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Sharma A, Sharma S, Kumar N, Rana RS, Sharma P, Kumar P, Rani M. Morpho-molecular genetic diversity and population structure analysis in garden pea (Pisum sativum L.) genotypes using simple sequence repeat markers. PLoS One 2022; 17:e0273499. [PMID: 36112614 PMCID: PMC9480992 DOI: 10.1371/journal.pone.0273499] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2022] [Accepted: 08/09/2022] [Indexed: 11/18/2022] Open
Abstract
Garden pea (Pisum sativum L.) is a self-pollinated plant species which played an important role for the foundation of modern genetics. Genetic diversity among 56 garden pea genotypes was assessed using 12 morphological descriptors, 19 quantitative traits and 8 simple sequence repeat (SSR) markers. Eight morphological descriptors were found polymorphic, and highest Shannon diversity index was recorded for pod curvature (1.18). Mahalanobis D2 illustrating genetic divergence arranged 56 genotypes into six clusters, with the highest inter-cluster distance between clusters IV and VI (18.09). The average values of Na (number of alleles), Ne (effective number of alleles), I (Shannon's Information index), PIC (polymorphism information content), Ho (observed heterozygosity) and He (expected heterozygosity) were 3.13, 1.85, 0.71, 0.36, 0.002 and 0.41, respectively. Pair wise genetic distance among all pairs of the genotypes varied from 0.33 to 1.00 with an average of 0.76. Based on genetic distance, the genotypes were classified into two main clusters (A and B) by cluster analysis, whereas structure analysis divided the genotypes into four sub-populations. The SSR makers indicated that present of genetic variability among the studied genotypes. When, we compared the groups formed by agro-morphological and molecular data, no genotypes were observed, indicating that both stages of characterization are crucial for a better understanding of the genetic variability. Hybridization between genetically diverse genotypes can be exploited to expend the genetic variability and introduce new traits in the pea breeding program.
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Affiliation(s)
- Akhilesh Sharma
- Department of Vegetable Science & Floriculture, Chaudhary Sarwan Kumar Himachal Pradesh Krishi Vishvavidyalaya, Palampur, Himachal Pradesh, India
| | - Shimalika Sharma
- Department of Vegetable Science & Floriculture, Chaudhary Sarwan Kumar Himachal Pradesh Krishi Vishvavidyalaya, Palampur, Himachal Pradesh, India
| | - Nimit Kumar
- Department of Genetics and Plant Breeding, Chaudhary Sarwan Kumar Himachal Pradesh Krishi Vishvavidyalaya, Palampur, Himachal Pradesh, India
| | - Ranbir Singh Rana
- Centre for Geo Informatics Research and Training, Chaudhary Sarwan Kumar Himachal Pradesh Krishi Vishvavidyalaya, Palampur, Himachal Pradesh, India
| | - Parveen Sharma
- Department of Vegetable Science & Floriculture, Chaudhary Sarwan Kumar Himachal Pradesh Krishi Vishvavidyalaya, Palampur, Himachal Pradesh, India
| | - Prabhat Kumar
- PIU-NAHEP, Krishi Anusandhan Bhavan-II, Indian Council of Agricultural Research, Pusa, New Delhi, India
| | - Menisha Rani
- Department of Vegetable Science & Floriculture, Chaudhary Sarwan Kumar Himachal Pradesh Krishi Vishvavidyalaya, Palampur, Himachal Pradesh, India
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Haliloglu K, Turkoglu A, Tan M, Poczai P. SSR-Based Molecular Identification and Population Structure Analysis for Forage Pea ( Pisum sativum var. arvense L.) Landraces. Genes (Basel) 2022; 13:1086. [PMID: 35741848 PMCID: PMC9222440 DOI: 10.3390/genes13061086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 06/09/2022] [Accepted: 06/16/2022] [Indexed: 12/10/2022] Open
Abstract
Plant genetic diversity has a significant role in providing traits that can help meet future challenges, such as the need to adapt crops to changing climatic conditions or outbreaks of disease. Our aim in this study was to evaluate the diversity of 61 forage pea specimens (P. sativum ssp. arvense L.) collected from the northeastern Anatolia region of Turkey using 28 simple sequence repeat (SSR) markers. These primers generated a total of 82 polymorphic bands. The number of observed alleles (Na) per primer varied from 2 to 4 with a mean of 2.89 alleles/locus. The mean value of expected heterozygosity (Exp-Het = 0.50) was higher than the mean value of observed heterozygosity (Obs-Het = 0.22). The mean of polymorphic information content (PIC) was 0.41 with a range of 0.03-0.70. The mean number of effective alleles (Ne) was found to be 2.15, Nei's expected heterozygosity (H) 0.49, and Shannon's information index (I) 0.81. Cluster analysis through the unweighted pair-group mean average (UPGMA) method revealed that 61 forage pea landraces were divided into three main clusters. Genetic dissimilarity between the genotypes, calculated with the use of NTSYS-pc software, varied between 0.10 (G30 and G34) and 0.66 (G1 and G32). Principal coordinate analysis (PCoA) revealed that three principal coordinates explained 51.54% of the total variation. Moreover, population structure analysis showed that all genotypes formed three sub-populations. Expected heterozygosity values varied between 0.2669 (the first sub-population) and 0.3223 (third sub-population), with an average value of 0.2924. Average population differentiation measurement (Fst) was identified as 0.2351 for the first sub-population, 0.3838 for the second sub-population, and 0.2506 for the third sub-population. In general, current results suggest that SSR markers could be constantly used to illuminate the genetic diversity of forage pea landraces and can potentially be incorporated into future studies that examine the diversity within a larger collection of forage pea genotypes from diverse regions.
