Dataset Information

Genome analyses reveal population structure and a purple stigma color gene candidate in finger millet.

ABSTRACT: Finger millet is a key food security crop widely grown in eastern Africa, India and Nepal. Long considered a 'poor man's crop', finger millet has regained attention over the past decade for its climate resilience and the nutritional qualities of its grain. To bring finger millet breeding into the 21^st century, here we present the assembly and annotation of a chromosome-scale reference genome. We show that this ~1.3 million years old allotetraploid has a high level of homoeologous gene retention and lacks subgenome dominance. Population structure is mainly driven by the differential presence of large wild segments in the pericentromeric regions of several chromosomes. Trait mapping, followed by variant analysis of gene candidates, reveals that loss of purple coloration of anthers and stigma is associated with loss-of-function mutations in the finger millet orthologs of the maize R1/B1 and Arabidopsis GL3/EGL3 anthocyanin regulatory genes. Proanthocyanidin production in seed is not affected by these gene knockouts.

SUBMITTER: Devos KM

PROVIDER: S-EPMC10284860 | biostudies-literature | 2023 Jun

REPOSITORIES: biostudies-literature

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Genome analyses reveal population structure and a purple stigma color gene candidate in finger millet.

Devos Katrien M KM Qi Peng P Bahri Bochra A BA Gimode Davis M DM Jenike Katharine K Manthi Samuel J SJ Lule Dagnachew D Lux Thomas T Martinez-Bello Liliam L Pendergast Thomas H TH Plott Chris C Saha Dipnarayan D Sidhu Gurjot S GS Sreedasyam Avinash A Wang Xuewen X Wang Hao H Wright Hallie H Zhao Jianxin J Deshpande Santosh S de Villiers Santie S Dida Mathews M MM Grimwood Jane J Jenkins Jerry J Lovell John J Mayer Klaus F X KFX Mneney Emmarold E EE Ojulong Henry F HF Schatz Michael C MC Schmutz Jeremy J Song Bo B Tesfaye Kassahun K Odeny Damaris A DA

Nature communications 20230621 1

Finger millet is a key food security crop widely grown in eastern Africa, India and Nepal. Long considered a 'poor man's crop', finger millet has regained attention over the past decade for its climate resilience and the nutritional qualities of its grain. To bring finger millet breeding into the 21<sup>st</sup> century, here we present the assembly and annotation of a chromosome-scale reference genome. We show that this ~1.3 million years old allotetraploid has a high level of homoeologous gene ...[more]

PMID: 37344528

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Project description:Eleusine coracana (L.) Gaertn., commonly known as finger millet, is a multipurpose crop used for food and feed. Genomic tools are required for the characterization of crop gene pools and their genomics-led breeding. High-throughput sequencing-based characterization of finger millet germplasm representing diverse agro-ecologies was considered an effective method for determining its genetic diversity, thereby suggesting potential candidates for breeding. In this study, the genotyping-by-sequencing (GBS) method was used to simultaneously identify novel single nucleotide polymorphism (SNP) markers and genotype 288 finger millet accessions collected from Ethiopia and Zimbabwe. The accessions were characterized at individual and group levels using 5,226 bi-allelic SNPs, with a minimum allele frequency (MAF) of above 0.05, distributed across 2,500 scaffolds of the finger millet reference genome. The polymorphism information content (PIC) of the SNPs was 0.23 on average, and a quarter of them have PIC values over 0.32, making them highly informative. The grouping of the 288 accessions into seven populations based on geographic proximity and the potential for germplasm exchange revealed a narrow range of observed heterozygosity (Ho; 0.09-0.11) and expected heterozygosity (He) that ranged over twofold, from 0.11 to 0.26. Alleles unique to the different groups were also identified, which merit further investigation for their potential association with desirable traits. The analysis of molecular variance (AMOVA) revealed a highly significant genetic differentiation among groups of accessions classified based on the geographic region, country of origin, days to flowering, panicle type, and Al tolerance (p < 0.01). The high genetic differentiation between Ethiopian and Zimbabwean accessions was evident in the AMOVA, cluster, principal coordinate, and population structure analyses. The level of genetic diversity of finger millet accessions varies moderately among locations within Ethiopia, with accessions from the northern region having the lowest level. In the neighbor-joining cluster analysis, most of the improved cultivars included in this study were closely clustered, probably because they were developed using genetically less diverse germplasm and/or selected for similar traits, such as grain yield. The recombination of alleles via crossbreeding genetically distinct accessions from different regions of the two countries can potentially lead to the development of superior cultivars.

