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The Identification and Characterization of the KNOX Gene Family as an Active Regulator of Leaf Development in Trifolium repens. Genes (Basel) 2022; 13:genes13101778. [PMID: 36292663 PMCID: PMC9601826 DOI: 10.3390/genes13101778] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Revised: 09/23/2022] [Accepted: 09/26/2022] [Indexed: 11/04/2022] Open
Abstract
Leaves are the primary and critical feed for herbivores. They directly determine the yield and quality of legume forage. Trifolium repens (T. repens) is an indispensable legume species, widely cultivated in temperate pastures due to its nutritional value and nitrogen fixation. Although the leaves of T. repens are typical trifoliate, they have unusual patterns to adapt to herbivore feeding. The number of leaflets in T. repens affects its production and utilization. The KNOX gene family encodes transcriptional regulators that are vital in regulating and developing leaves. Identification and characterization of TrKNOX gene family as an active regulator of leaf development in T. repens were studied. A total of 21 TrKNOX genes were identified from the T. repens genome database and classified into three subgroups (Class I, Class II, and Class M) based on phylogenetic analysis. Nineteen of the genes identified had four conserved domains, except for KNOX5 and KNOX9, which belong to Class M. Varying expression levels of TrKNOX genes were observed at different developmental stages and complexities of leaves. KNOX9 was observed to upregulate the leaf complexity of T. repens. Research on TrKNOX genes could be novel and further assist in exploring their functions and cultivating high-quality T. repens varieties.
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Egan LM, Hofmann RW, Ghamkhar K, Hoyos-Villegas V. Prospects for Trifolium Improvement Through Germplasm Characterisation and Pre-breeding in New Zealand and Beyond. FRONTIERS IN PLANT SCIENCE 2021; 12:653191. [PMID: 34220882 PMCID: PMC8242581 DOI: 10.3389/fpls.2021.653191] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Accepted: 05/10/2021] [Indexed: 06/13/2023]
Abstract
Trifolium is the most used pastoral legume genus in temperate grassland systems, and a common feature in meadows and open space areas in cities and parks. Breeding of Trifolium spp. for pastoral production has been going on for over a century. However, the breeding targets have changed over the decades in response to different environmental and production pressures. Relatively small gains have been made in Trifolium breeding progress. Trifolium breeding programmes aim to maintain a broad genetic base to maximise variation. New Zealand is a global hub in Trifolium breeding, utilising exotic germplasm imported by the Margot Forde Germplasm Centre. This article describes the history of Trifolium breeding in New Zealand as well as the role and past successes of utilising genebanks in forage breeding. The impact of germplasm characterisation and evaluation in breeding programmes is also discussed. The history and challenges of Trifolium breeding and its effect on genetic gain can be used to inform future pre-breeding decisions in this genus, as well as being a model for other forage legumes.
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Affiliation(s)
- Lucy M. Egan
- CSIRO Agriculture and Food, Narrabri, NSW, Australia
- Faculty of Agriculture and Life Sciences, Lincoln University, Lincoln, New Zealand
| | - Rainer W. Hofmann
- Faculty of Agriculture and Life Sciences, Lincoln University, Lincoln, New Zealand
| | - Kioumars Ghamkhar
- AgResearch Grasslands Research Centre, Palmerston North, New Zealand
| | - Valerio Hoyos-Villegas
- Department of Plant Science, Faculty of Agricultural and Environmental Sciences, McGill University, Montreal, QC, Canada
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Wu F, Ma S, Zhou J, Han C, Hu R, Yang X, Nie G, Zhang X. Genetic diversity and population structure analysis in a large collection of white clover ( Trifolium repens L.) germplasm worldwide. PeerJ 2021; 9:e11325. [PMID: 33987011 PMCID: PMC8101478 DOI: 10.7717/peerj.11325] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Accepted: 03/31/2021] [Indexed: 12/31/2022] Open
Abstract
White clover is an important temperate legume forage with high nutrition. In the present study, 448 worldwide accessions were evaluated for the genetic variation and polymorphisms using 22 simple sequence repeat (SSR) markers. All the markers were highly informative, a total of 341 scored bands were amplified, out of which 337 (98.83%) were polymorphic. The PIC values ranged from 0.89 to 0.97 with an average of 0.95. For the AMOVA analysis, 98% of the variance was due to differences within the population and the remaining 2% was due to differences among populations. The white clover accessions were divided into different groups or subgroups based on PCoA, UPGMA, and STRUCTURE analyses. The existence of genetic differentiation between the originally natural and introduced areas according to the PCoA analysis of the global white clover accessions. There was a weak correlation between genetic relationships and geographic distribution according to UPGMA and STRUCTURE analyses. The results of the present study will provide the foundation for future breeding programs, genetic improvement, core germplasm collection establishment for white clover.