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Affiliation(s)
- Kamil Haliloglu
- Department of Field Crops, Faculty of Agriculture, Ataturk University, 25240 Erzurum, Turkey;
- Department of Biology, Faculty of Science, Cankiri Karatekin University, 18200 Çankırı, Turkey
| | - Aras Turkoglu
- Department of Field Crops, Faculty of Agriculture, Necmettin Erbakan University, 42310 Konya, Turkey
| | - Mustafa Tan
- Havsa Vocational College Park and Garden Plants, Trakya University, 22030 Edirne, Turkey;
| | - Peter Poczai
- Botany Unit, Finnish Museum of Natural History, University of Helsinki, P.O. Box 7, FI-00014 Helsinki, Finland
- Institute of Advanced Studies Kőszeg (iASK), 9731 Kőszeg, Hungary
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Sari H, Sari D, Eker T, Toker C. De novo super-early progeny in interspecific crosses Pisum sativum L. × P. fulvum Sibth. et Sm. Sci Rep 2021; 11:19706. [PMID: 34611237 PMCID: PMC8492716 DOI: 10.1038/s41598-021-99284-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Accepted: 09/23/2021] [Indexed: 02/08/2023] Open
Abstract
Earliness in crop plants has a crucial role in avoiding the stress of drought and heat, which are the most important challenging stressors in crop production and are predicted to increase in the near future due to global warming. Furthermore, it provides a guarantee of vegetable production in the short growing season of agricultural lands in the northern hemisphere and at high altitudes. The growing human population needs super early plant cultivars for these agricultural lands to meet future global demands. This study examined de novo super-early progeny, referred to as much earlier than that of the earlier parent, which flowered in 13-17 days and pod setting in 18-29 days after germination, discovered in F2 and studied up to F5 derived from interspecific crosses between garden pea (P. sativum L.) and the most distant relative of pea (P. fulvum Sibth. et Sm.). De novo super-early progeny were found to be earlier by about one month than P. sativum and two months than P. fulvum under short day conditions in the F5 population. In respect of days to flowering and pod setting, de novo super-early progeny had a relatively high level of narrow sense heritability (h2 = 82% and 80%, respectively), indicating that the selections for earliness in segregating populations was effective for improvement of extreme early maturing varieties. De novo super-early progeny could be grown under heat stress conditions due to the escape ability. Vegetable types were not only high yielding but also free of any known undesirable traits from the wild species, such as pod dehiscence and non-uniform maturity. It could be considered complementary to "speed breeding", possibly obtaining more than six generations per year in a suitable climate chamber. Not only de novo super-early progeny but also transgressive segregation for agro-morphological traits can be created via interspecific crosses between P. sativum and P. fulvum, a precious unopened treasure in the second gene pool. Useful progeny obtained from crossing wild species with cultivated species reveal the importance of wild species.
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Affiliation(s)
- Hatice Sari
- Department of Field Crops, Faculty of Agriculture, Akdeniz University, Antalya, 07070, Turkey.
| | - Duygu Sari
- Department of Field Crops, Faculty of Agriculture, Akdeniz University, Antalya, 07070, Turkey
| | - Tuba Eker
- Department of Field Crops, Faculty of Agriculture, Akdeniz University, Antalya, 07070, Turkey
| | - Cengiz Toker
- Department of Field Crops, Faculty of Agriculture, Akdeniz University, Antalya, 07070, Turkey
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Bogdanova VS, Shatskaya NV, Mglinets AV, Kosterin OE, Vasiliev GV. Discordant evolution of organellar genomes in peas (Pisum L.). Mol Phylogenet Evol 2021; 160:107136. [PMID: 33684529 DOI: 10.1016/j.ympev.2021.107136] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Revised: 02/25/2021] [Accepted: 02/26/2021] [Indexed: 01/30/2023]
Abstract
Plastids and mitochondria have their own small genomes, which do not undergo meiotic recombination and may have evolutionary fates different from each other and that of the nuclear genome. For the first time, we sequenced mitochondrial genomes of pea (Pisum L.) from 42 accessions mostly representing diverse wild germplasm from throughout the wild pea geographical range. Six structural types of the pea mitochondrial genome were revealed. From the same accessions, plastid genomes were sequenced. Phylogenetic trees based on the plastid and mitochondrial genomes were compared. The topologies of these trees were highly discordant, implying not less than six events of hybridisation between diverged wild peas in the past, with plastids and mitochondria differently inherited by the descendants. Such discordant inheritance of organelles could have been driven by plastid-nuclear incompatibility, which is known to be widespread in crosses involving wild peas and affects organellar inheritance. The topology of the phylogenetic tree based on nucleotide sequences of a nuclear gene, His5, encoding a histone H1 subtype, corresponded to the current taxonomy and resembled that based on the plastid genome. Wild peas (Pisum sativum subsp. elatius s.l.) inhabiting Southern Europe were shown to be of hybrid origin, resulting from crosses of peas related to those presently inhabiting the eastern Mediterranean in a broad sense. These results highlight the roles of hybridisation and cytonuclear conflict in shaping plant microevolution.
