Understanding genetic diversity in drought-adaptive hybrid parental lines in pearl millet.

Information on genetic diversity and population structure is helpful to strategize enhancing the genetic base of hybrid parental lines in breeding programs. The present study determined the population structure and genetic diversity of 109 pearl millet hybrid parental lines, known for their better adaptation and performance in drought-prone environments, using 16,472 single nucleotide polymorphic (SNP) markers generated from GBS (genotyping-by-sequencing) platforms. The SNPs were distributed uniformly across the pearl millet genome and showed considerable genetic diversity (0.337), expected heterozygosity (0.334), and observed heterozygosity (0.031). Most of the pairs of lines (78.36%) had Identity-by-State (IBS) based genetic distances of more than 0.3, indicating a significant amount of genetic diversity among the parental lines. Bayesian model-based population stratification, neighbor-joining phylogenetic analysis, and principal coordinate analysis (PCoA) differentiated all hybrid parental lines into two clear-cut major groups, one each for seed parents (B-lines) and pollinators (R-lines). Majority of parental lines sharing common parentages were found grouped in the same cluster. Analysis of molecular variance (AMOVA) revealed 7% of the variation among subpopulations, and 93% of the variation was attributable to within sub-populations. Chromosome 3 had the highest number of LD regions. Genomic LD decay distance was 0.69 Mb and varied across the different chromosomes. Genetic diversity based on 11 agro-morphological and grain quality traits also suggested that the majority of the B- and R-lines were grouped into two major clusters with few overlaps. In addition, the combined analysis of phenotypic and genotypic data showed similarities in the population grouping patterns. The present study revealed the uniqueness of most of the inbred lines, which can be a valuable source of new alleles and help breeders to utilize these inbred lines for the development of hybrids in drought-prone environments

Induced Mutagenesis Enhances Lodging Resistance and Photosynthetic Efficiency of Kodomillet (Paspalum Scrobiculatum)

The present research was focused in the development of photosynthetically efficient (PhE) and non-lodging mutants by utilizing ethyl methane sulphonate (EMS) and gamma radiation in the kodomillet variety CO 3, prone to lodging. Striking variations in a number of anatomical characteristics of leaf anatomy for PhE and culm thickness for lodging resistance was recorded in M2 (second mutant) generation. The identified mutants were subjected to transcriptomic studies to understand their molecular basis. Expression profiling was undertaken for pyruvate phosphate dikinase (PPDK), Nicotinamide Adenine Dinucleotide Phosphate Hydrogen—(NADPH) and NADP-dependent malate dehydrogenase (NADP-MDH) in the mutants CO 3-100-7-12 (photosynthetically efficient) and in CO 3-200-13-4 (less efficient). For lodging trait, two mutants CO 3-100-18-22 (lodged) and CO 3-300-7-4 (non-lodged) were selected for expression profiling using genes GA2ox6 and Rht-B. The studies confirmed the expression of PPDK increased 30-fold, NADP-ME2 ~1-fold and NADP-MDH10 was also highly expressed in the mutant CO 3-100-7-12. These expression profiles suggest that kodomillet uses an NADP-malic enzyme subtype C4 photosynthetic system. The expression of Rht-B was significantly up regulated in CO 3-300-7-4. The study highlights the differential expression patterns of the same gene in different lines at different time points of stress as well as non-stress conditions. This infers that the mutation has some effect on their expression; otherwise the expression levels will be unaltered. Enhancement in grain yield could be best achieved by developing a phenotype with high PhE and culm with thick sclerenchyma cells

Violin plot based on pairwise Mahalanobis distances of 84 parental lines based on molecular marker; B-lines (34), R-lines (50) and between B- and R-lines.

Violin plot based on pairwise Mahalanobis distances of 84 parental lines based on molecular marker; B-lines (34), R-lines (50) and between B- and R-lines.</p

Nei’s genetic distance matrix for 109 parental inbred lines obtained from 16,472 SNPs.

Nei’s genetic distance matrix for 109 parental inbred lines obtained from 16,472 SNPs.</p

The Linkage Disequilibrium pattern based on 16,472 SNPs identified via GBS; is depicted in a Triangle plot for all seven chromosomes.

Illustrating LD among SNPs across each chromosome. Pairwise LD values were graphically represented on the X- and Y-axes, with the above diagonal indicating the squared correlation coefficient (r2), and the below diagonal indicating the corresponding P-value. (DOCX)</p

Fig 6 -

Linkage Disequilibrium pattern based on SNP identified via GBS (a) Triangle plot representing LD among SNPs for Chr 3 regions which showed a high LD pattern, Pairwise LD values were plotted on the X- and Y- axes; the above diagonal represents the squared correlation coefficient (r2), and the below diagonal represents the corresponding P-value; (b) Linkage Disequilibrium Decay (LDD) plots which show a decline in r2 between SNP pairs presented as a function of physical distance in pairs for the entire genome.</p

Inferred ancestry of individuals and degree of admixture among 109 hybrid parental lines.

Inferred ancestry of individuals and degree of admixture among 109 hybrid parental lines.</p

Roger’s Genetic distance (Below diagonal) based on SNP data and Mahalonbis Distance (above diagonal) based on phenotypic data for 84 Hybrid parental lines.

Roger’s Genetic distance (Below diagonal) based on SNP data and Mahalonbis Distance (above diagonal) based on phenotypic data for 84 Hybrid parental lines.</p