Pearl millet genome sequence provides a resource to improve agronomic traits in arid environments - PubMed (original) (raw)

. 2017 Oct;35(10):969-976.

doi: 10.1038/nbt.3943. Epub 2017 Sep 18.

Chengcheng Shi 2, Mahendar Thudi 1, Cedric Mariac 3, Jason Wallace 4, Peng Qi 4, He Zhang 2, Yusheng Zhao 5, Xiyin Wang 4, Abhishek Rathore 1, Rakesh K Srivastava 1, Annapurna Chitikineni 1, Guangyi Fan 2, Prasad Bajaj 1, Somashekhar Punnuri 6, S K Gupta 1, Hao Wang 7, Yong Jiang 5, Marie Couderc 3, Mohan A V S K Katta 1, Dev R Paudel 8, K D Mungra 9, Wenbin Chen 2, Karen R Harris-Shultz 10, Vanika Garg 1, Neetin Desai 11 12, Dadakhalandar Doddamani 1, Ndjido Ardo Kane 13, Joann A Conner 14, Arindam Ghatak 11 15, Palak Chaturvedi 11, Sabarinath Subramaniam 16 17, Om Parkash Yadav 18, Cécile Berthouly-Salazar 3 19, Falalou Hamidou 20 21, Jianping Wang 8, Xinming Liang 2, Jérémy Clotault 3 22, Hari D Upadhyaya 1, Philippe Cubry 3, Bénédicte Rhoné 3 23, Mame Codou Gueye 13, Ramanjulu Sunkar 24, Christian Dupuy 25, Francesca Sparvoli 26, Shifeng Cheng 2, R S Mahala 27, Bharat Singh 6, Rattan S Yadav 28, Eric Lyons 16, Swapan K Datta 29, C Tom Hash 20, Katrien M Devos 4, Edward Buckler 7 30, Jeffrey L Bennetzen 4, Andrew H Paterson 4, Peggy Ozias-Akins 14, Stefania Grando 1, Jun Wang 2, Trilochan Mohapatra 31, Wolfram Weckwerth 11 32, Jochen C Reif 5, Xin Liu 2 33, Yves Vigouroux 3 22, Xun Xu 2 33 34

Affiliations

Pearl millet genome sequence provides a resource to improve agronomic traits in arid environments

Rajeev K Varshney et al. Nat Biotechnol. 2017 Oct.

Abstract

Pearl millet [Cenchrus americanus (L.) Morrone] is a staple food for more than 90 million farmers in arid and semi-arid regions of sub-Saharan Africa, India and South Asia. We report the ∼1.79 Gb draft whole genome sequence of reference genotype Tift 23D2B1-P1-P5, which contains an estimated 38,579 genes. We highlight the substantial enrichment for wax biosynthesis genes, which may contribute to heat and drought tolerance in this crop. We resequenced and analyzed 994 pearl millet lines, enabling insights into population structure, genetic diversity and domestication. We use these resequencing data to establish marker trait associations for genomic selection, to define heterotic pools, and to predict hybrid performance. We believe that these resources should empower researchers and breeders to improve this important staple crop.

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Conflict of interest statement

The authors declare no competing financial interests.

Figures

Figure 1

Figure 1. Pearl millet genome.

Genome features in 1-Mb intervals across the seven pseudomolecules. Units on the circumference are megabase values of pseudomolecules. (1) Repeat density, (2) tandem repeat density, (3) gene density, (4) GC content and (5) SNPs identified by resequencing PMiGAP lines in 1-Mb bins. The genome assembly furnished an average GC content of 47.9% and contained 38,579 gene models with mean coding sequence length of 1,014.71 bp.

Figure 2

Figure 2. Gene conservation and gene family expansion and contraction in pearl millet.

(a) Venn diagrams show the number of genes shared between different grass species and among grass families; pearl millet shares 14,398 genes with sorghum and foxtail millet; 13,027 genes with maize and rice; 11,369 genes with barley and wheat. (b) 384 gene families are substantially expanded and 1,692 gene families are contracted in pearl millet compared with other plant genomes.

Figure 3

Figure 3. Domestication and genetic diversity in elite and wild accessions of pearl millet.

(a) Principal component analysis of 376 pearl millet lines (345 PMiGAP lines and 31 wild accessions) using 450,000 high-quality SNPs. Four different groups were identified: cultivated lines (red) and wild lines from east (blue), west (orange) and central Africa (pink). (b) Neighbor joining (NJ) tree based on 450,000 high-quality SNPs. This analysis also identified separate groups of cultivated and wild lines from east, west and central parts of Africa. (c) Morphological differences between wild (i, ii) and cultivated accessions (iii, iv) of pearl millet. Wild accessions have numerous bristled spikes in the inflorescence and low seed density (i), and a plant architecture characterized by numerous basal and aerial branches (ii), with a plant height of around 1 m. Cultivated accessions have exposed seeds and a high seed density per spike (iii), with a few basal branches and no aerial branches (iv).

Figure 4

Figure 4. Prediction of hybrid performance.

Grain yield of 64 different pearl millet hybrids, produced by crossing 20 male and 23 female lines, was evaluated at five locations (Jamnagar, Anand, SK Nagar, Mahuva, Kothara in India) during 2004–2013. Phenotyping data (Supplementary Data set 1), together with 302,110 high-quality SNP marker data obtained from 580 B and R- lines (Supplementary Table 27), were used to predict hybrid performance. Ridge regression-BLUP, which takes additive and dominance effects into account, was used to predict hybrid performance. (a) Prediction accuracy was studied using 500 cross-validation tests. In each cross-validation, 48 hybrids were randomly selected as a training set and the remaining 16 hybrids were used as a test set. (b) Promising hybrid combinations that include parental lines that have not been used in breeding efforts previously were identified for testing and release as better hybrids. (c) Heat map showing putative heterotic groups.

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