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Affiliation(s)
- Vera S Bogdanova
- Institute of Cytology and Genetics of the Siberian Division of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Natalia V Shatskaya
- Institute of Cytology and Genetics of the Siberian Division of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Anatoliy V Mglinets
- Institute of Cytology and Genetics of the Siberian Division of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Oleg E Kosterin
- Institute of Cytology and Genetics of the Siberian Division of the Russian Academy of Sciences, Novosibirsk, Russia; Novosibirsk State University, Novosibirsk, Russia.
| | - Gennadiy V Vasiliev
- Institute of Cytology and Genetics of the Siberian Division of the Russian Academy of Sciences, Novosibirsk, Russia
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Islam M, Abdullah, Zubaida B, Amin N, Khan RI, Shafqat N, Masood R, Waseem S, Tahir J, Ahmed I, Naeem M, Ahmad H. Agro-Morphological, Yield, and Genotyping-by-Sequencing Data of Selected Wheat ( Triticum aestivum) Germplasm From Pakistan. Front Genet 2021; 12:617772. [PMID: 34163518 PMCID: PMC8216712 DOI: 10.3389/fgene.2021.617772] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Accepted: 03/19/2021] [Indexed: 11/13/2022] Open
Affiliation(s)
- Madiha Islam
- Department of Biotechnology and Genetic Engineering, Hazara University, Mansehra, Pakistan
| | - Abdullah
- Department of Biochemistry, Quaid-i-Azam University, Islamabad, Pakistan
| | - Bibi Zubaida
- Department of Biotechnology and Genetic Engineering, Hazara University, Mansehra, Pakistan
| | - Nageena Amin
- Institute of Molecular Biology and Biotechnology, Bahauddin Zakariya University, Multan, Pakistan
| | - Rashid Iqbal Khan
- Institute of Horticultural Sciences, University of Agriculture, Faisalabad, Pakistan
| | - Noshin Shafqat
- Department of Agriculture, Hazara University, Mansehra, Pakistan
| | - Rabia Masood
- Department of Botany, Hazara University, Mansehra, Pakistan
| | | | - Jibran Tahir
- Terrestrial Bioscience New Zealand Limited, Auckland, New Zealand
| | - Ibrar Ahmed
- Alpha Genomics Private Limited, Islamabad, Pakistan
| | - Muhammad Naeem
- Federal Seed Certification and Registration Department, Islamabad, Pakistan
| | - Habib Ahmad
- Department of Biotechnology and Genetic Engineering, Hazara University, Mansehra, Pakistan
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Tilwari A, Sharma R. Random amplified polymorphic DNA and inter simple sequence repeat markers reveals genetic diversity between micro propagated, wild and field cultivated genotypes of Gloriosa superba: an endangered medicinal plant. Mol Biol Rep 2021; 48:2437-2452. [PMID: 33768370 DOI: 10.1007/s11033-021-06278-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Accepted: 03/11/2021] [Indexed: 12/27/2022]
Abstract
Gloriosa superba L., an endangered medicinal plant with global interest due to presence of colchicine, an important alkaloid used in formulations of Indian and Traditional medicine. The plant has become endangered due to its unscientifically exploitation and high medicinal values. In the Present study 10 randomly amplified polymorphic DNA (RAPD) and 6 ISSR markers were employed to assess genetic divergence among micro propagated, wild and field cultivated plants of Gloriosa superba collected from different parts of India. In RAPD analysis, all the 10 accession with 10 RAPD primers amplified 466 fragments, with 96.43 % polymorphism and with an average of 46.6 bands per primer. The size of amplicons varied from 1656 to 100 bp. While, ISSR primers produced 328 fragments of which 298 were polymorphic with an average of 49.7 bands per primer with 91.83% polymorphism. The size of amplicons ranges from 2395 to 181 bp. RAPD, ISSR markers were also assessed by calculating polymorphic information content (PIC) to discriminate the genotypes, Average PIC value for RAPD, ISSR and combined RAPD + ISSR markers obtained was ≤ 0.50 suggesting the informativeness of markers. Jaccard's coefficient ranges from 0.18 to 0.75 (RAPD) and 0.17 to 0.61 (ISSR) and 0.21-0.52 for pooled ISSR and RAPD markers. The clustering pattern based on UPGMA analysis of the genotypes in the combined analysis revealed that the majority of the genotypes remained similar to the ISSR dendrogram, while the RAPD-based dendrogram showed some variation in the clustering of genotypes. The result of PCA scattered plot obtained were in agreement with the UPGMA dendrogram, which further confirms the genetic relationships explain by cluster analysis. Results confirmed that the genotype studied had good genetic diversity and can be used for identification, conservation, and future breeding program of Gloriosa species and consequently for the benefit of the pharmaceutical industries.
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Affiliation(s)
- Anita Tilwari
- Centre of Excellence in Biotechnology, M.P. Council of Science and Technology, Vigyan Bhawan, Nehru Nagar, Bhopal, Madhya Pradesh, 462003, India.