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Affiliation(s)
- Feifei Wu
- Department of Grassland Science, Animal Science and Technology College, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Sainan Ma
- Department of Grassland Science, Animal Science and Technology College, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Jie Zhou
- Department of Grassland Science, Animal Science and Technology College, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Chongyang Han
- Department of Grassland Science, Animal Science and Technology College, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Ruchang Hu
- Department of Grassland Science, Animal Science and Technology College, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Xinying Yang
- Department of Grassland Science, Animal Science and Technology College, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Gang Nie
- Department of Grassland Science, Animal Science and Technology College, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Xinquan Zhang
- Department of Grassland Science, Animal Science and Technology College, Sichuan Agricultural University, Chengdu, Sichuan, China
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Iqbal MM, Huynh M, Udall JA, Kilian A, Adhikari KN, Berger JD, Erskine W, Nelson MN. The first genetic map for yellow lupin enables genetic dissection of adaptation traits in an orphan grain legume crop. BMC Genet 2019; 20:68. [PMID: 31412771 PMCID: PMC6694670 DOI: 10.1186/s12863-019-0767-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2019] [Accepted: 07/17/2019] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Yellow lupin (Lupinus luteus L.) is a promising grain legume for productive and sustainable crop rotations. It has the advantages of high tolerance to soil acidity and excellent seed quality, but its current yield potential is poor, especially in low rainfall environments. Key adaptation traits such as phenology and enhanced stress tolerance are often complex and controlled by several genes. Genomic-enabled technologies may help to improve our basic understanding of these traits and to provide selective markers in breeding. However, in yellow lupin there are very limited genomic resources to support research and no published information is available on the genetic control of adaptation traits. RESULTS We aimed to address these deficiencies by developing the first linkage map for yellow lupin and conducting quantitative trait locus (QTL) analysis of yield under well-watered (WW) and water-deficit (WT) conditions. Two next-generation sequencing marker approaches - genotyping-by-sequencing (GBS) and Diversity Array Technology (DArT) sequencing - were employed to genotype a recombinant inbred line (RIL) population developed from a bi-parental cross between wild and domesticated parents. A total of 2,458 filtered single nucleotide polymorphism (SNP) and presence / absence variation (PAV) markers were used to develop a genetic map comprising 40 linkage groups, the first reported for this species. A number of significant QTLs controlling total biomass and 100-seed weight under two water (WW and WD) regimes were found on linkage groups YL-03, YL-09 and YL-26 that together explained 9 and 28% of total phenotypic variability. QTLs associated with length of the reproductive phase and time to flower were found on YL-01, YL-21, YL-35 and YL-40 that together explained a total of 12 and 44% of total phenotypic variation. CONCLUSION These genomic resources and the QTL information offer significant potential for use in marker-assisted selection in yellow lupin.
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Affiliation(s)
- Muhammad Munir Iqbal
- School of Agriculture and Environment, The University of Western Australia, Perth, WA, Australia.
- Centre for Plant Genetics and Breeding and Institute of Agriculture, The University of Western Australia, Perth, WA, Australia.
