S K Gupta

Pearl millet genome sequence provides a resource to improve agronomic traits in arid environments

Pearl millet [Cenchrus americanus (L.) Morrone] is a staple food for more than 90 million farmers in arid and semi-arid regions of sub-Saharan Africa, India and South Asia. We report the ∼1.79 Gb draft whole genome sequence of reference genotype Tift 23D2B1-P1-P5, which contains an estimated 38,579 genes. We highlight the substantial enrichment for wax biosynthesis genes, which may contribute to heat and drought tolerance in this crop. We resequenced and analyzed 994 pearl millet lines, enabling insights into population structure, genetic diversity and domestication. We use these resequencing data to establish marker trait associations for genomic selection, to define heterotic pools, and to predict hybrid performance. We believe that these resources should empower researchers and breeders to improve this important staple crop.

Pathogenic Variation in the Pearl Millet Blast Pathogen Magnaporthe grisea and Identification of Resistance to Diverse Pathotypes

Blast, also known as leaf spot, caused by Pyricularia grisea (teleomorph: Magnaporthe grisea), has emerged as a serious disease affecting both forage and grain production in pearl millet in India. Pathogenic variation was studied in a greenhouse using 25 M. grisea isolates collected from four major pearl-millet-growing states in India (Rajasthan, Haryana, Maharashtra, and Uttar Pradesh) on 10 pearl millet genotypes (ICMB 02444, ICMB 02777, ICMB 06444, ICMB 93333, ICMB 96666, ICMB 97222, ICMB 99444, 863B, ICMR 06222, and ICMB 95444). Differential reactions to the test isolates were recorded on ICMB 02444, ICMB 93333, ICMB 97222, 863B, and ICMR 06222. The 25 isolates were grouped into five different pathotypes based on their reaction types (virulent = score ≥ 4 and avirulent = score ≤ 3 on a 1-to-9 scale). For the identification of resistance sources, a pearl millet mini-core comprising 238 accessions was evaluated under greenhouse conditions against five M. grisea isolates (Pg118, Pg119, Pg56, Pg53, and Pg45) representing the five pathotypes. Of 238 accessions, 32 were found to be resistant to at least one pathotype. Resistance to multiple pathotypes (two or more) was recorded in several accessions, while three accessions (IP 7846, IP 11036, and IP 21187) exhibited resistance to four of the five pathotypes. Four early-flowering (≤50 days) blast-resistant mini-core accessions (IP 7846, IP 4291, IP 15256, and IP 22449) and four accessions (IP 5964, IP 11010, IP 13636, and IP 20577) having high scores (≥7) for grain and green fodder yield potential and overall plant aspect were found to be promising for utilization in pearl millet improvement programs. Identification of five pathotypes of M. grisea and sources of resistance to these pathotypes will provide a foundation for breeding for blast resistance in pearl millet in India.

Phenotypic Data from Inbred Parents Can Improve Genomic Prediction in Pearl Millet Hybrids

Pearl millet is a non-model grain and fodder crop adapted to extremely hot and dry environments globally. In India, a great deal of public and private sectors’ investment has focused on developing pearl millet single cross hybrids based on the cytoplasmic-genetic male sterility (CMS) system, while in Africa most pearl millet production relies on open pollinated varieties. Pearl millet lines were phenotyped for both the inbred parents and hybrids stage. Many breeding efforts focus on phenotypic selection of inbred parents to generate improved parental lines and hybrids. This study evaluated two genotyping techniques and four genomic selection schemes in pearl millet. Despite the fact that 6× more sequencing data were generated per sample for RAD-seq than for tGBS, tGBS yielded more than 2× as many informative SNPs (defined as those having MAF > 0.05) than RAD-seq. A genomic prediction scheme utilizing only data from hybrids generated prediction accuracies (median) ranging from 0.73-0.74 (1000-grain weight), 0.87-0.89 (days to flowering time), 0.48-0.51 (grain yield) and 0.72-0.73 (plant height). For traits with little to no heterosis, hybrid only and hybrid/inbred prediction schemes performed almost equivalently. For traits with significant mid-parent heterosis, the direct inclusion of phenotypic data from inbred lines significantly (P < 0.05) reduced prediction accuracy when all lines were analyzed together. However, when inbreds and hybrid trait values were both scored relative to the mean trait values for the respective populations, the inclusion of inbred phenotypic datasets moderately improved genomic predictions of the hybrid genomic estimated breeding values. Here we show that modern approaches to genotyping by sequencing can enable genomic selection in pearl millet. While historical pearl millet breeding records include a wealth of phenotypic data from inbred lines, we demonstrate that the naive incorporation of this data into a hybrid breeding program can reduce prediction accuracy, while controlling for the effects of heterosis per se allowed inbred genotype and trait data to improve the accuracy of genomic estimated breeding values for pearl millet hybrids.

Inheritance of fertility restoration of A5 cytoplasmic-nuclear male sterility system in pearl millet [Pennisetum glaucum (L.) R. Br.]

The A5 cytoplasmic-nuclear male sterility (CMS), the most stable cytoplasm available in pearl millet [Pennisetum glaucum (L). R. Br.] is yet to be utilized on large scale by breeders owing to limited fertility restoration in the available germplasm for this cytoplasm. An understanding of the inheritance of fertility restoration can make significant contributions to restorer breeding efficiency of this CMS system. This study investigated inheritance of fertility restoration of this CMS system in which three diverse isonuclear A-lines (P1) were crossed with two A5 restorer lines (P2) to produce 4 F1s and their respective F2s and two backcrosses. These were evaluated for male sterility (S) and fertility (F) for two seasons at International Crops Research Institute for the Semi-Arid Tropics (ICRISAT) Patancheru. The segregation patterns in the F2 (54F:10S) and BCP1 (3F:1S) were broadly suggestive of trigenic inheritance of male fertility restoration, where dominant alleles at any two of the three duplicate complimentary loci will lead to fertility restoration.

Allelic relationship between restorer genes for A1 and A4 CMS systems in pearl millet

Understanding the allelic complementation of restoration among the stable restorer lines will contribute to robust pearl millet restorer breeding program. Thus, present study aimed to test allelic relationship between four diverse restorer lines each for A1 and A4 cytoplasmic male sterility (CMS) systems to find linkage between restorer genes carried by different restorers of each CMS systems. Six testcrosses were developed for each CMS system by crossing each of A1 and A4 male sterile lines (81A1 and 81 A4) with all possible combination of F1s among four A1 restorers and A4 restorers, respectively. Almost all the plants in these testcrosses showed complete male fertility indicating presence of same fertility restoration gene (allelic) is present in all the four restorer lines of A1 CMS system. Similar results were found for A4 CMS system. This single gene system within A1 and A4 provides the opportunity to breeders to incorporate this allelic restorer gene into any of the advanced lines for its rapid conversion into new restorer lines besides to search for new restorer gene for future diversification.