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Phenotyping Mediterranean Durum Wheat Landraces for Resistance to Zymoseptoria tritici in Tunisia. Genes (Basel) 2022; 13:genes13020355. [PMID: 35205399 PMCID: PMC8872163 DOI: 10.3390/genes13020355] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 01/21/2022] [Accepted: 02/09/2022] [Indexed: 02/01/2023] Open
Abstract
Durum wheat landraces have huge potential for the identification of genetic factors valuable for improving resistance to biotic stresses. Tunisia is known as a hot spot for Septoria tritici blotch disease (STB), caused by the fungus Zymoseptoria tritici (Z. tritici). In this context, a collection of 3166 Mediterranean durum wheat landraces were evaluated at the seedling and adult stages for STB resistance in the 2016–2017 cropping season under field conditions in Kodia (Tunisia). Unadapted/susceptible accessions were eliminated to reach the final set of 1059 accessions; this was termed the Med-collection, which comprised accessions from 13 countries and was also screened in the 2018–2019 cropping season. The Med-collection showed high frequency of resistance reactions, among which over 50% showed an immune reaction (HR) at both seedling and adult growth stages. Interestingly, 92% of HR and R accessions maintained their resistance levels across the two years, confirming the highly significant correlation found between seedling- and adult-stage reactions. Plant Height was found to have a negative significant effect on adult-stage resistance, suggesting that either this trait can influence disease severity, or that it can be due to environmental/epidemiological factors. Accessions from Italy showed the highest variability, while those from Portugal, Spain and Tunisia showed the highest levels of resistance at both growth stages, suggesting that the latter accessions may harbor novel QTLs effective for STB resistance.
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Gore PG, Gupta V, Singh R, Tripathi K, Kumar R, Kumari G, Madhavan L, Dikshit HK, Venkateswaran K, Pandey A, Singh N, Bhat KV, Nair RM, Pratap A. Insights into the genetic diversity of an underutilized Indian legume, Vigna stipulacea (Lam.) Kuntz., using morphological traits and microsatellite markers. PLoS One 2022; 17:e0262634. [PMID: 35045093 PMCID: PMC8769370 DOI: 10.1371/journal.pone.0262634] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Accepted: 12/31/2021] [Indexed: 11/26/2022] Open
Abstract
Vigna stipulacea (Lam.) Kuntz., commonly known as Minni payaru is an underutilized legume species and has a great potential to be utilized as food crop. To evaluate and select the best germplasm to be harnessed in the breeding programme, we assessed the genetic diversity of V. stipulacea (94 accessions) conserved in the Indian National Genebank, based on morphological traits and microsatellite markers. Significant variation was recorded for the morphological traits studied. Euclidean distance using UPGMA method grouped all accessions into two major clusters. Accessions were identified for key agronomic traits such as, early flowering (IC331436, IC251436, IC331437); long peduncle length (IC553518, IC550531, IC553557, IC553540, IC550532, IC553564); and more number of seeds per pod (IC553529, IC622865, IC622867, IC553528). To analyse the genetic diversity among the germplasm 33 SSR primers were used anda total of 116 alleles were detected. The number of alleles varied from two to seven, with an average of 3.52 per loci. The polymorphic information content values varied from 0.20 to 0.74, with a mean of 0.40. The high number of alleles per locus and the allelic diversity in the studied germplasm indicated a relatively wider genetic base of V. stipulacea. Phylogenetic analysis clustered accessions into seven clades. Population structure analysis grouped them into five genetic groups, which were partly supported by PCoA and phylogenetic tree. Besides, PCoA and AMOVA also decoded high genetic diversity among the V. stipulacea accessions. Thus, morphological and microsatellite markers distinguished V. stipulacea accessions and assessed their genetic diversity efficiently. The identified promising accessions can be utilized in Vigna improvement programme through introgression breeding and/or can be used for domestication and enhanced utilization of V. stipulacea.
