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T. V. N, S. RP, R. L. R. Population structure and genetic diversity characterization of soybean for seed longevity. PLoS One 2022; 17:e0278631. [PMID: 36472991 PMCID: PMC9725150 DOI: 10.1371/journal.pone.0278631] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Accepted: 11/19/2022] [Indexed: 12/12/2022] Open
Abstract
Seed longevity is an important trait in the context of germplasm conservation and economics of seed production. The identification of populations with high level of genetic variability for seed longevity and associated traits will become a valuable resource for superior alleles for seed longevity. In this study, Genotyping-by-sequencing (GBS)-single nucleotide polymorphism (SNP) approach, simple sequence repeats (SSR) markers and agro-morphological traits have been explored to investigate the diversity and population structure of assembled 96 genotypes. The GBS technique performed on 96 genotypes of soybean (Glycine max (L.) Merrill) resulted in 37,897 SNPs on sequences aligned to the reference genome sequence. The average genome coverage was 6.81X with a mapping rate of 99.56% covering the entire genome. Totally, 29,955 high quality SNPs were identified after stringent filtering and most of them were detected in non-coding regions. The 96 genotypes were phenotyped for eight quantitative and ten qualitative traits by growing in field by following augmented design. The STRUCTURE (Bayesian-model based algorithm), UPGMA (Un-weighed Pair Group Method with Arithmetic mean) and principal component analysis (PCA) approaches using SSR, SNP as well as quantitative and qualitative traits revealed population structure and diversity in assembled population. The Bayesian-model based STRUCTURE using SNP markers could effectively identify clusters with higher seed longevity associated with seed coat colour and size which were subsequently validated by UPGMA and PCA based on SSR and agro-morphological traits. The results of STRUCTURE, PCA and UPGMA cluster analysis showed high degree of similarity and provided complementary data that helped to identify genotypes with higher longevity. Six black colour genotypes, viz., Local black soybean, Kalitur, ACC Nos. 39, 109, 101 and 37 showed higher seed longevity during accelerated ageing. Higher coefficient of variability observed for plant height, number of pods per plant, seed yield per plant, 100 seed weight and seed longevity confirms the diversity in assembled population and its suitability for quantitative trait loci (QTL) mapping.
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Affiliation(s)
- Naflath T. V.
- Department of Seed Science and Technology, College of Agriculture, UAS, GKVK, Bangalore, Karnataka, India
| | - Rajendra Prasad S.
- Department of Seed Science and Technology, College of Agriculture, UAS, GKVK, Bangalore, Karnataka, India
| | - Ravikumar R. L.
- Department of Plant Biotechnology, College of Agriculture, UAS, GKVK, Bangalore, Karnataka, India
- * E-mail:
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Genetic and Genomic Diversity in a Tarwi (Lupinus mutabilis Sweet) Germplasm Collection and Adaptability to Mediterranean Climate Conditions. AGRONOMY-BASEL 2019. [DOI: 10.3390/agronomy10010021] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Lupinus mutabilis (tarwi) is a species of Andean origin with high protein and oil content and regarded as a potential crop in Europe. The success in the introduction of this crop depends in part on in depth knowledge of the intra-specific genetic variability of the collections, enabling the establishment of breeding and conservation programs. In this study, we used morphological traits, Inter-Simple Sequence Repeat markers and genome size to assess genetic and genomic diversity of 23 tarwi accessions under Mediterranean conditions. Phenotypic analyses and yield component studies point out accession LM268 as that achieving the highest seed production, producing large seeds and efficiently using primary branches as an important component of total yield, similar to the L. albus cultivars used as controls. By contrast, accession JKI-L295 presents high yield concentrated on the main stem, suggesting a semi-determinate development pattern. Genetic and genomic analyses revealed important levels of diversity, however not relatable to phenotypic diversity, reflecting the recent domestication of this crop. This is the first study of genome size diversity within L. mutabilis, revealing an average size of 2.05 pg/2C (2001 Mbp) with 9.2% variation (1897–2003 Mbp), prompting further studies for the exploitation of this diversity.