| | - Rajesh Sharma
- Centre of Excellence in Biotechnology, M.P. Council of Science and Technology, Vigyan Bhawan, Nehru Nagar, Bhopal, Madhya Pradesh, 462003, India
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DNA Fingerprinting and Species Identification Uncovers the Genetic Diversity of Katsouni Pea in the Greek Islands Amorgos and Schinoussa. PLANTS 2020; 9:plants9040479. [PMID: 32283704 PMCID: PMC7238155 DOI: 10.3390/plants9040479] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/21/2020] [Revised: 04/04/2020] [Accepted: 04/05/2020] [Indexed: 11/17/2022]
Abstract
Pea (P. sativum L.), one of the most important legume crops worldwide, has been traditionally cultivated in Lesser Cyclades since ancient times. The commonly known traditional pea cultivar, ‘Katsouni’, is endemic to the islands of Amorgos and Schinoussa and is of great local economic importance. Despite the widespread cultivation of ‘Katsouni’ in both islands, it is still unknown whether the current Schinoussa and Amorgos pea populations are distinct landraces, and if they have common evolutionary origin. To assist conservation and breeding of the pea crop, the genetic diversity and phylogenetic relationships of 39 pea samples from Amorgos and 86 from Schinoussa were studied using DNA barcoding and ISSR marker analyses. The results indicate that both populations are different landraces with distinct geographical distribution and are more closely related to P. sativum subsp. elatius than the P. abyssinicum and P. fulvum species. Further characterization of the ‘Katsouni’ landraces for functional polymorphisms regarding pathogen resistance, revealed susceptibility to the powdery mildew (Erysiphe pisi DC.). This work represents the first investigation on the genetic diversity and population structure of the ‘Katsouni’ cultivar. Exploiting the local genetic diversity of traditional landraces is fundamental for conservation practices and crop improvement through breeding strategies.
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Gali KK, Sackville A, Tafesse EG, Lachagari VR, McPhee K, Hybl M, Mikić A, Smýkal P, McGee R, Burstin J, Domoney C, Ellis TN, Tar'an B, Warkentin TD. Genome-Wide Association Mapping for Agronomic and Seed Quality Traits of Field Pea ( Pisum sativum L.). FRONTIERS IN PLANT SCIENCE 2019; 10:1538. [PMID: 31850030 PMCID: PMC6888555 DOI: 10.3389/fpls.2019.01538] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Accepted: 11/04/2019] [Indexed: 05/24/2023]
Abstract
Genome-wide association study (GWAS) was conducted to identify loci associated with agronomic (days to flowering, days to maturity, plant height, seed yield and seed weight), seed morphology (shape and dimpling), and seed quality (protein, starch, and fiber concentrations) traits of field pea (Pisum sativum L.). A collection of 135 pea accessions from 23 different breeding programs in Africa (Ethiopia), Asia (India), Australia, Europe (Belarus, Czech Republic, Denmark, France, Lithuania, Netherlands, Russia, Sweden, Ukraine and United Kingdom), and North America (Canada and USA), was used for the GWAS. The accessions were genotyped using genotyping-by-sequencing (GBS). After filtering for a minimum read depth of five, and minor allele frequency of 0.05, 16,877 high quality SNPs were selected to determine marker-trait associations (MTA). The LD decay (LD1/2max,90) across the chromosomes varied from 20 to 80 kb. Population structure analysis grouped the accessions into nine subpopulations. The accessions were evaluated in multi-year, multi-location trials in Olomouc (Czech Republic), Fargo, North Dakota (USA), and Rosthern and Sutherland, Saskatchewan (Canada) from 2013 to 2017. Each trait was phenotyped in at least five location-years. MTAs that were consistent across multiple trials were identified. Chr5LG3_566189651 and Chr5LG3_572899434 for plant height, Chr2LG1_409403647 for lodging resistance, Chr1LG6_57305683 and Chr1LG6_366513463 for grain yield, Chr1LG6_176606388, Chr2LG1_457185, Chr3LG5_234519042 and Chr7LG7_8229439 for seed starch concentration, and Chr3LG5_194530376 for seed protein concentration were identified from different locations and years. This research identified SNP markers associated with important traits in pea that have potential for marker-assisted selection towards rapid cultivar improvement.
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Affiliation(s)
- Krishna Kishore Gali
- Crop Development Centre, Department of Plant Sciences, University of Saskatchewan, Saskatoon, SK, Canada
| | - Alison Sackville
- Crop Development Centre, Department of Plant Sciences, University of Saskatchewan, Saskatoon, SK, Canada
| | - Endale G. Tafesse
- Crop Development Centre, Department of Plant Sciences, University of Saskatchewan, Saskatoon, SK, Canada
| | | | - Kevin McPhee
- Department of Plant Sciences and Plant Pathology, Montana State University, Bozeman, MT, United States
| | - Mick Hybl
- Crop Research Institute/Department of Genetic Resources for Vegetables, Medicinal and Special Plants, Olomouc, Czechia
| | - Alexander Mikić
- Forage Crops Department, Institute of Field and Vegetable Crops, Novi Sad, Serbia
| | - Petr Smýkal
- Department of Botany, Palacký University, Olomouc, Czechia
| | - Rebecca McGee
- Grain Legume Genetics and Physiology Research Unit, USDA, ARS, Pullman, WA, United States
| | | | - Claire Domoney
- Department of Metabolic Biology, John Innes Centre, Norwich, United Kingdom
| | - T.H. Noel Ellis
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Bunyamin Tar'an
- Crop Development Centre, Department of Plant Sciences, University of Saskatchewan, Saskatoon, SK, Canada
| | - Thomas D. Warkentin
- Crop Development Centre, Department of Plant Sciences, University of Saskatchewan, Saskatoon, SK, Canada
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Bogdanova VS, Mglinets AV, Shatskaya NV, Kosterin OE, Solovyev VI, Vasiliev GV. Cryptic divergences in the genus Pisum L. (peas), as revealed by phylogenetic analysis of plastid genomes. Mol Phylogenet Evol 2018; 129:280-290. [PMID: 30195476 DOI: 10.1016/j.ympev.2018.09.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Revised: 09/02/2018] [Accepted: 09/03/2018] [Indexed: 10/28/2022]
Abstract
Organellar genomes may shed light on complicated patterns of plant evolution at inter- and intraspecies level. Primary structure of plastid genomes sequenced in this study and taken from public databases was characterised and compared in 22 diverse, mostly wild representatives of the genus Pisum (peas). Phylogenetic trees reconstructed via Bayesian approach on the basis of entire plastid genomes resembled those reconstructed on the basis of a nuclear gene His5 coding for a minor histone H1 subtype. They reveal Pisum fulvum as an early divergence of the genus but do not support other taxonomical subdivisions. The positions of three accessions, classified as P. sativum subsp. elatius (the wild subspecies of the common pea), appeared quite unexpected. On the entire plastid genome tree, two accessions, from the Black Sea area of Turkey and Georgia, clustered with representatives of another species, P. fulvum, while the other, from Greece, was the first divergence of the P. sativum branch. We suppose these unusual plastid genomes to be ancient lineages ascending to a 'missing link' between P. fulvum and P. sativum, represented by accession Pe 013 from Turkey. Accessions with common pea appearance but deeply diverged plastids could occur through occasional crossing of diverged pea lines in the past and biparental plastid inheritance, both events being possible in peas.