| | - Mark Huynh
- The College of Life Sciences, Brigham Young University, Provo, UT, USA
| | - Joshua A Udall
- USDA-ARS Southern Plains Agricultural Research Center, 2881 F&B Rd., College Station, TX, 77845, USA
| | - Andrzej Kilian
- Diversity Arrays Technology, University of Canberra, Canberra, Australia
| | - Kedar N Adhikari
- School of Life and Environmental Sciences, I A Watson Grains Research Centre, The University of Sydney, Narrabri, NSW, Australia
| | | | - William Erskine
- School of Agriculture and Environment, The University of Western Australia, Perth, WA, Australia
- Centre for Plant Genetics and Breeding and Institute of Agriculture, The University of Western Australia, Perth, WA, Australia
| | - Matthew N Nelson
- Agriculture and Food, CSIRO, Floreat, WA, Australia
- The UWA Institute of Agriculture, Perth, WA, Australia
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Genetic diversity between two Egyptian clover varieties and QTL analysis for some agro-morphological traits. Mol Biol Rep 2018; 46:897-908. [PMID: 30547389 DOI: 10.1007/s11033-018-4546-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Accepted: 11/30/2018] [Indexed: 10/27/2022]
Abstract
Genetic diversity between two ecotypes of Egyptian clover varieties, namely Fahl (mono-cut) and Helaly (multi-cut) have been assessed based on forage yield and yield components as well as molecular marker systems. The two parental genotypes were crossed to produce seeds of F1 and F2 progenies. Analyses of variance indicated significant differences between four populations (P1 (Fahl), P2 (Helaly), F1 and F2) for fresh forage yield, number of florets/inflorescence, number of seeds/inflorescence and 1000 seed weight. The mean of F1 hybrid indicated over-dominance of the higher performance. The phenotypic and genotypic coefficients of variation were high for fresh forage yield, intermediate for 1000-seed weight and low for number of florets/inflorescence and number of seeds/inflorescence. Four molecular marker systems with 80 primers, 30 RAPD, 10 ISSR, 10 SRAP and 30 SSR were used for studying the genetic diversity between the two parents, out of which 64 primers (26 RAPD, 7 ISSR, 7 SRAP and 24 SSR) were polymorphic between the parents. The four molecular marker systems generated unique DNA bands for each parent. Twenty-one primers which produced higher unique bands in both parents were surveyed on bulked DNA from the extremes of four agro-morphological traits within and between the two ecotypes in F2 generations. Twenty-one primers produced bands distinguish between the bulked extremes for at least one trait within each ecotype or between the two ecotypes. All polymorphic primers were subjected to QTL analysis, out of them 23 only were mapped on three linkage groups with four agro-morphological traits and showed 24 putative QTLs.
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Inostroza L, Bhakta M, Acuña H, Vásquez C, Ibáñez J, Tapia G, Mei W, Kirst M, Resende M, Munoz P. Understanding the Complexity of Cold Tolerance in White Clover using Temperature Gradient Locations and a GWAS Approach. THE PLANT GENOME 2018; 11. [PMID: 30512038 DOI: 10.3835/plantgenome2017.11.0096] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
White clover ( L.) is the most important grazing perennial forage legume in temperate climates. However, its limited capacity to survive and restore growth after low temperatures during winter constrains the productivity and wide adoption of the crop. Despite the importance of cold tolerance for white clover cultivar development, the genetic basis of this trait remains largely unknown. Hence, in this study, we performed the first genome-wide association study (GWAS) analyses in white clover to identify quantitative trait loci (QTL) for cold-tolerance-related traits. Seeds from 192 divergent genotypes from six populations in the Patagonia region of South America were collected and seed-derived plants were further clonally propagated. Clonal trials were established in three locations representing temperature gradient associated with elevation. Given the allotetraploid nature of the white clover genome, distinct genetic models (diploid and tetraploid) were tested. Only the tetraploid parameterization was able to detect the 53 loci associated with cold-tolerance traits. Out of the 53 single nucleotide polymorphism (SNP) trait associations, 17 controlled more than one trait or were stable across multiple sites. This work represents the first report of QTL for cold-tolerance-related traits, providing insights into its genetic basis and candidate genomic regions for further functional validation studies.
