Mapping and identification of quantitative trait loci controlling test weight and seed yield of pearl millet in multi agro-climatic zones of India

Abstract

Pearl millet [ Pennisetum glaucum (L.) R. Br.] is a climate-resilient nutri-cereal and is a staple food for the inhabitants of arid and semi-arid regions of the world. Yield stability is a major problem and requires exploiting key breeding strategies for the improvement of yield component traits in pearl millet. The main objective of the present study was the genomic dissection of yield and its component traits by identifying multi-environmental QTL in order to increase the efficiency and accuracy of pearl millet breeding. An experiment was designed for mapping agronomically important traits in 210 Recombinant inbred lines (RIL) derived from the cross PPMI 683 × PPMI 627. These RILs were evaluated in three diverse pearl millet growing regions in India for three consecutive years. Over the consecutive years and locations, thousand seed weight (TSW) showed a significant positive association with other agronomic traits. QTL analysis revealed three significant common QTL for TSW. the flanking markers of common QTL were Xpsmp2273- Xipes0203; Xpsmp2077- Xpsmp2059 and ICMP3058- Xipes0147 . The identified common QTL markers explained the total phenotypic variance of 27.57, 22.61,7.59% for QTL 1 on LG 1; 21.38, 24.13,12.14% for QTL 2 on LG 2, and 7.34, 15.26, 9.6% for QTL 3 on LG 6 across three consecutive years (2014–2016) at Delhi (E1), Dharwad (E2) and Jodhpur (E3), respectively. Two constitutive expressing QTL markers for Seed Yield per Plant (SYPP) were found at a significant threshold LOD value of 3.5 and flanked by the markers: Xpsmp2273- Xipes0203 and Xpsmp2077- Xpsmp2059 with a total phenotypic variance of 28.24 , 19.95%, and 6.31% for QTL 1 on LG 1; 19.78, 21.38, 7.17% for QTL 2 on LG 2 across consecutive years at Delhi, Dharwad and Jodhpur, respectively. In total, 34 and 29 significant digenic interactions were detected for TSW and SYPP, respectively. In the present study, using quantitative genetic variation for TSW and SYPP, major and stable QTLs were found across environments. Some potential genes that may affect the traits were identified in the comparative genomics scan using rice and Arabidopsis. Three significant and stable QTLs for TSW and two for SYPP were detected across all environments. The digenic interactions were detected for TSW (34) and SYPP (29) at Delhi, Dharwad, and Jodhpur. The mapped QTL for TSW and SYPP in the current study could be exploited to develop elite hybrid parental genotypes/cultivars through marker-assisted selection and genomic selection in breeding programs. • In an era of climate change, pearl millet has promising prospects to achieve economic returns. • Major and stable QTLs for TSW (3 QTLs) and SYPP (2 QTLs) were detected across the environments. • Two genomic regions with pleiotropic effects for TSW and SYPP at Delhi, Dharwad, and Jodhpur were detected. • Digenic interactions were detected for TSW (34) and SYPP (29) at Delhi, Dharwad, and Jodhpur. • All favorable QTLs to break down genetic barriers to yield for sustainable food security.