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Affiliation(s)
- Padmavati G Gore
- Division of Plant Genetic Resources, ICAR - Indian Agricultural Research Institute, New Delhi, India
- ICAR-National Bureau of Plant Genetic Resources, New Delhi, India
| | - Veena Gupta
- ICAR-National Bureau of Plant Genetic Resources, New Delhi, India
| | - Rakesh Singh
- ICAR-National Bureau of Plant Genetic Resources, New Delhi, India
| | - Kuldeep Tripathi
- ICAR-National Bureau of Plant Genetic Resources, New Delhi, India
| | - Ramesh Kumar
- ICAR-National Bureau of Plant Genetic Resources, New Delhi, India
| | - Gita Kumari
- ICAR-Indian Institute of Pulses Research, Kanpur, Uttar Pradesh, India
| | - Latha Madhavan
- ICAR-National Bureau of Plant Genetic Resources, Thrissur, Kerala, India
| | - Harsh Kumar Dikshit
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | | | - Anjula Pandey
- ICAR-National Bureau of Plant Genetic Resources, New Delhi, India
| | - Neeta Singh
- ICAR-National Bureau of Plant Genetic Resources, New Delhi, India
| | - Kangila V Bhat
- ICAR-National Bureau of Plant Genetic Resources, New Delhi, India
| | | | - Aditya Pratap
- ICAR-Indian Institute of Pulses Research, Kanpur, Uttar Pradesh, India
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Hao M, Zhang L, Ning S, Huang L, Yuan Z, Wu B, Yan Z, Dai S, Jiang B, Zheng Y, Liu D. The Resurgence of Introgression Breeding, as Exemplified in Wheat Improvement. FRONTIERS IN PLANT SCIENCE 2020; 11:252. [PMID: 32211007 PMCID: PMC7067975 DOI: 10.3389/fpls.2020.00252] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Accepted: 02/18/2020] [Indexed: 05/21/2023]
Abstract
Breeding progress in most crops has relied heavily on the exploitation of variation within the species' primary gene pool, a process which is destined to fail once the supply of novel variants has been exhausted. Accessing a crop's secondary gene pool, as represented by its wild relatives, has the potential to greatly expand the supply of usable genetic variation. The crop in which this approach has been most strongly championed is bread wheat (Triticum aestivum), a species which is particularly tolerant of the introduction of chromosomal segments of exotic origin thanks to the genetic buffering afforded by its polyploid status. While the process of introgression can be in itself cumbersome, a larger problem is that linkage drag and/or imperfect complementation frequently impose a yield and/or quality penalty, which explains the reluctance of breeders to introduce such materials into their breeding populations. Thanks to the development of novel strategies to induce introgression and of genomic tools to facilitate the selection of desirable genotypes, introgression breeding is returning as a mainstream activity, at least in wheat. Accessing variation present in progenitor species has even been able to drive genetic advance in grain yield. The current resurgence of interest in introgression breeding can be expected to result in an increased deployment of exotic genes in commercial wheat cultivars.
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Affiliation(s)
- Ming Hao
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Ya’an, China
- Triticeae Research Institute, Sichuan Agricultural University, Ya’an, China
| | - Lianquan Zhang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Ya’an, China
- Triticeae Research Institute, Sichuan Agricultural University, Ya’an, China
| | - Shunzong Ning
- Triticeae Research Institute, Sichuan Agricultural University, Ya’an, China
| | - Lin Huang
- Triticeae Research Institute, Sichuan Agricultural University, Ya’an, China
| | - Zhongwei Yuan
- Triticeae Research Institute, Sichuan Agricultural University, Ya’an, China
| | - Bihua Wu
- Triticeae Research Institute, Sichuan Agricultural University, Ya’an, China
| | - Zehong Yan
- Triticeae Research Institute, Sichuan Agricultural University, Ya’an, China
| | - Shoufen Dai
- Triticeae Research Institute, Sichuan Agricultural University, Ya’an, China
| | - Bo Jiang
- Triticeae Research Institute, Sichuan Agricultural University, Ya’an, China
| | - Youliang Zheng
- Triticeae Research Institute, Sichuan Agricultural University, Ya’an, China
| | - Dengcai Liu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Ya’an, China
- Triticeae Research Institute, Sichuan Agricultural University, Ya’an, China
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Genetic variability in landraces populations and the risk to lose genetic variation. The example of landrace 'Kyperounda' and its implications for ex situ conservation. PLoS One 2019; 14:e0224255. [PMID: 31661501 PMCID: PMC6818954 DOI: 10.1371/journal.pone.0224255] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Accepted: 10/09/2019] [Indexed: 11/19/2022] Open
Abstract
Genetic characterization enhances the development of rational conservation strategies and the utilization of germplasm to plant breeding programs. In the present study, 19 microsatellite markers were employed to evaluate the genetic diversity and the genetic affiliations across 20 Cypriot durum wheat (Triticum turgidum L. subsp. durum) landraces, 13 landraces from the broader Mediterranean basin and 22 modern varieties. Cluster analysis depicted a clear separation among modern varieties and landraces, regardless of their origin. Landraces presented the highest genetic variation (average discriminating power of 0.89) and a high number of private alleles (131) was detected; underlying the unique genetic mark-up of this genepool. AMOVA revealed that the highest variability was detected within the landraces originating from Cyprus and landraces from the broader Mediterranean basin. The Cypriot landrace ‘Kyperounda’ was selected for further evaluation of its’ intra-genetic variation and it was determined that genetic diversity was higher in accessions conserved as sublines (He 0.643–0.731) than bulks (He 0.384–0.469). Bayesian analysis revealed substantial admixture within ‘Kyperounda’ accessions, depicted also by Principal Coordinate Analysis. The findings of the current manuscript emphasize that high intra-genetic diversity is retained when landraces are conserved as sublines in ex situ collections, while landraces that are conserved as bulks have a higher risk of bottleneck. Hence, a more exhausting diversity evaluation is needed in order to fully utilize landraces in breeding schemes and to prevent the loss of genetic variation.
