Genome wide association scans for markers- S3_162065732 associated with root dry weight (RDW) and flowering period water use (WU) and S3_225760139 associated with root volume (RV) and Shoot biomass (SB) under drought stress condition.

<p>Genome wide association scans for markers- S3_162065732 associated with root dry weight (RDW) and flowering period water use (WU) and S3_225760139 associated with root volume (RV) and Shoot biomass (SB) under drought stress condition.</p

Genome wide association scans for markers- S3_128533521 and S7_151238865 associated with Grain yield (GY), Shoot biomass (SB) and Transpiration efficiency (TE) under well water condition.

<p>Genome wide association scans for markers- S3_128533521 and S7_151238865 associated with Grain yield (GY), Shoot biomass (SB) and Transpiration efficiency (TE) under well water condition.</p

Accessions selected possessing desirable allelic combination for multiple traits and there phenotypic expressions under DS and WW condition.

<p><b>WW</b>- Well watered condition, <b>DS</b>- Drought stress condition, <b>GY</b>- Grain yield, <b>SB</b>- Shoot biomass, <b>TE</b>- Water use efficiency, WU-Flowering period water use <b>RDW</b>-Root dry weight, <b>RV</b>-Root volume.</p

Linkage disequilibrium (LD) decay in the CAAM panel based on the SNPs

<p>Linkage disequilibrium (LD) decay in the CAAM panel based on the SNPs</p

Summary of Marker trait association (MTAs) under well-watered (WW) and drought stress condition (DS).

<p><b>W</b>- Well watered condition, <b>DS</b>- Drought stress condition, <b>GY</b>- Grain yield, <b>SB</b>- Shoot biomass, <b>WU</b>- Flowering period water use, <b>TE</b>- Transpiration efficiency, <b>RD</b>-Rooting depth, <b>RDW</b>-Root dry weight, <b>RL</b>-Root length, <b>RSA</b>-Root surface area, <b>RV</b>- Root volume, <b>RLD</b>- Root length density, <b>PV</b>- phenotypic variation.</p

Clustering of CAAM panel based on discriminant analysis of principal component using the genetic data.

<p>Clustering of CAAM panel based on discriminant analysis of principal component using the genetic data.</p

Improved pearl millet genomes representing the global heterotic pool offer a framework for molecular breeding applications

Abstract High-quality reference genome assemblies, representative of global heterotic patterns, offer an ideal platform to accurately characterize and utilize genetic variation in the primary gene pool of hybrid crops. Here we report three platinum grade de-novo, near gap-free, chromosome-level reference genome assemblies from the active breeding germplasm in pearl millet with a high degree of contiguity, completeness, and accuracy. An improved Tift genome (Tift23D2B1-P1-P5) assembly has a contig N50 ~ 7,000-fold (126 Mb) compared to the previous version and better alignment in centromeric regions. Comparative genome analyses of these three lines clearly demonstrate a high level of collinearity and multiple structural variations, including inversions greater than 1 Mb. Differential genes in improved Tift genome are enriched for serine O-acetyltransferase and glycerol-3-phosphate metabolic process which play an important role in improving the nutritional quality of seed protein and disease resistance in plants, respectively. Multiple marker-trait associations are identified for a range of agronomic traits, including grain yield through genome-wide association study. Improved genome assemblies and marker resources developed in this study provide a comprehensive framework/platform for future applications such as marker-assisted selection of mono/oligogenic traits as well as whole-genome prediction and haplotype-based breeding of complex traits