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Muhaidat R, Brake MH, Al Zoubi M, Colautti RI, Al-Nasser A, Awawdeh M, Al-Batayneh K, Al Khateeb W, McKown AD, Lahham J, El-Oqlah A. Integrating morphological characters, molecular markers, and distribution patterns to assess the identity of Blepharis species from Jordan. BOTANICAL STUDIES 2018; 59:18. [PMID: 30046932 PMCID: PMC6060189 DOI: 10.1186/s40529-018-0234-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Accepted: 07/16/2018] [Indexed: 06/08/2023]
Abstract
BACKGROUND Blepharis constitutes an important part of the vegetation of the Jordanian arid and semi-arid regions, yet whether one or more species of this genus occurs in the Jordanian area is uncertain. We addressed this question by assessing morphological characters and testing Inter-Simple Sequence Repeat (ISSR) markers from three populations of Blepharis: two northern (lower slopes of Kufranjah valley and the Dead Sea region) and one southern (Wadi al Yutm). RESULTS Shoots from randomly chosen Blepharis plants were harvested from each of the three populations for morphological and molecular analyses. In the northern populations, spikes were lax and bract width was significantly shorter than length of the longest lateral spine compared to the southern population. A multivariate linear discriminant analysis distinguished the northern populations from the southern one by internode length, bract width, longest lateral spine length, and bract width to spine length ratio. The ISSR analysis revealed that 44 markers across eight primers were polymorphic with major allele frequency of 83.6% and an average of 5.5 polymorphic markers per primer. The genetic resemblance among individuals ranged from 0.27 to 0.96. The three Blepharis populations were accordingly clustered into two distinct groups, similar to the analysis of morphological differences and corresponding with the "northern" and "southern" population designations. CONCLUSIONS Our results strongly indicate the occurrence of two discrete Blepharis species in Jordan and reject the hypothesis that the genus is represented by only one species. We propose that the Blepharis species in Jordan are B. attenutata Napper (represented by the northern populations) and B. ciliaris (L.) B. L. Burtt (represented by the southern population). These findings are important for informing and revising floristic work within the region and an updated key has been included in our findings.
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Affiliation(s)
- Riyadh Muhaidat
- Department of Biological Sciences, Faculty of Science, Yarmouk University, P. O. Box 21163, Irbid, Jordan
| | - Mohammad H. Brake
- Science Department, Faculty of Science, Jerash University, Jerash, Jordan
| | - Mazhar Al Zoubi
- Department of Basic Sciences, Faculty of Medicine, Yarmouk University, P. O. Box 21163, Irbid, Jordan
| | - Robert I. Colautti
- Department of Biology, Queen’s University, 116 Barrie Street, Kingston, ON K7L 3N6 Canada
| | - Amjad Al-Nasser
- Department of Statistics, Faculty of Science, Yarmouk University, P. O. Box 21163, Irbid, Jordan
| | - Muheeb Awawdeh
- Department of Environmental and Earth Sciences, Faculty of Science, Yarmouk University, P. O. Box 21163, Irbid, Jordan
| | - Khalid Al-Batayneh
- Department of Biological Sciences, Faculty of Science, Yarmouk University, P. O. Box 21163, Irbid, Jordan
| | - Wesam Al Khateeb
- Department of Biological Sciences, Faculty of Science, Yarmouk University, P. O. Box 21163, Irbid, Jordan
| | - Athena D. McKown
- Department of Forest and Conservation Sciences, Faculty of Forestry, University of British Columbia, Forest Sciences Centre, 2424 Main Mall, Vancouver, BC V6T 1Z4 Canada
| | - Jamil Lahham
- Department of Biological Sciences, Faculty of Science, Yarmouk University, P. O. Box 21163, Irbid, Jordan
| | - Ahmad El-Oqlah
- Department of Biological Sciences, Faculty of Science, Yarmouk University, P. O. Box 21163, Irbid, Jordan
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Identification of novel microsatellite markers in okra (Abelmoschus esculentus (L.) Moench) through next-generation sequencing and their utilization in analysis of genetic relatedness studies and cross-species transferability. J Genet 2018. [DOI: 10.1007/s12041-018-0893-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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