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Affiliation(s)
- Vera S Bogdanova
- Institute of Cytology and Genetics of Siberian Division of Russian Academy of Sciences, Novosibirsk, Russia
| | - Anatoliy V Mglinets
- Institute of Cytology and Genetics of Siberian Division of Russian Academy of Sciences, Novosibirsk, Russia
| | - Natalia V Shatskaya
- Institute of Cytology and Genetics of Siberian Division of Russian Academy of Sciences, Novosibirsk, Russia
| | - Oleg E Kosterin
- Institute of Cytology and Genetics of Siberian Division of Russian Academy of Sciences, Novosibirsk, Russia; Novosibirsk State University, Novosibirsk, Russia.
| | - Vladimir I Solovyev
- Institute of Cytology and Genetics of Siberian Division of Russian Academy of Sciences, Novosibirsk, Russia; Novosibirsk State University, Novosibirsk, Russia
| | - Gennadiy V Vasiliev
- Institute of Cytology and Genetics of Siberian Division of Russian Academy of Sciences, Novosibirsk, Russia
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Trněný O, Brus J, Hradilová I, Rathore A, Das RR, Kopecký P, Coyne CJ, Reeves P, Richards C, Smýkal P. Molecular Evidence for Two Domestication Events in the Pea Crop. Genes (Basel) 2018; 9:genes9110535. [PMID: 30404223 PMCID: PMC6265838 DOI: 10.3390/genes9110535] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Revised: 10/25/2018] [Accepted: 10/29/2018] [Indexed: 12/02/2022] Open
Abstract
Pea, one of the founder crops from the Near East, has two wild species: Pisum sativum subsp. elatius, with a wide distribution centered in the Mediterranean, and P. fulvum, which is restricted to Syria, Lebanon, Israel, Palestine and Jordan. Using genome wide analysis of 11,343 polymorphic single nucleotide polymorphisms (SNPs) on a set of wild P. elatius (134) and P. fulvum (20) and 74 domesticated accessions (64 P. sativum landraces and 10 P. abyssinicum), we demonstrated that domesticated P. sativum and the Ethiopian pea (P. abyssinicum) were derived from different P. elatius genepools. Therefore, pea has at least two domestication events. The analysis does not support a hybrid origin of P. abyssinicum, which was likely introduced into Ethiopia and Yemen followed by eco-geographic adaptation. Both P. sativum and P. abyssinicum share traits that are typical of domestication, such as non-dormant seeds. Non-dormant seeds were also found in several wild P. elatius accessions which could be the result of crop to wild introgression or natural variation that may have been present during pea domestication. A sub-group of P. elatius overlaps with P. sativum landraces. This may be a consequence of bidirectional gene-flow or may suggest that this group of P. elatius is the closest extant wild relative of P. sativum.
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Affiliation(s)
- Oldřich Trněný
- Agricultural Research Ltd., 66441 Troubsko, Czech Republic.
| | - Jan Brus
- Department of Geoinformatics, Palacký University, 783 71 Olomouc, Czech Republic.
| | - Iveta Hradilová
- Department of Botany, Palacký University, 783 71 Olomouc, Czech Republic.
| | - Abhishek Rathore
- The International Crops Research Institute for the Semi-Arid Tropics, Hyderabad, Telangana 502324, India.
| | - Roma R Das
- The International Crops Research Institute for the Semi-Arid Tropics, Hyderabad, Telangana 502324, India.
| | - Pavel Kopecký
- Crop Research Institute, The Centre of the Region Haná for biotechnological and Agricultural Research, 783 71 Olomouc, Czech Republic.
| | - Clarice J Coyne
- United States Department of Agriculture, Washington State University, Pullman, WA 99164-6402, USA.
| | - Patrick Reeves
- United States Department of Agriculture, National Laboratory for Genetic Resources Preservation, Fort Collins, CO 80521, USA.
| | - Christopher Richards
- United States Department of Agriculture, National Laboratory for Genetic Resources Preservation, Fort Collins, CO 80521, USA.
| | - Petr Smýkal
- Department of Botany, Palacký University, 783 71 Olomouc, Czech Republic.