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Development of Genomic Resources in the Species of Trifolium L. and Its Application in Forage Legume Breeding. AGRONOMY-BASEL 2012. [DOI: 10.3390/agronomy2020116] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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Isobe SN, Hisano H, Sato S, Hirakawa H, Okumura K, Shirasawa K, Sasamoto S, Watanabe A, Wada T, Kishida Y, Tsuruoka H, Fujishiro T, Yamada M, Kohara M, Tabata S. Comparative Genetic Mapping and Discovery of Linkage Disequilibrium Across Linkage Groups in White Clover (Trifolium repens L.). G3 (BETHESDA, MD.) 2012; 2:607-17. [PMID: 22670230 PMCID: PMC3362943 DOI: 10.1534/g3.112.002600] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/09/2011] [Accepted: 03/16/2012] [Indexed: 11/18/2022]
Abstract
White clover (Trifolium repens L.) is an allotetraploid species (2n = 4X = 32) that is widely distributed in temperate regions and cultivated as a forage legume. In this study, we developed expressed sequence tag (EST)-derived simple sequence repeat (SSR) markers, constructed linkage maps, and performed comparative mapping with other legume species. A total of 7982 ESTs that could be assembled into 5400 contigs and 2582 singletons were generated. Using the EST sequences that were obtained, 1973 primer pairs to amplify EST-derived SSR markers were designed and used for linkage analysis of 188 F(1) progenies, which were generated by a cross between two Japanese plants, '273-7' and 'T17-349,' with previously published SSR markers. An integrated linkage map was constructed by combining parental-specific maps, which consisted of 1743 SSR loci on 16 homeologous linkage groups with a total length of 2511 cM. The primer sequences of the developed EST-SSR markers and their map positions are available on http://clovergarden.jp/. Linkage disequilibrium (LD) was observed on 9 of 16 linkage groups of a parental-specific map. The genome structures were compared among white clover, red clover (T. pratense L.), Medicago truncatula, and Lotus japonicus. Macrosynteny was observed across the four legume species. Surprisingly, the comparative genome structure between white clover and M. truncatula had a higher degree of conservation than that of the two clover species.
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Affiliation(s)
- Sachiko N. Isobe
- Department of Plant Genome Research, Kazusa DNA Research Institute, Kisarazu, Chiba 292-0818, Japan
| | - Hiroshi Hisano
- Department of Plant Genome Research, Kazusa DNA Research Institute, Kisarazu, Chiba 292-0818, Japan
| | - Shusei Sato
- Department of Plant Genome Research, Kazusa DNA Research Institute, Kisarazu, Chiba 292-0818, Japan
| | - Hideki Hirakawa
- Department of Plant Genome Research, Kazusa DNA Research Institute, Kisarazu, Chiba 292-0818, Japan
| | - Kenji Okumura
- Forage Crop Breeding Research Team, National Agricultural Research Center for Hokkaido Region, Sapporo, Hokkaido 062-8555, Japan
| | - Kenta Shirasawa
- Department of Plant Genome Research, Kazusa DNA Research Institute, Kisarazu, Chiba 292-0818, Japan
| | - Shigemi Sasamoto
- Department of Plant Genome Research, Kazusa DNA Research Institute, Kisarazu, Chiba 292-0818, Japan
| | - Akiko Watanabe
- Department of Plant Genome Research, Kazusa DNA Research Institute, Kisarazu, Chiba 292-0818, Japan
| | - Tsuyuko Wada
- Department of Plant Genome Research, Kazusa DNA Research Institute, Kisarazu, Chiba 292-0818, Japan
| | - Yoshie Kishida
- Department of Plant Genome Research, Kazusa DNA Research Institute, Kisarazu, Chiba 292-0818, Japan
| | - Hisano Tsuruoka
- Department of Plant Genome Research, Kazusa DNA Research Institute, Kisarazu, Chiba 292-0818, Japan
| | - Tsunakazu Fujishiro
- Department of Plant Genome Research, Kazusa DNA Research Institute, Kisarazu, Chiba 292-0818, Japan
| | - Manabu Yamada
- Department of Plant Genome Research, Kazusa DNA Research Institute, Kisarazu, Chiba 292-0818, Japan
| | - Mistuyo Kohara
- Department of Plant Genome Research, Kazusa DNA Research Institute, Kisarazu, Chiba 292-0818, Japan
| | - Satoshi Tabata
- Department of Plant Genome Research, Kazusa DNA Research Institute, Kisarazu, Chiba 292-0818, Japan
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Espinoza LDCL, Huguet T, Julier B. Multi-population QTL detection for aerial morphogenetic traits in the model legume Medicago truncatula. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2012; 124:739-54. [PMID: 22075808 DOI: 10.1007/s00122-011-1743-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2011] [Accepted: 10/28/2011] [Indexed: 05/02/2023]
Abstract
Medicago truncatula, as a model species, is useful to study the genetic control of traits of agronomic interest in legumes species. Aerial morphogenesis is a key component of forage and seed yield. It was measured in four mapping populations originating from five parental lines. Single and multi-population quantitative trait locus (QTL) detections were carried out. A large variation was observed within populations and transgressive segregation was noted. Most traits showed high heritabilities in all seasons. Length of primary branches (LPB, cm) was positively correlated to branch elongation rate (BER, cm day(-1)) and aerial dry matter (ADM, g). Flowering time (FT, °C day(-1)) showed negative correlations with length of main stem (LMS, cm) and BER. One hundred and forty-one QTLs for BER, LMS, FT, LPB, diameter of primary branches (DPB), number of primary branches (NPB), number of nodes (NI) and ADM were identified and localized over all eight chromosomes. Single and multi-population analyses showed that the most important regions for aerial morphogenetic traits were chromosomes 1, 2, 7 and 8. Multi-population analysis revealed three regions of major QTLs affecting aerial morphogenetic traits (LPB, LMS, NPB, BER and FT). A region involved in flowering time variation was revealed on chromosome 6 on a single population. These results were used to identify candidate genes that could control variation for aerial morphogenesis traits in this species and in related crop legume species.
