Genome-wide association study uncovers genomic regions associated with grain iron, zinc and protein content in pearl millet

Abstract

Pearl millet hybrids biofortified with iron (Fe) and zinc (Zn) promise to be part of a long-term strategy to combat micronutrient malnutrition in the arid and semi-arid tropical (SAT) regions of the world. Biofortification through molecular breeding is the way forward to achieving a rapid trait-based breeding strategy. This genome-wide association study (GWAS) was conducted to identify significant marker-trait associations (MTAs) for Fe, Zn, and protein content (PC) for enhanced biofortification breeding. A diverse panel of 281 advanced inbred lines was evaluated for Fe, Zn, and PC over two seasons. Phenotypic evaluation revealed high variability (Fe: 32–120 mg kg−1, Zn: 19–87 mg kg−1, PC: 8–16%), heritability (hbs2 ≥ 90%) and significantly positive correlation among Fe, Zn and PC (P = 0.01), implying concurrent improvement. Based on the Diversity Arrays Technology (DArT) seq assay, 58,719 highly informative SNPs were filtered for association mapping. Population structure analysis showed six major genetic groups (K = 6). A total of 78 MTAs were identified, of which 18 were associated with Fe, 43 with Zn, and 17 with PC. Four SNPs viz., Pgl04_64673688, Pgl05_135500493, Pgl05_144482656, and Pgl07_101483782 located on chromosomes Pgl04 (1), Pgl05 (2) and Pgl07 (1), respectively were co-segregated for Fe and Zn. Promising genes, ‘Late embryogenesis abundant protein’, ‘Myb domain’, ‘pentatricopeptide repeat’, and ‘iron ion binding’ coded by 8 SNPs were identified. The SNPs/genes identified in the present study presents prospects for genomics assisted biofortification breeding in pearl millet.

Genome-wide association mapping for component traits of drought and heat tolerance in wheat

“…To avoid such biasness, a stringent selection procedure of Bonferroni correction was applied like Kumar et al ( 2018 ), and in total 57 MTAs were retained. If geographical and environmental variation among different locations was significantly high, a location-wise association study was carried out to avoid flattening of the genetic variation as mentioned in previous references (Pujar et al, 2020 ; Rathan et al, 2022 ). MTAs observed in more than one location with Bonferroni corrected p-value in at least one location (Stable MTAs) are presumed to be the true association, which is supported by the presence of the candidate gene ( Table 6 ).…”

Genetic diversity and distinctness based on morphological and SSR markers in peanut

“…2020 ; Pandey et al. 2017a; Agarwal et al., 2018), ddRADseq, DArT, and DArT‐sEquation (Pujar et al., 2020; Vishwakarma et al., 2016) and high density single nucleotide polymorphism (SNP) array (Gangurde et al., 2020; Pandey et al., 2017b) which provided a much cheaper, time saving, and highly precise option for performing distinctiveness studies in plants including peanut. Besides, it has the advantage of not being restricted by gene expression during different developmental stages of plant growth.…”

“…This procedure is not only time consuming but also very expensive and laborious. The last decade has witnessed drastic reduction in prices of sequencing and genotyping due to advancement in sequencing technologies such genotyping-by-sequencing (GBS) (Dodia et al, 2019;Kulkarni et al, 2020), whole genome resequencing (WGRS) (Kumar et al 2020 ;Pandey et al 2017a;Agarwal et al, 2018), ddRADseq, DArT, and DArT-sEquation (Pujar et al, 2020;Vishwakarma et al, 2016) and high density single nucleotide polymorphism (SNP) array (Gangurde et al, 2020;Pandey et al, 2017b) which provided a much cheaper, time saving, and highly precise option for performing distinctiveness studies in plants including peanut. Besides, it has the advantage of not being restricted by gene expression during different developmental stages of plant growth.…”

Mainstreaming orphan millets for advancing climate smart agriculture to secure nutrition and health

“…Several whole-genome scan studies, e.g., genome-wide association studies (GWAS) and genomic selection (GS), facilitated by genotyping-by-sequencing (GBS), RAD-sequencing, and whole-genome re-sequencing (WGRS), were also performed in millets. Several stresses and nutritional, grain quality, related single nucleotide polymorphism (SNP), and simple sequence repeat (SSR) markers were identified (Gimode et al, 2016;Hittalmani et al, 2017;Sharma et al, 2018;Pujar et al, 2020). Regardless of this progress, knowledge on the genetic determinants of stress tolerance and the molecular machinery underlying stress tolerance is largely unknown in millets.…”