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Naik A, Prajapat P, Krishnamurthy R, Pathak JM. Assessment of genetic diversity in Costus pictus accessions based on RAPD and ISSR markers. 3 Biotech 2017; 7:70. [PMID: 28452016 DOI: 10.1007/s13205-017-0667-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2017] [Accepted: 02/21/2017] [Indexed: 11/28/2022] Open
Abstract
Costus pictus, belonging to the family Costaceae, is one of the valuable medicinal plants with its anti-diabetic property. Despite ever-increasing demand from the pharmaceutical industry, this species is being less exploited at molecular level. Hence, an effort has been made in the present study to characterize the 15 accessions of C. pictus collected from different geographical regions of India through random amplified polymorphic DNA (RAPD) and inter-simple sequence repeats (ISSR) markers. A total of 25 RAPD and 20 ISSR primers were used in the present study. The RAPD analysis generated 343 loci, of which 124 were polymorphic with an average of 4.96 loci per primer. While, ISSR primers produced 177 loci, of which 77 were polymorphic with an average of 3.85 loci per primer. The similarity coefficients ranged from 0.86-0.99, 0.84-0.95 and 0.86-0.96 for RAPD, ISSR and combined RAPD-ISSR, respectively. The UPGMA dendrogram generated using these data showed low level of divergence among the accessions from South and West regions. Further, accession-specific bands were also revealed by RAPD and ISSR markers which might be contributed to specific trait. This investigation was an understanding of genetic variation within the C. pictus accessions. The present finding indicates that both the marker tools RAPD and ISSR combined or individually can be used in determining the genetic relationship between the accessions. It may be concluded that data of hereditary differences appeared among the C. pictus accessions could be utilized for their conservation and reproducing programs.
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Affiliation(s)
- Ami Naik
- C. G. Bhakta Institute of Biotechnology, Uka Tarsadia University, Tarsadia, Surat, Gujarat, 396350, India
| | - Pravin Prajapat
- ICAR-Directorate of Medicinal and Aromatic Plants Research, Boriavi, Gujarat, 387310, India
| | - R Krishnamurthy
- C. G. Bhakta Institute of Biotechnology, Uka Tarsadia University, Tarsadia, Surat, Gujarat, 396350, India.
| | - J M Pathak
- Zandu Foundation for Health Care, Pardi, Valsad, Gujarat, 396145, India
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Holdsworth WL, Gazave E, Cheng P, Myers JR, Gore MA, Coyne CJ, McGee RJ, Mazourek M. A community resource for exploring and utilizing genetic diversity in the USDA pea single plant plus collection. HORTICULTURE RESEARCH 2017; 4:17017. [PMID: 28503311 PMCID: PMC5405346 DOI: 10.1038/hortres.2017.17] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2017] [Revised: 04/07/2017] [Accepted: 04/09/2017] [Indexed: 05/04/2023]
Abstract
Globally, pea (Pisum sativum L.) is an important temperate legume crop for food, feed and fodder, and many breeding programs develop cultivars adapted to these end-uses. In order to assist pea development efforts, we assembled the USDA Pea Single Plant Plus Collection (PSPPC), which contains 431 P. sativum accessions with morphological, geographic and taxonomic diversity. The collection was characterized genetically in order to maximize its value for trait mapping and genomics-assisted breeding. To that end, we used genotyping-by-sequencing-a cost-effective method for de novo single-nucleotide polymorphism (SNP) marker discovery-to generate 66 591 high-quality SNPs. These data facilitated the identification of accessions divergent from mainstream breeding germplasm that could serve as sources of novel, favorable alleles. In particular, a group of accessions from Central Asia appear nearly as diverse as a sister species, P. fulvum, and subspecies, P. sativum subsp. elatius. PSPPC genotypes can be paired with new and existing phenotype data for trait mapping; as proof-of-concept, we localized Mendel's A gene controlling flower color to its known position. We also used SNP data to define a smaller core collection of 108 accessions with similar levels of genetic diversity as the entire PSPPC, resulting in a smaller germplasm set for research screening and evaluation under limited resources. Taken together, the results presented in this study along with the release of a publicly available SNP data set comprise a valuable resource for supporting worldwide pea genetic improvement efforts.
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Affiliation(s)
- William L. Holdsworth
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA
| | - Elodie Gazave
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA
| | - Peng Cheng
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA 99164, USA
| | - James R. Myers
- Department of Horticulture, Oregon State University, Corvallis, OR 97331, USA
| | - Michael A. Gore
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA
| | - Clarice J. Coyne
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA 99164, USA
- US Department of Agriculture, Agricultural Research Service, Western Regional Plant Introduction Station, Pullman, WA 99164, USA
| | - Rebecca J. McGee
- US Department of Agriculture, Agricultural Research Service, Grain Legume Genetics and Physiology Research Unit, Pullman, WA 99164, USA
| | - Michael Mazourek
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA
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Kumar A, Mishra P, Baskaran K, Shukla AK, Shasany AK, Sundaresan V. Higher efficiency of ISSR markers over plastid psbA-trnH region in resolving taxonomical status of genus Ocimum L. Ecol Evol 2016; 6:7671-7682. [PMID: 30128120 PMCID: PMC6093152 DOI: 10.1002/ece3.2483] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Revised: 08/19/2016] [Accepted: 08/22/2016] [Indexed: 11/23/2022] Open
Abstract
High level of morphological as well as chemical variability exists within the genus Ocimum, and its taxonomy and phylogenetic relationships are still doubtful. For evaluating interspecific genetic relationships among the Ocimum species, genotyping with intersimple sequence repeat (ISSR) markers and sequence analyses of noncoding psbA‐trnH intergenic region belonging to chloroplast DNA were carried out. Although ISSR markers are highly efficient and reproducible, they have not been used extensively in phylogenetic studies. The use of the plastidial barcode candidate was expected to provide more variable and informative insight into evolutionary rates, and was thus employed as a phylogenetic marker to assess interspecific relationships. This study revealed that the ISSR markers were more efficient than psbA‐trnH sequences in resolving the current status of Ocimum L. genus. Distance‐ and character‐based methodological approaches applied on the molecular data with biparental and maternal inheritance were used for deducing the phylogenetic relationships among Ocimum species. Average polymorphic information content (0.344) and resolving power (6.285) depicted through ISSR markers proved to be efficient in discriminating the studied species of Ocimum. The primers used in this study revealed 99.585% polymorphism across the species demonstrating the polymorphic nature of ISSR markers.