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Winfield MO, Allen AM, Wilkinson PA, Burridge AJ, Barker GL, Coghill J, Waterfall C, Wingen LU, Griffiths S, Edwards KJ. High-density genotyping of the A.E. Watkins Collection of hexaploid landraces identifies a large molecular diversity compared to elite bread wheat. PLANT BIOTECHNOLOGY JOURNAL 2018; 16:165-175. [PMID: 28500796 PMCID: PMC5785351 DOI: 10.1111/pbi.12757] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Revised: 05/04/2017] [Accepted: 05/06/2017] [Indexed: 05/03/2023]
Abstract
The importance of wheat as a food crop makes it a major target for agricultural improvements. As one of the most widely grown cereal grains, together with maize and rice, wheat is the leading provider of calories in the global diet, constituting 29% of global cereal production in 2015. In the last few decades, however, yields have plateaued, suggesting that the green revolution, at least for wheat, might have run its course and that new sources of genetic variation are urgently required. The overall aim of our work was to identify novel variation that may then be used to enable the breeding process. As landraces are a potential source of such diversity, here we have characterized the A.E. Watkins Collection alongside a collection of elite accessions using two complementary high-density and high-throughput genotyping platforms. While our results show the importance of using the appropriate SNP collection to compare diverse accessions, they also show that the Watkins Collection contains a substantial amount of novel genetic diversity which has either not been captured in current breeding programmes or which has been lost through previous selection pressures. As a consequence of our analysis, we have identified a number of accessions which carry an array of novel alleles along with a number of interesting chromosome rearrangements which confirm the variable nature of the wheat genome.
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Affiliation(s)
- Mark O. Winfield
- University of BristolBristol Life Sciences Building24 Tyndall AvenueBristolUK
| | - Alexandra M. Allen
- University of BristolBristol Life Sciences Building24 Tyndall AvenueBristolUK
| | - Paul A. Wilkinson
- University of BristolBristol Life Sciences Building24 Tyndall AvenueBristolUK
| | - Amanda J. Burridge
- University of BristolBristol Life Sciences Building24 Tyndall AvenueBristolUK
| | - Gary L.A. Barker
- University of BristolBristol Life Sciences Building24 Tyndall AvenueBristolUK
| | - Jane Coghill
- University of BristolBristol Life Sciences Building24 Tyndall AvenueBristolUK
| | - Christy Waterfall
- University of BristolBristol Life Sciences Building24 Tyndall AvenueBristolUK
| | | | | | - Keith J. Edwards
- University of BristolBristol Life Sciences Building24 Tyndall AvenueBristolUK
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Chen C, He W, Nassirou TY, Nsabiyumva A, Dong X, Adedze YMN, Jin D. Molecular characterization and genetic diversity of different genotypes of Oryza sativa and Oryza glaberrima. ELECTRON J BIOTECHN 2017. [DOI: 10.1016/j.ejbt.2017.08.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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Phenotypic and genotypic intra-diversity among Anatolian durum wheat “Kunduru” landraces. BIOCHEM SYST ECOL 2016. [DOI: 10.1016/j.bse.2016.01.008] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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Novoselskaya-Dragovich AY. Genetics and genomics of wheat: Storage proteins, ecological plasticity, and immunity. RUSS J GENET+ 2015. [DOI: 10.1134/s102279541505004x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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Abdin MZ, Arya L, Verma M. Transferability of cucumber microsatellite markers used for phylogenetic analysis and population structure study in bottle gourd (Lagenaria siceraria (Mol.) Standl.). Appl Biochem Biotechnol 2014; 175:2206-23. [PMID: 25471016 DOI: 10.1007/s12010-014-1395-z] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2014] [Accepted: 11/12/2014] [Indexed: 11/29/2022]
Abstract
Improved breeding for developing fruit quality in bottle gourd (Lagenaria siceraria (Mol.) Standl.) necessitates knowledge regarding its genetic diversity. To achieve this, a set of 108 locus-specific SSR markers has been developed in bottle gourd by cross-species transferability from 995 mapped Cucumis sativus SSR markers. During screening, 280 primer pairs amplified in the bottle gourd germplasm, which were further evaluated in a diverse set of 42 lines, resulting in 19 polymorphic, 89 monomorphic, 15 with multiple bands, and the rest 157 showed no or very non-specific amplification. The 19 polymorphic primer pairs produced a total of 54 alleles. Gene diversity, Shannon's information index, and Nei's coefficient of differentiation were calculated suggesting a moderate genetic variation at the species level. A model-based population structure analysis divided these germplasm into two subpopulations. This marker set will be applicable for evaluating the genetic structure for association mapping, DNA fingerprinting, and mounting linkage maps and will be a practical tool set for further genetics. This study provides one of the first quantitative views of population genetic variation in bottle gourd.