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Affiliation(s)
- Luz del Carmen Lagunes Espinoza
- INRA, UR 4, Unité de Recherche Pluridisciplinaire Prairies et Plantes Fourragères, Le Chêne, RD 150, BP 80006, 86600, Lusignan, France
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Mapping of QTLs governing agronomic and yield traits in chickpea. J Appl Genet 2010; 52:9-21. [PMID: 21181334 DOI: 10.1007/s13353-010-0016-y] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2010] [Revised: 08/04/2010] [Accepted: 08/07/2010] [Indexed: 10/18/2022]
Abstract
Chickpea is one of the most important leguminous cool season food crops, cultivated prevalently in South Asia and Middle East. The main objective of this study was to identify quantitative trait loci (QTLs) associated with seven agronomic and yield traits in two recombinant inbred line populations of chickpea derived from the crosses JG62 × Vijay (JV population) and Vijay × ICC4958 (VI population) from at least three environments. Single locus QTL analysis involved composite interval mapping (CIM) for individual traits and multiple-trait composite interval mapping (MCIM) for correlated traits to detect pleiotropic QTLs. Two-locus analysis was conducted to identify the main effect QTLs (M-QTLs), epistatic QTLs (E-QTLs) and QTL × environment interactions. Through CIM analysis, a total of 106 significant QTLs (41 in JV and 65 in VI populations) were identified for the seven traits, of which one QTL each for plant height and days to maturity was common in both the populations. Six pleiotropic QTLs that were consistent over the environments were also identified. LG2 in JV and LG1a in VI contained at least one QTL for each trait. Hence, concentrating on these LGs in molecular breeding programs is most likely to bring simultaneous improvement in these traits.
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Wang J, Drayton MC, George J, Cogan NOI, Baillie RC, Hand ML, Kearney GA, Erb S, Wilkinson T, Bannan NR, Forster JW, Smith KF. Identification of genetic factors influencing salt stress tolerance in white clover (Trifolium repens L.) by QTL analysis. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2010; 120:607-19. [PMID: 19865805 DOI: 10.1007/s00122-009-1179-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2009] [Accepted: 10/04/2009] [Indexed: 05/20/2023]
Abstract
Allotetraploid (2n = 4x = 32) white clover (Trifolium repens L.) is the most commonly cultivated legume component of temperate pastures, sown in swards with a companion grass species. Genetic control of growth performance of white clover on saline land is highly important for dairy industries, due to increasing soil salinity problems. The objective of this study was to identify quantitative trait loci (QTLs) for salinity tolerance in terms of vegetative growth under stress. Two parental genetic maps consisting of 213 and 159 marker loci and spanning 1,973.0 and 1,837.6 cM, respectively, were constructed using simple sequence repeat (SSR) and single nucleotide polymorphism (SNP) markers from a two-way pseudo-test cross F(1) population derived from pair-crossing of the Haifa(2) and LCL(2) genotypes. A total of 8 unique genomic regions on 8 linkage groups (LGs) of the Haifa(2) parental map and 6 unique regions on 5 LGs in the LCL(2) parental map were associated with plant growth under salt stress and relative growth under stress, as compared to control conditions. The results of this study indicate that salt tolerance in white clover is controlled by multiple QTLs, some at common locations, but each of limited magnitude. Location of these QTLs provides the genetic basis and potential for pyramiding of salt tolerance genes in breeding improvement.