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Affiliation(s)
- Amit Kumar
- Department of Plant Biology and Systematics CSIR - Central Institute of Medicinal and Aromatic Plants, Research Centre Bengaluru India
| | - Priyanka Mishra
- Department of Plant Biology and Systematics CSIR - Central Institute of Medicinal and Aromatic Plants, Research Centre Bengaluru India
| | - Kuppusamy Baskaran
- Department of Plant Biology and Systematics CSIR - Central Institute of Medicinal and Aromatic Plants, Research Centre Bengaluru India
| | - Ashutosh K Shukla
- Biotechnology Division CSIR - Central Institute of Medicinal and Aromatic Plants Lucknow India
| | - Ajit K Shasany
- Biotechnology Division CSIR - Central Institute of Medicinal and Aromatic Plants Lucknow India
| | - Velusamy Sundaresan
- Department of Plant Biology and Systematics CSIR - Central Institute of Medicinal and Aromatic Plants, Research Centre Bengaluru India
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Solberg SØ, Brantestam AK, Olsson K, Leino MW, Weibull J, Yndgaard F. Diversity in local cultivars of Pisum sativum collected from home gardens in Sweden. BIOCHEM SYST ECOL 2015. [DOI: 10.1016/j.bse.2015.09.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Patel HK, Fougat RS, Kumar S, Mistry JG, Kumar M. Detection of genetic variation in Ocimum species using RAPD and ISSR markers. 3 Biotech 2015; 5:697-707. [PMID: 28324522 PMCID: PMC4569613 DOI: 10.1007/s13205-014-0269-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2014] [Accepted: 11/20/2014] [Indexed: 11/29/2022] Open
Abstract
There is a lack of information on the molecular characterization of Ocimum species and hence, efforts have been made under the present study to characterize 17 Ocimum genotypes belonging to 5 different species (O. basilicum, O. americanum, O. sanctum, O. gratissimum and O. Polystachyon) through random amplified polymorphic DNA (RAPD) and inter simple sequence repeats (ISSR) markers. PCR amplification using 20 RAPD primers generated a total of 506 loci, of which 490 (96.47 %) loci were found polymorphic. The PIC value for RAPD ranged from 0.907 (OPF 14) to 0.954 (OPC 11) with an average of 0.937. The ISSR primers generated a total of 238 loci, of them 234 (98.17 %) loci were polymorphic. The PIC value ranged from 0.892 (UBC 808) to 0.943 (ISSR A12) with an average of 0.923. The average Jaccard’s similarity coefficient based on RAPD and ISSR analysis was 0.58 and 0.52, respectively. Clustering pattern of dendrogram generated using the pooled RAPD and ISSR data showed all Ocimum genotypes in their respective species groups at a cutoff value of 0.49 and 0.42, respectively. Many unique species-specific alleles were amplified by RAPD and ISSR markers. In both marker systems, a maximum number of unique alleles were observed in O. sanctum. The results of the present investigation provided valid guidelines for collection, conservation and characterization of Ocimum genetic resources.
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Teshome A, Bryngelsson T, Dagne K, Geleta M. Assessment of genetic diversity in Ethiopian field pea (Pisum sativum L.) accessions with newly developed EST-SSR markers. BMC Genet 2015; 16:102. [PMID: 26286720 PMCID: PMC4541747 DOI: 10.1186/s12863-015-0261-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2015] [Accepted: 08/06/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Field pea (Pisum sativum L.) is among the prominent crops in the world as food and feed. There are relatively few simple sequence repeat (SSR) markers developed from expressed sequence tags (ESTs) in P. sativum. RESULTS In the present study, 15 new EST-SSR markers were developed from publicly available ESTs. These markers have successfully amplified their target loci across seven Pisum sativum subsp. sativum accessions. Eleven (73%) of these SSRs were trinucleotide repeats, two (13%) dinucleotide and two (13%) were hexanucleotide repeats. Across-taxa transferability of these new markers was also tested on other subspecies of Pisum as well as on P. fulvum, Vicia faba and Lens culinaris. In Pisum sativum subsp. sativum, 13 of the 15 markers were polymorphic and 12 of them subsequently used for genetic diversity analysis. Forty six accessions, of which 43 were from Ethiopia, were subjected to genetic diversity analysis using these newly developed markers. All accessions were represented by 12 individuals except two (NGB103816 and 237508) that were represented by 9 and 11 individuals, respectively. A total of 37 alleles were detected across all accessions. PS10 was the most polymorphic locus with six alleles, and the average number of alleles per locus over the 12 polymorphic loci was 3.1. Several rare and private alleles were also revealed. The most distinct accession (32048) had private alleles at three loci with 100% frequency. CONCLUSION These newly developed EST-SSR primer-pairs successfully amplified expected loci in P. sativum subsp. sativum as well as in other subspecies of the genus Pisum and related genera. High levels of genetic variation were detected in field pea accessions from Ethiopia using these markers. This result implies the potential of the Ethiopian field pea gene pool for improvement of field peas in various desirable traits. In addition, these markers could be a valuable asset in resolving the inconsistency in the taxonomic status of the different subspecies of genus Pisum as well as for characterization of field pea accessions in different gene banks around the world for breeding and conservation purposes.
