approaches to augment the grain yield. Here, we studied the drought response of 48 inbreds representing four different maturity groups at the flow-ering stage. A set of 74 drought-responsive genes were separated into five major phylogenic groups belonging to eight functional groups, namely ABA signaling, hormone signaling, ion and osmotic homeostasis, TF-mediated regulation, molecular adaptation, signal transduction, physiological ad-aptation, detoxification, which were comprehensively studied. Among the conserved motifs of the drought-responsive genes, the protein kinases and MYB domain proteins were the most conserved ones. Comparative in-silico analysis of the drought genes across millet crops showed foxtail millet had most orthologs with pearl millet. Of 698 haplotypes identified across millet crops, MyC2 and Myb4 had maximum haplotypes. The protein–protein interaction network identified ABI2, P5CS, CDPK, DREB, MYB, and CYP707A3 as major hub genes. The expression assay showed the presence of common as well as unique drought-responsive genes across maturity groups. Drought tolerant genotypes in respective maturity groups were identified from the expression pattern of genes. Among several gene families, ABA signaling, TFs, and signaling proteins were the prospective con-tributors to drought tolerance across maturity groups. The functionally validated genes could be used as promising candidates in backcross breeding, genomic selection, and gene-editing schemes in pearl millet and other millet crops to increase the yield in drought-prone arid and semi-arid ecol-ogies