Genome-wide association analyses of agronomic traits and Striga hermonthica resistance in pearl millet

Abstract

Pearl millet (Pennisetum glaucum [L.] R. Br.) is a nutrient-dense, relatively drought-tolerant cereal crop cultivated in dry regions worldwide. The crop is under-researched, and its grain yield is low (< 0.8 tons ha−1) and stagnant in the major production regions, including Burkina Faso. The low productivity of pearl millet is mainly attributable to a lack of improved varieties, Striga hermonthica [Sh] infestation, downy mildew infection, and recurrent heat and drought stress. Developing high-yielding and Striga-resistant pearl millet varieties that satisfy the farmers’ and market needs requires the identification of yield-promoting genes linked to economic traits to facilitate marker-assisted selection and gene pyramiding. The objective of this study was to undertake genome-wide association analyses of agronomic traits and Sh resistance among 150 pearl millet genotypes to identify genetic markers for marker-assisted breeding and trait introgression. The pearl millet genotypes were phenotyped in Sh hotspot fields and screen house conditions. Twenty-nine million single nucleotide polymorphisms (SNPs) initially generated from 345 pearl millet genotypes were filtered, and 256 K SNPs were selected and used in the present study. Phenotypic data were collected on days to flowering, plant height, number of tillers, panicle length, panicle weight, thousand-grain weight, grain weight, number of emerged Striga and area under the Striga number progress curve (ASNPC). Agronomic and Sh parameters were subjected to combined analysis of variance, while genome-wide association analysis was performed on phenotypic and SNPs data. Significant differences (P < 0.001) were detected among the assessed pearl millet genotypes for Sh parameters and agronomic traits. Further, there were significant genotype by Sh interaction for the number of Sh and ASNPC. Twenty-eight SNPs were significantly associated with a low number of emerged Sh located on chromosomes 1, 2, 3, 4, 6, and 7. Four SNPs were associated with days-to-50%-flowering on chromosomes 3, 5, 6, and 7, while five were associated with panicle length on chromosomes 2, 3, and 4. Seven SNPs were linked to thousand-grain weight on chromosomes 2, 3, and 6. The putative SNP markers associated with a low number of emerged Sh and agronomic traits in the assessed genotypes are valuable genomic resources for accelerated breeding and variety deployment of pearl millet with Sh resistance and farmer- and market-preferred agronomic traits.

Chromosome-scale pearl millet genomes reveal aCARLACTONOIC ACID METHYL TRANSFERASEas key determinant of strigolactone pattern and Striga susceptibility

“…Genome-wide association studies on Striga resistance in sorghum and maize, both closely related to millets, as well as in pearl millet itself, have surprisingly not yielded many strigolactone biosynthetic genes (Mallu et al, 2022; Kavuluko et al, 2021; Badu-Apraku et al, 2020; Rouamba et al, 2023). Although a comparison of the candidate genes from these studies with their homologs between Aw and P10 did not yield any results for pre-attachment resistance, it did indicate potential post-attachment resistance candidates (Supplementary table 5; Supplementary figure 7).…”

The role of phenomics and genomics in delineating the genetic basis of complex traits in millets

“…This can be achieved by finding the genotype-phenotype interaction. In several studies for various millet crop species, an extensive number of DNA marker-trait associations have been revealed to date (Bančič et al 2023;Srivastava et al 2019;Rouamba et al 2023;Habyarimana et al 2019Habyarimana et al , 2020.…”

Towards Striga-resistant Gene pool in Nigerian Pearl millet landraces

“…Striga also known as Striga hermonthica (Del.) Benth, poses a significant challenge to pearl millet production in various tropical and subtropical regions of Africa (Rouamba, Shimelis, Drabo, et al, 2023). This parasitic weed can cause substantial yield losses, ranging from 20 to 80% in Africa and up to 100% in severe cases, thereby negatively impacting food security [1].…”

“…This parasitic weed can cause substantial yield losses, ranging from 20 to 80% in Africa and up to 100% in severe cases, thereby negatively impacting food security [1]. Previous studies by [2], [3], [4], [5], [7], [8], [9] and [10] have highlighted the detrimental effects of Striga on pearl millet production. To address this issue, the present study aims to identify the sources of resistance and explore the key morphological and agronomic traits associated with pearl millet's ability to resist Striga infestation.…”