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Affiliation(s)
- Junping Wang
- Biosciences Research Division, Department of Primary Industries, Hamilton Centre, Hamilton, VIC 3300, Australia
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Weller JL, Hecht V, Liew LC, Sussmilch FC, Wenden B, Knowles CL, Vander Schoor JK. Update on the genetic control of flowering in garden pea. JOURNAL OF EXPERIMENTAL BOTANY 2009; 60:2493-9. [PMID: 19414500 DOI: 10.1093/jxb/erp120] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
The garden pea has been a model for the genetics of flowering for several decades and numerous flowering loci have been identified, but until recently little was known about the molecular nature of these loci. This paper presents an update on recent work on the molecular genetics of flowering in pea, outlining progress in gene and mutant isolation, expression analyses, grafting and other physiological studies, and candidate gene assessment. Work so far has led to the identification of the LATE1 and DNE loci as orthologues of Arabidopsis GIGANTEA and ELF4, respectively, and candidate genes for several other loci are being evaluated. Expression analysis of an expanded FT-like gene family suggests a more complex role for this group of genes. These results provide the first insight into the circadian clock, photoperiod response mechanism, and mobile signals in pea, and identify both conserved and divergent features in comparison with Arabidopsis.
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Affiliation(s)
- James L Weller
- School of Plant Science, University of Tasmania, Private Bag 55, Hobart, Tasmania 7001, Australia.
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George J, Sawbridge TI, Cogan NOI, Gendall AR, Smith KF, Spangenberg GC, Forster JW. Comparison of genome structure between white clover and Medicago truncatula supports homoeologous group nomenclature based on conserved synteny. Genome 2009; 51:905-11. [PMID: 18956023 DOI: 10.1139/g08-076] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Computational analysis has been used to align the genetic map of white clover (Trifolium repens L.) with the draft genome sequence of the model legume species Medicago truncatula Gaertn. In silico comparison based on white clover expressed sequence tags that contain simple sequence repeat loci revealed substantial macrosynteny between the genomes of these two species, which are closely related within the Trifolieae tribe of the Fabaceae family. Six of the eight homoeologous chromosome groups (HGs) of allotetraploid white clover show predominant relationships with single M. truncatula (Mt) chromosomes, while the two remaining groups may have participated in an evolutionary reciprocal translocation event. On this basis, a new chromosome nomenclature system for allotetraploid white clover is proposed such that HG A = 3, HG B = 8, HG C = 7, HG D = 4, HG E = 1, HG F = 2, HG G = 5, and HG H = 6. A rationalized linkage map ordering system has also been demonstrated. Improved knowledge of the relationships between agricultural and model forage legume genomes will facilitate prediction of gene location for key agronomic traits for pasture production.
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Affiliation(s)
- Julie George
- Department of Primary Industries, Biosciences Research Division, Victorian AgriBiosciences Centre, La Trobe University Research and Development Park, Bundoora, Victoria 3083, Australia
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Zhang Y, He J, Zhao PX, Bouton JH, Monteros MJ. Genome-wide identification of microsatellites in white clover (Trifolium repens L.) using FIASCO and phpSSRMiner. PLANT METHODS 2008; 4:19. [PMID: 18631390 PMCID: PMC2517061 DOI: 10.1186/1746-4811-4-19] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2008] [Accepted: 07/16/2008] [Indexed: 05/23/2023]
Abstract
BACKGROUND Allotetraploid white clover (Trifolium repens L.) is an important forage legume widely cultivated in most temperate regions. Only a small number of microsatellite markers are publicly available and can be utilized in white clover breeding programs. The objectives of this study were to develop an integrated approach for microsatellite development and to evaluate the approach for the development of new SSR markers for white clover. RESULTS Genomic libraries containing simple sequence repeat (SSR) sequences were constructed using a modified Fast Isolation by AFLP of Sequences COntaining repeats (FIASCO) procedure and phpSSRMiner was used to develop the microsatellite markers. SSR motifs were isolated using two biotin-labeled probes, (CA)17 and (ATG)12. The sequences of 6,816 clones were assembled into 1,698 contigs, 32% of which represented novel sequences based on BLASTN searches. Approximately 32%, 28%, and 16% of these SSRs contained hexa-, tri-, and di-nucleotide repeats, respectively. The most frequent motifs were the CA and ATG complementary repeats and the associated compound sequences. Primer pairs were designed for 859 SSR loci based on sequences from these genomic libraries and from GenBank white clover nucleotide sequences. A total of 191 SSR primers developed from the two libraries were tested for polymorphism in individual clones from the parental genotypes GA43 ('Durana'), 'SRVR' and six F1 progeny from a mapping population. Ninety two percent produced amplicons and 66% of these were polymorphic. CONCLUSION The combined approach of identifying SSR-enriched fragments by FIASCO coupled with the primer design and in silico amplification using phpSSRMiner represents an efficient and low cost pipeline for the large-scale development of microsatellite markers in plants.The approach described here could be readily adapted and utilized in other non-related species with none or limited genomic resources.
