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Heterotic pools in African and Asian origin populations of pearl millet [Pennisetum glaucum (L.) R. Br.].

ABSTRACT: Forty-five African or Asian origin pearl millet populations bred either in Africa or Asia were investigated to generate information on heterotic pools. They were clustered into seven groups (G1 to G7) when genotyped, using 29 highly polymorphic SSRs. Fourteen parental populations representing these seven marker-based groups were crossed in diallel mating design to generate 91 population hybrids. The hybrids evaluated at three locations in India showed mean panmictic mid-parent heterosis (PMPH) and better-parent heterosis (PBPH) for grain yield ranging from - 21.7 to 62.08% and - 32.51 to 42.99%, respectively. Higher grain yield and heterosis were observed in G2 × G6 (2462 kg ha^-1, 43.2%) and G2 × G5 (2455 kg ha^-1, 42.8%) marker group crosses compared to the most popular Indian open-pollinated variety (OPV) ICTP 8203. Two heterotic groups, Pearl millet Population Heterotic Pool-1 (PMPHP-1) comprising G2 populations and Pearl millet Population Heterotic Pool-2 (PMPHP-2) comprising G5 and G6 populations, were identified based on hybrid performance, heterosis and combining ability among marker group crosses. Population hybrids from two heterotic groups, PMPHP-1 × PMPHP-2 demonstrated PMPH of 14.75% and PBPH of 6.8%. Populations of PMPHP-1 had linkages with either African or Asian origin populations, whereas PMPHP-2 composed of populations originating in Africa and later bred for Asian environments. Results indicated that parental populations from the two opposite heterotic groups can be used as base populations to derive superior inbred lines to develop high yielding hybrids/cultivars.

SUBMITTER: Patil KS

PROVIDER: S-EPMC8190140 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Project description:Pearl millet is a staple food for people in arid and semi-arid regions of Africa and South Asia due to its high drought tolerance and nutritional qualities. A better understanding of the genomic diversity and population structure of pearl millet germplasm is needed to support germplasm conservation and genetic improvement of this crop. Here we characterized two pearl millet diversity panels, (i) a set of global accessions from Africa, Asia, and the America, and (ii) a collection of landraces from multiple agro-ecological zones in Senegal.We identified 83,875 single nucleotide polymorphisms (SNPs) in 500 pearl millet accessions, comprised of 252 global accessions and 248 Senegalese landraces, using genotyping by sequencing (GBS) of PstI-MspI reduced representation libraries. We used these SNPs to characterize genomic diversity and population structure among the accessions. The Senegalese landraces had the highest levels of genetic diversity (?), while accessions from southern Africa and Asia showed lower diversity levels. Principal component analyses and ancestry estimation indicated clear population structure between the Senegalese landraces and the global accessions, and among countries in the global accessions. In contrast, little population structure was observed across in the Senegalese landraces collections. We ordered SNPs on the pearl millet genetic map and observed much faster linkage disequilibrium (LD) decay in Senegalese landraces compared to global accessions. A comparison of pearl millet GBS linkage map with the foxtail millet (Setaria italica) and sorghum (Sorghum bicolor) genomes indicated extensive regions of synteny, as well as some large-scale rearrangements in the pearl millet lineage.We identified 83,875 SNPs as a genomic resource for pearl millet improvement. The high genetic diversity in Senegal relative to other regions of Africa and Asia supports a West African origin of this crop, followed by wide diffusion. The rapid LD decay and lack of confounding population structure along agro-ecological zones in Senegalese pearl millet will facilitate future association mapping studies. Comparative population genomics will provide insights into panicoid crop evolution and support improvement of these climate-resilient crops.

Project description:BACKGROUND: Pearl millet landraces display an important variation in their cycle duration. This diversity contributes to the stability of crop production in the Sahel despite inter-annual rainfall fluctuation. Conservation of phenological diversity is important for the future of pearl millet improvement and sustainable use. Identification of genes contributing to flowering time variation is therefore relevant. In this study we focused on three flowering candidate genes, PgHd3a, PgDwarf8 and PgPHYC. We tested for signatures of past selective events within polymorphism patterns of these three genes that could have been associated with pearl millet domestication and/or landraces differentiation. In order to implement ad hoc neutrality tests, a plausible demographic history of pearl millet domestication was inferred through Approximate Bayesian Computation by using eight neutral STS loci. RESULTS: Domesticated pearl millet exhibited 84% of the nucleotide diversity level found in the wild population. No specific polymorphisms were found either in the wild or in the domestic populations. The bayesian approach and previous studies suggest that gene flow between wild relatives and domesticated pearl millets is a main factor explaining these results. Early and late landraces did not show significant genetic differentiation at both the neutral and the candidate loci. A positive selection was evidenced in PgHd3a and PgDwarf8 genes of domestic forms but not in the wild population. CONCLUSION: Our results strongly suggest that PgHd3a and PgDwarf8 were likely targeted by selection during domestication. However, a potential role of any of the three candidate genes in the phenological differentiation between early and late landraces was not supported by our data. Reasons why these results contrast with previous results that have shown a slight but significant association between PgPHYC polymorphisms and variation in flowering time in pearl millet are discussed.

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Heterotic pools in African and Asian origin populations of pearl millet [Pennisetum glaucum (L.) R. Br.].

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