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Morphological and genetic diversity analysis of rice accessions (Oryza sativa L.) differing in iron toxicity tolerance. ACTA ACUST UNITED AC 2013. [DOI: 10.1007/s12892-012-0104-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Zhao H, Yu J, You FM, Luo M, Peng J. Transferability of microsatellite markers from Brachypodium distachyon to Miscanthus sinensis, a potential biomass crop. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2011; 53:232-45. [PMID: 21205191 DOI: 10.1111/j.1744-7909.2010.01026.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Miscanthus sinensis has high biomass yield and contributed two of the three genomes in M. x giganteus, a bioenergy crop widely studied in Europe and North America, and thus is a potential biomass crop and an important germplasm for Miscanthus breeding. Molecular markers are essential for germplasm evaluation, genetic analyses and new cultivar development in M. sinensis. In the present study, we reported transferability of simple sequence repeat (SSR) markers from Brachypodium distachyon to M. sinensis. A set of 57 SSR markers evenly distributed across the B. distachyon genome were deliberately designed. Out of these B. distachyon SSR markers, 86.0% are transferable to M. sinensis. The SSR loci amplified in M. sinensis were validated by re-sequencing the amplicons. The polymorphism information content (PIC) of the transferable SSR markers varied from 0.073 to 0.375 with a mean of 0.263, assessed based on 21 M. sinensis genotypes. Phylogenetic tree based on 162 alleles detected by 49 SSR markers could unambiguously distinguish B. distachyon from M. sinensis, and cluster 21 M. sinensis genotypes into three groups that are basically in coincidence with their geographical distribution and ecotype classifications. The markers developed by the comparative genomic approach could be useful for germplasm evaluation, genetic analysis, and marker-assisted breeding in Miscanthus.
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Affiliation(s)
- Hua Zhao
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, the Chinese Academy of Sciences, Wuhan 430074, China
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Tam SM, Lefebvre V, Palloix A, Sage-Palloix AM, Mhiri C, Grandbastien MA. LTR-retrotransposons Tnt1 and T135 markers reveal genetic diversity and evolutionary relationships of domesticated peppers. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2009; 119:973-89. [PMID: 19618162 DOI: 10.1007/s00122-009-1102-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2009] [Accepted: 06/25/2009] [Indexed: 05/03/2023]
Abstract
Plant genetic resources often constitute the foundation of successful breeding programs. Pepper (Capsicum annuum L.) is one of the most economically important and diversely utilized Solanaceous crop species worldwide, but less studied compared to tomato and potato. We developed and used molecular markers based on two copia-type retrotransposons, Tnt1 and T135, in a set of Capsicum species and wild relatives from diverse geographical origins. Results showed that Tnt1 and T135 insertion polymorphisms are very useful for studying genetic diversity and relationships within and among pepper species. Clusters of accessions correspond to cultivar types based on fruit shape, pungency, geographic origin and pedigree. Genetic diversity values, normally reflective of past transposition activity and population dynamics, showed positive correlation with the average number of insertions per accession. Similar evolutionary relationships are observed to that inferred by previous karyosystematics studies. These observations support the possibility that retrotransposons have contributed to genome inflation during Capsicum evolution.
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Affiliation(s)
- Sheh May Tam
- Laboratoire de Biologie Cellulaire, UR501, Institut Jean-Pierre Bourgin, INRA, 78026, Versailles Cedex, France
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Carvalho A, Lima-Brito J, Maçãs B, Guedes-Pinto H. Genetic Diversity and Variation Among Botanical Varieties of Old Portuguese Wheat Cultivars Revealed by ISSR Assays. Biochem Genet 2009; 47:276-94. [DOI: 10.1007/s10528-009-9227-5] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2008] [Accepted: 09/08/2008] [Indexed: 10/21/2022]
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Zheleva D, Todorovska E, Christov N, Ivanov P, Ivanova I, Todorov I. Assessing the Genetic Variation of Bulgarian Bread Wheat Varieties by Biochemical and Molecular Markers. BIOTECHNOL BIOTEC EQ 2007. [DOI: 10.1080/13102818.2007.10817466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
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