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Affiliation(s)
- Yan Zhang
- Forage Improvement Division, The Samuel Roberts Noble Foundation, 2510 Sam Noble Parkway, Ardmore, OK, 73402, USA
| | - Ji He
- Plant Biology Division, The Samuel Roberts Noble Foundation, 2510 Sam Noble Parkway, Ardmore, OK, 73402, USA
| | - Patrick X Zhao
- Plant Biology Division, The Samuel Roberts Noble Foundation, 2510 Sam Noble Parkway, Ardmore, OK, 73402, USA
| | - Joseph H Bouton
- Forage Improvement Division, The Samuel Roberts Noble Foundation, 2510 Sam Noble Parkway, Ardmore, OK, 73402, USA
| | - Maria J Monteros
- Forage Improvement Division, The Samuel Roberts Noble Foundation, 2510 Sam Noble Parkway, Ardmore, OK, 73402, USA
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15
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Gondo T, Sato S, Okumura K, Tabata S, Akashi R, Isobe S. Quantitative trait locus analysis of multiple agronomic traits in the model legumeLotus japonicus. Genome 2007; 50:627-37. [PMID: 17893740 DOI: 10.1139/g07-040] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The first quantitative trait locus (QTL) analysis of multiple agronomic traits in the model legume Lotus japonicus was performed with a population of recombinant inbred lines derived from Miyakojima MG-20 × Gifu B-129. Thirteen agronomic traits were evaluated in 2004 and 2005: traits of vegetative parts (plant height, stem thickness, leaf length, leaf width, plant regrowth, plant shape, and stem color), flowering traits (flowering time and degree), and pod and seed traits (pod length, pod width, seeds per pod, and seed mass). A total of 40 QTLs were detected that explained 5%–69% of total variation. The QTL that explained the most variation was that for stem color, which was detected in the same region of chromosome 2 in both years. Some QTLs were colocated, especially those for pod and seed traits. Seed mass QTLs were located at 5 locations that mapped to the corresponding genomic positions of equivalent QTLs in soybean, pea, chickpea, and mung bean. This study provides fundamental information for breeding of agronomically important legume crops.
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Affiliation(s)
- Takahiro Gondo
- University of Miyazaki, Frontier Science Research Center, 1-1 Nishi Gakuen-Kibanadai, Miyazaki 889-2192, Japan
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16
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Zhang Y, Sledge MK, Bouton JH. Genome mapping of white clover (Trifolium repens L.) and comparative analysis within the Trifolieae using cross-species SSR markers. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2007; 114:1367-78. [PMID: 17356868 PMCID: PMC1950584 DOI: 10.1007/s00122-007-0523-3] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2006] [Accepted: 02/02/2007] [Indexed: 05/04/2023]
Abstract
Allotetraploid white clover (Trifolium repens L.), a cool-season perennial legume used extensively as forage for livestock, is an important target for marker-assisted breeding. A genetic linkage map of white clover was constructed using simple sequence repeat (SSR) markers based on sequences from several Trifolieae species, including white clover, red clover (T. pratense L.), Medicago truncatula (Gaertn.) and soybean (Glycine max L.). An F(1) population consisting of 179 individuals, from a cross between two highly heterozygous genotypes, GA43 and Southern Regional Virus Resistant, was used for genetic mapping. A total of 1,571 SSR markers were screened for amplification and polymorphism using DNA from two parents and 14 F(1)s of the mapping population. The map consists of 415 loci amplified from 343 SSR primer pairs, including 83 from white clover, 181 from red clover, 77 from M. truncatula, and two from soybean. Linkage groups for all eight homoeologous chromosome pairs of allotetraploid white clover were detected. Map length was estimated at 1,877 cM with 87% genome coverage. Map density was approximately 5 cM per locus. Segregation distortion was detected in six segments of the genome (homoeologous groups A1, A2, B1, B2, C1, and D1). A comparison of map locations of markers originating from white clover, red clover, and alfalfa (M. sativa L.) revealed putative macro-colinearity between the three Trifolieae species. This map can be used to link quantitative trait loci with SSR markers, and accelerate the improvement of white clover by marker-assisted selection and breeding.
