Deciphering Genomic Regions for High Grain Iron and Zinc Content Using Association Mapping in Pearl Millet

Abstract

Micronutrient malnutrition, especially deficiency of two mineral elements, iron [Fe] and zinc [Zn] in the developing world needs urgent attention. Pearl millet is one of the best crops with many nutritional properties and is accessible to the poor. We report findings of the first attempt to mine favorable alleles for grain iron and zinc content through association mapping in pearl millet. An association mapping panel of 130 diverse lines was evaluated at Delhi, Jodhpur and Dharwad, representing all the three pearl millet growing agro-climatic zones of India, during 2014 and 2015. Wide range of variation was observed for grain iron (32.3–111.9 ppm) and zinc (26.6–73.7 ppm) content. Genotyping with 114 representative polymorphic SSRs revealed 0.35 mean gene diversity. STRUCTURE analysis revealed presence of three sub-populations which was further supported by Neighbor-Joining method of clustering and principal coordinate analysis (PCoA). Marker-trait associations (MTAs) were analyzed with 267 markers (250 SSRs and 17 genic markers) in both general linear model (GLM) and mixed linear model (MLM), however, MTAs resulting from MLM were considered for more robustness of the associations. After appropriate Bonferroni correction, Xpsmp 2261 (13.34% R2-value), Xipes 0180 (R2-value of 11.40%) and Xipes 0096 (R2-value of 11.38%) were consistently associated with grain iron and zinc content for all the three locations. Favorable alleles and promising lines were identified for across and specific environments. PPMI 1102 had highest number (7) of favorable alleles, followed by four each for PPMFeZMP 199 and PPMI 708 for across the environment performance for both grain Fe and Zn content, while PPMI 1104 had alleles specific to Dharwad for grain Fe and Zn content. When compared with the reference genome Tift 23D2B1-P1-P5, Xpsmp 2261 amplicon was identified in intergenic region on pseudomolecule 5, while the other marker, Xipes 0810 was observed to be overlapping with aspartic proteinase (Asp) gene on pseudomolecule 3. Thus, this study can help in breeding new lines with enhanced micronutrient content using marker-assisted selection (MAS) in pearl millet leading to improved well-being especially for women and children.

Genetic variability, genotype × environment interaction and correlation analysis for grain iron and zinc contents in recombinant inbred line population of pearl millet [Pennisetum glaucum (L). R.

“…It is highly resilient to diverse climate conditions and is cultivated in marginal environments of arid and semi-arid tropics of sub-Saharan Africa and Asia (Ramya et al 2018). It shows a higher degree of tolerance to severe drought, heat stress and high temperature (Anuradha et al 2017;Govindaraj et al 2018). Pearl millet grains are the rich source of the several macro-and micro-nutrients (like iron, zinc, phosphorus, and magnesium), high fiber content, αamylose, metabolizable energy, proteins, essential amino acids, thus ensuring food and nutritional security (Nambiar et al 2011;Kumar et al 2018).…”

Genome-Wide Association Studies and Genomic Selection in Pearl Millet: Advances and Prospects

“…Association studies reveal that Xibmsp11/AP6.1, an SNP marker on an acetyl CoA carboxylase gene, is strongly associated with GY, GHI (grain harvest index), and PY (panicle yield) under both treatments; whereas InDel markers viz., Xibmcp09/AP10.1 & Xibmcp09/AP10.2 of a chlorophyll a/b binding protein gene are associated with GY and stay-green traits. Using association mapping, key alleles for grain iron and zinc were demonstrated by Anuradha et al (2017). Developing MTAs (Marker Trait Associations) between 250 SSR and 17 genic markers with grain iron and zinc content for 130 diversified lines across different environs revealed that the Xicmp3092 marker had a strong association with grain iron content on LG 7, and markers Xpsmp2086 & Xpsmp2213 and Xipes0224 showed association with grain zinc content on LG 4 and LG 6, respectively; conserved association for grain iron and zinc, however, was exhibited by Xipes0180, Xpsmp2261, and Xipes0096 on LG 3, LG 5, and LG 7, respectively.…”

Genomic Designing of Pearl Millet: A Resilient Crop for Arid and Semi-arid Environments

“…This climate variability is expected to increase crop vulnerability in different agro-ecologies with drastic consequences on food security and economic growth. Pearl millet is a climate-smart crop with nutritious grains (Anuradha et al 2017) and ideal for environments prone to drought and extreme heat, thereby reinforcing the fight against food insecurity in the arid and semiarid environments (Bailey et al 1979;Buerkert et al 2001;Jukanti et al 2016).…”