Faloye, Benjamin Busuyi
(2024)
Understanding drought tolerance of Bambara groundnut (Vigna subterranea (L.)Verdc.)in different agro-ecologies of Nigeria.
PhD thesis, University of Nottingham.
Abstract
Bambara groundnut (BG) (Vigna subterranea (L.) Verdc.) is a legume seed crop with high nutritional contents. It is a drought tolerant crop plant, and it is predominantly found in sub-Saharan Africa. Assessment of the available diversity using morphological and molecular approaches is an essential step to understand the genetics of complex traits including drought tolerance and to develop new high-yielding and climate-resilient varieties.
In the arid and semi-arid zones of Nigeria, drought is the major abiotic stress limiting crop performance. To study the response of BG to drought stress, multi-year field drought trials were conducted in research fields of Ahmadu Bello University (ABU), Mokwa, Niger state (lat. 9.345064, long. 5.031372), Ibadan, Oyo state (lat. 7.486354, long. 3.903728), and Zaria, Kaduna state (lat. 11.18656, long. 7.615368). A set of one hundred and thirty-five accessions of BG with diverse origins were established and characterized for drought under well-watered (WW) and water stressed (WS) regimes in two consecutive years 2019/2020 and 2020/2021. The experiment was laid out in an α-lattice design of 3 replicates per regime with 15 rows and 9 blocks per replicate. A 10m distance separated the regimes and WW and WS regimes were irrigated until flower emergence when water supply was withdrawn from WS plots. Twelve quantitative traits, namely: number of days to the first flower, days to 50% flowering, plant height (cm), plant spread (cm), number of petioles per plant, number of pods per plant, number of seeds per plant, seed weight per plant (g), 100 seeds weight (g), and shell weight per plant (g) were recorded using BG descriptors.
ANOVA revealed significant variations for most traits. Genotype, and treatment x genotype were highly significant (p<0.05). Drought stress imposed at flower emergence generally suppressed growth and yield. Consequently, significant yield reduction was observed in WS compared to WW conditions. The mean BLUPs values of seed weight accounted for 6.15g under WS and 8.49g under WW condition respectively. There was a highly significant correlation (p<0.05) between pod weight per plant and number of pods per plant.
A genome-wide association study (GWAS) was conducted on the same set of 135 BG accessions. The estimated best linear unbiased estimates (BLUEs) mean value was calculated for yield-traits and pod-shell trait in each location and across the locations. The BLUEs value of each accession and high-quality 5,395 genome-wide SNPs were used for marker-trait association analysis using both GLM and MLM models. A total of 15 SNPs QTL were significantly associated with five phenotypic traits (number of seeds per plant, number of pods per plant, seed weight per plant, shell weight per plant, and pod weight per plant). The threshold of –log (p) > 5 was used to consider a significant association between SNP marker and trait. Out of 15 SNP QTL, 12 SNP QTL were common in both GLM and MLM statistical methods employed for the GWAS analysis. Six of these SNP markers were found in both WW and WS regimes. Eight unique SNP markers were found only in WS and were absent from WW regimes. The phenotypic variance explained (R square) by these QTLs were ranged 0.01-0.15 (GLM) and 0.10-0.14 (MLM) in GLM and MLM approaches respectively. By the MLM approach, six SNPs were associated with the number of pods per plant, five associated with number of seeds per plant, one associated with pod weight and seed weight while four were associated with shell weight.
A trimmed sequence (70-100 bp reads) of associated SNPs was blasted to Legume Information System database (https://www.legumeinfo.org) to identify candidate genes (1Mb region: 500Kb downstream and 500 Kb upstream) in reference genome of relative-legume crops cowpea (Vigna unguiculata) and mung bean (Vigna radiata). A total of 56 candidate genes were identified and they were located closely to the 15 SNPS QTLs associated with the number of pods per plant and number of seeds per plant. A candidate gene Vigun05g235600 (GTPase-activating protein 1-like) and four other candidate genes; Vigun04g138400, Vigun04g138600, Vigun04g139100, and Vigun04g139400 (receptor- like protein kinase 2) have been reported for their role under abiotic stresses including drought tolerance in field crops. A candidate gene search identified six significant candidate genes in proximity to the SNP markers associated with the number of pods per plant and number of seeds per plant; four SNPs were left for shell weight in the MLM. Seven SNPs QTL of total 15 QTLs showed pleiotropic effects and were associated with both pods per plant and seeds per plant traits. Two pairs of SNP markers were exhibiting pleiotropic effects on seeds per plant and shell weight. This is the first GWAS study reported for yield related traits under WS in BG. The associated SNPs could help to understand the genetic yield traits in BG for future genomic-assisted breeding research. The outstanding accessions under WS conditions could serve as parent lines for drought improvement while the significant positive correlations between pairs of the traits suggests the possibility of simultaneous improvement of the traits to enhance seed yield.
| Item Type: |
Thesis (University of Nottingham only)
(PhD)
|
| Supervisors: |
Massawe, Festo
Mayes, Sean |
| Keywords: |
drought tolerance, Bambara groundnut, single nucleotide polymorphism, genome wide association study |
| Subjects: |
Q Science > QK Botany |
| Faculties/Schools: |
University of Nottingham, Malaysia > Faculty of Science and Engineering — Science > School of Biosciences |
| Item ID: |
78442 |
| Depositing User: |
Faloye, Benjamin
|
| Date Deposited: |
27 Jul 2024 04:40 |
| Last Modified: |
27 Jul 2024 04:40 |
| URI: |
https://eprints.nottingham.ac.uk/id/eprint/78442 |
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