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Genome-wide diversity and structure variation among lablab [Lablab purpureus (L.) Sweet] accessions and their implication in a Forage breeding program

ABSTRACT: Most orphan crops have not been fully sequenced, hence we rely on genome sequences of related species to align markers to different chromosomes. This hinders their utilisation in plant population improvement programs. Utilising the advances in the science of sequencing technologies, the population structure, relatedness, and genetic diversity among accessions can be assessed quickly for better exploitation in forage breeding programs. Using DArTseq technology, we studied the genetic and structural variation in 65 Lablab purpureus (L.) Sweet conserved gene-bank accessions using 9320 DArTseq-based SNPs and 15,719 SilicoDart markers. These markers had a low discriminating ability with mean polymorphic information content (P.I.C.) of 0.14 with DArTseq-based SNPs and 0.13 with SilicoDart markers. However, the markers had a high mean call rate of 73% with DArTseq-based SNPs and 97% with SilicoDart markers. Analysis of molecular variance revealed a high within populations variance (99.4%), indicating a high gene exchange or low genetic differentiation (PhiPT = 0.0057) among the populations. Structure analysis showed three allelic pools in variable clusters of ΔK = 3 and 6. Phylogenetic tree of lablab accessions showed three main groups with variable membership coefficients. Most pairs of accessions (40.3%) had genetic distances between 0.10 and 0.15 for SilicoDart markers, while for DArTseq-based SNPs, (46.5%) had genetic distances between 0.20 and 0.25. Phylogenetic clustering and minimum spanning analysis divided the 65 accessions into three groups, irrespective of their origin. For the first time, this study produced high-density markers with good genom coverage. The utilisation of these accessions in a forage program will base on the information from molecular-based grouping. The outcomes uncovered the presence of noteworthy measure of variety in Uganda, CIAT and ILRI accessions, thus demonstrating an opportunity for further marker-trait-association studies.

Supplementary Information

The online version contains supplementary material available at 10.1007/s10722-021-01171-y.

SUBMITTER: Sserumaga J

PROVIDER: S-EPMC8550355 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Project description:BackgroundPhytochromes are the best characterized photoreceptors that perceive Red (R)/Far-Red (FR) signals and mediate key developmental responses in plants. It is well established that photoperiodic control of flowering is regulated by PHY A (phytochrome A) gene. So far, the members of PHY A gene family remains unexplored in Lablab purpureus, and therefore, their functions are still not deciphered. PHYA3 is the homologue of phytochrome A and known to be involved in dominant suppression of flowering under long day conditions by downregulating florigens in Glycine max. The present study is the first effort to identify and characterize any photoreceptor gene (PHYA3, in this study) in Lablab purpureus and decipher its phylogeny with related legumes.ResultsPHYA3 was amplified in Lablab purpureus cv GNIB-21 (photo-insensitive and determinate) by utilizing primers designed from GmPHYA3 locus of Glycine max. This study was successful in partially characterizing PHYA3 in Lablab purpureus (LprPHYA3) which is 2 kb longer and belongs to exon 1 region of PHYA3 gene. Phylogenetic analysis of the nucleotide and protein sequences of PHYA genes through MEGA X delineated the conservation and evolution of Lablab purpureus PHYA3 (LprPHYA3) probably from PHYA genes of Vigna unguiculata, Glycine max and Vigna angularis. A conserved basic helix-loop-helix motif bHLH69 was predicted having DNA binding property. Domain analysis of GmPHYA protein and predicted partial protein sequence corresponding to exon-1 of LprPHYA3 revealed the presence of conserved domains (GAF and PAS domains) in Lablab purpureus similar to Glycine max.ConclusionPartial characterization of LprPHYA3 would facilitate the identification of complete gene in Lablab purpureus utilizing sequence information from phylogenetically related species of Fabaceae. This would allow screening of allelic variants for LprPHYA3 locus and their role in photoperiod responsive flowering. The present study could aid in modulating photoperiod responsive flowering in Lablab purpureus and other related legumes in near future through genome editing.

Project description:Climate change is posing severe challenges in Africa, where resilient crops are urgently needed to withstand drought periods and unreliable rainfall. Multi-purpose legume species, such as lablab (Lablab purpureus (L.) Sweet), have been under-utilized yet have the potential to overcome climate challenges. While lablab is native to Africa, there are few characterized varieties and it is under-utilized by smallholder farmers due to a lack of information and access to varieties. Knowledge is especially lacking on the performance of this crop by genotype, management, and environment. We conducted a two-year field study at two sites to evaluate 29 lablab cultivars under sole and maize intercrop management, with 14 cultivars selected for in-depth study. Cultivars were evaluated on vegetative biomass and grain yield production, with N fixation assessed for one site year. Biomass and grain production differed across environments and cultivars, with only biomass affected by intercropping. Average grain yield was substantially reduced to only 37 kg ha-1 in environments with maximum temperatures greater than 33°C, but biomass production yielded comparable amounts across high temperatures and in dry (<500 mm rainfall) environments. Tradeoffs were found between biomass and grain yield across high yielding cultivars, with the top three grain accessions averaging 612 kg ha-1 of grain and 1.97 Mg ha-1 biomass whereas the top three biomass accessions produced 327 kg ha-1 grain and 2.52 Mg ha-1 biomass across all environments. In a comparison of production and N fixation measurements, cultivars were identified which may have high performance in both. Suitability of lablab for grain and biomass production were visualized across Tanzania in a map comparing max temperature thresholds for grain and biomass against average regional livestock populations. This provides a way forward for identifying potential areas for lablab cultivation as a novel means to enhance fodder and pulse production with smallholder farmers.

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Genome-wide diversity and structure variation among lablab [Lablab purpureus (L.) Sweet] accessions and their implication in a Forage breeding program

Supplementary Information

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