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Affiliation(s)
- Yan Zhang
- Forage Improvement Division, The Samuel Roberts Noble Foundation, 2510, Sam Noble Parkway, Ardmore, OK 73401, USA.
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17
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George J, Dobrowolski MP, van Zijll de Jong E, Cogan NOI, Smith KF, Forster JW. Assessment of genetic diversity in cultivars of white clover (Trifolium repens L.) detected by SSR polymorphisms. Genome 2007; 49:919-30. [PMID: 17036067 DOI: 10.1139/g06-079] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
White clover (Trifolium repens L.) is an important temperate pasture legume that plays a key role as a companion to grass species, such as perennial ryegrass (Lolium perenne L.). Due to the outbreeding nature of white clover, cultivars are highly heterogeneous. Genetic diversity was assessed using 16 elite cultivars from Europe, North and South America, Australia, and New Zealand. Fifteen simple sequence repeat markers that detect single, codominant polymorphic genetic loci were selected for the study. The genetic relationships among individuals were compared using phenetic clustering, and those among cultivars were compared using nonmetric multidimensional scaling. Intrapopula tion variability exceeded interpopulation variability, with substantial overlap among populations and weak interpopula tion differentiation. No obvious or significant differentiation was observed on the basis of morphology or geographic origin of the cultivars. The number of parental genotypes used to derive each cultivar was not a major determinant of genome-wide genetic diversity. The outcomes of this assessment of genetic variation in elite white clover germplasm pools have important implications for the feasibility of molecular marker-based cultivar discrimination, and will be used to assist the design of linkage disequilibrium mapping strategies for marker-trait association.
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Affiliation(s)
- Julie George
- Primary Industries Research Victoria, Victorian AgriBiosciences Centre, La Troble Research and Development Park, Bundoora, Victpria, Australia
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18
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Cogan NOI, Drayton MC, Ponting RC, Vecchies AC, Bannan NR, Sawbridge TI, Smith KF, Spangenberg GC, Forster JW. Validation of in silico-predicted genic SNPs in white clover (Trifolium repens L.), an outbreeding allopolyploid species. Mol Genet Genomics 2007; 277:413-25. [PMID: 17216492 DOI: 10.1007/s00438-006-0198-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2006] [Accepted: 11/27/2006] [Indexed: 10/23/2022]
Abstract
White clover (Trifolium repens L.) is an obligate outbreeding allotetraploid forage legume. Gene-associated SNPs provide the optimum genetic system for improvement of such crop species. An EST resource obtained from multiple cDNA libraries constructed from numerous genotypes of a single cultivar has been used for in silico SNP discovery and validation. A total of 58 from 236 selected sequence clusters (24.5%) were fully validated as containing polymorphic SNPs by genotypic analysis across the parents and progeny of several two-way pseudo-testcross mapping families. The clusters include genes belonging to a broad range of predicted functional categories. Polymorphic SNP-containing ESTs have also been used for comparative genomic analysis by comparison with whole genome data from model legume species, as well as Arabidopsis thaliana. A total of 29 (50%) of the 58 clusters detected putative ortholoci with known chromosomal locations in Medicago truncatula, which is closely related to white clover within the Trifolieae tribe of the Fabaceae. This analysis provides access to translational data from model species. The efficiency of in silico SNP discovery in white clover is limited by paralogous and homoeologous gene duplication effects, which are resolved unambiguously by the transmission test. This approach will also be applicable to other agronomically important cross-pollinating allopolyploid plant species.
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Affiliation(s)
- N O I Cogan
- Primary Industries Research Victoria, Victorian AgriBiosciences Centre, La Trobe Research and Development Park, Bundoora, VIC, 3083, Australia
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