Project description:Finger millet [Eleusine coracana (L.) Gaertn.] is an important climate-resilient nutrient-dense crop grown as a staple food grain in Asia and Africa. Utilizing the full potential of the crop mainly depends on an in-depth exploration of the vast diversity in its germplasm. In this study, the global finger millet germplasm diversity panel of 314 accessions was genotyped, using the DArTseq approach to assess genetic diversity and population structure. We obtained 33,884 high-quality single nucleotide polymorphism (SNP) markers on 306 accessions after filtering. Finger millet germplasm showed considerable genetic diversity, and the mean polymorphic information content, gene diversity, and Shannon Index were 0.110, 0.114, and 0.194, respectively. The average genetic distance of the entire set was 0.301 (range 0.040 - 0.450). The accessions of the race elongata (0.326) showed the highest average genetic distance, and the least was in the race plana (0.275); and higher genetic divergence was observed between elongata and vulgaris (0.320), while the least was between compacta and plana (0.281). An average, landrace accessions had higher gene diversity (0.144) and genetic distance (0.299) than the breeding lines (0.117 and 0.267, respectively). A similar average gene diversity was observed in the accessions of Asia (0.132) and Africa (0.129), but Asia had slightly higher genetic distance (0.286) than African accessions (0.276), and the distance between these two regions was 0.327. This was also confirmed by a model-based STRUCTURE analysis, genetic distance-based clustering, and principal coordinate analysis, which revealed two major populations representing Asia and Africa. Analysis of molecular variance suggests that the significant population differentiation was mainly due to within individuals between regions or between populations while races had a negligible impact on population structure. Finger millet diversity is structured based on a geographical region of origin, while the racial structure made negligible contribution to population structure. The information generated from this study can provide greater insights into the population structure and genetic diversity within and among regions and races, and an understanding of genomic-assisted finger millet improvement.

Project description:Drought is one of the most significant abiotic stresses that affects the growth and productivity of crops worldwide. Finger millet [Eleusine coracana (L.) Gaertn.] is a C4 crop with high nutritional value and drought tolerance. However, the drought stress tolerance genetic mechanism of finger millet is largely unknown. In this study, transcriptomic (RNA-seq) and proteomic (iTRAQ) technologies were combined to investigate the finger millet samples treated with drought at different stages to determine drought response mechanism. A total of 80,602 differentially expressed genes (DEGs) and 3,009 differentially expressed proteins (DEPs) were identified in the transcriptomic and proteomic levels, respectively. An integrated analysis, which combined transcriptome and proteome data, revealed the presence of 1,305 DEPs were matched with the corresponding DEGs (named associated DEGs-DEPs) when comparing the control to samples which were treated with 19 days of drought (N1-N2 comparison group), 1,093 DEGs-DEPs between control and samples which underwent rehydration treatment for 36 hours (N1-N3 comparison group) and 607 DEGs-DEPs between samples which were treated with drought for 19 days and samples which underwent rehydration treatment for 36 hours (N2-N3 comparison group). Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis identified 80 DEGs-DEPs in the N1-N2 comparison group, 49 DEGs-DEPs in the N1-N3 comparison group, and 59 DEGs-DEPs in the N2-N3 comparison group, which were associated with drought stress. The DEGs-DEPs which were drought tolerance-related were enriched in hydrolase activity, glycosyl bond formation, oxidoreductase activity, carbohydrate binding and biosynthesis of unsaturated fatty acids. Co-expression network analysis revealed two candidate DEGs-DEPs which were found to be centrally involved in drought stress response. These results suggested that the coordination of the DEGs-DEPs was essential to the enhanced drought tolerance response in the finger millet.

Dataset Information

Genome analyses reveal population structure and a purple stigma color gene candidate in finger millet.

Publications

Genome analyses reveal population structure and a purple stigma color gene candidate in finger millet.

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