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Affiliation(s)
- Abel Teshome
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Box 101, SE-23053, Alnarp, Sweden.
| | - Tomas Bryngelsson
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Box 101, SE-23053, Alnarp, Sweden.
| | - Kifle Dagne
- Department of Microbial, Cellular and Molecular Biology, Addis Ababa University, P. O. Box 1176, Addis Ababa, Ethiopia.
| | - Mulatu Geleta
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Box 101, SE-23053, Alnarp, Sweden.
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Nasiri J, Naghavi MR, Kayvanjoo AH, Nasiri M, Ebrahimi M. Precision assessment of some supervised and unsupervised algorithms for genotype discrimination in the genus Pisum using SSR molecular data. J Theor Biol 2015; 368:122-32. [PMID: 25591889 DOI: 10.1016/j.jtbi.2015.01.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2014] [Revised: 11/06/2014] [Accepted: 01/01/2015] [Indexed: 10/24/2022]
Abstract
For the first time, prediction accuracies of some supervised and unsupervised algorithms were evaluated in an SSR-based DNA fingerprinting study of a pea collection containing 20 cultivars and 57 wild samples. In general, according to the 10 attribute weighting models, the SSR alleles of PEAPHTAP-2 and PSBLOX13.2-1 were the two most important attributes to generate discrimination among eight different species and subspecies of genus Pisum. In addition, K-Medoids unsupervised clustering run on Chi squared dataset exhibited the best prediction accuracy (83.12%), while the lowest accuracy (25.97%) gained as K-Means model ran on FCdb database. Irrespective of some fluctuations, the overall accuracies of tree induction models were significantly high for many algorithms, and the attributes PSBLOX13.2-3 and PEAPHTAP could successfully detach Pisum fulvum accessions and cultivars from the others when two selected decision trees were taken into account. Meanwhile, the other used supervised algorithms exhibited overall reliable accuracies, even though in some rare cases, they gave us low amounts of accuracies. Our results, altogether, demonstrate promising applications of both supervised and unsupervised algorithms to provide suitable data mining tools regarding accurate fingerprinting of different species and subspecies of genus Pisum, as a fundamental priority task in breeding programs of the crop.
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Affiliation(s)
- Jaber Nasiri
- Department of Agronomy and Plant Breeding, Division of Molecular Plant Genetics, College of Agricultural & Natural Resources, University of Tehran, Karaj, Tehran, Iran.
| | - Mohammad Reza Naghavi
- Department of Agronomy and Plant Breeding, College of Agricultural & Natural Resources, University of Tehran, Karaj, Tehran, Iran.
| | | | - Mojtaba Nasiri
- School of Life Sciences, Biomedical Science, Division of Molecular Biology, University of Sussex, Falmer, Brighton, UK.
| | - Mansour Ebrahimi
- Department of Biology, School of Basic Sciences, University of Qom, Qom, Iran.
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Burstin J, Salloignon P, Chabert-Martinello M, Magnin-Robert JB, Siol M, Jacquin F, Chauveau A, Pont C, Aubert G, Delaitre C, Truntzer C, Duc G. Genetic diversity and trait genomic prediction in a pea diversity panel. BMC Genomics 2015; 16:105. [PMID: 25765216 PMCID: PMC4355348 DOI: 10.1186/s12864-015-1266-1] [Citation(s) in RCA: 68] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2014] [Accepted: 01/22/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Pea (Pisum sativum L.), a major pulse crop grown for its protein-rich seeds, is an important component of agroecological cropping systems in diverse regions of the world. New breeding challenges imposed by global climate change and new regulations urge pea breeders to undertake more efficient methods of selection and better take advantage of the large genetic diversity present in the Pisum sativum genepool. Diversity studies conducted so far in pea used Simple Sequence Repeat (SSR) and Retrotransposon Based Insertion Polymorphism (RBIP) markers. Recently, SNP marker panels have been developed that will be useful for genetic diversity assessment and marker-assisted selection. RESULTS A collection of diverse pea accessions, including landraces and cultivars of garden, field or fodder peas as well as wild peas was characterised at the molecular level using newly developed SNP markers, as well as SSR markers and RBIP markers. The three types of markers were used to describe the structure of the collection and revealed different pictures of the genetic diversity among the collection. SSR showed the fastest rate of evolution and RBIP the slowest rate of evolution, pointing to their contrasted mode of evolution. SNP markers were then used to predict phenotypes -the date of flowering (BegFlo), the number of seeds per plant (Nseed) and thousand seed weight (TSW)- that were recorded for the collection. Different statistical methods were tested including the LASSO (Least Absolute Shrinkage ans Selection Operator), PLS (Partial Least Squares), SPLS (Sparse Partial Least Squares), Bayes A, Bayes B and GBLUP (Genomic Best Linear Unbiased Prediction) methods and the structure of the collection was taken into account in the prediction. Despite a limited number of 331 markers used for prediction, TSW was reliably predicted. CONCLUSION The development of marker assisted selection has not reached its full potential in pea until now. This paper shows that the high-throughput SNP arrays that are being developed will most probably allow for a more efficient selection in this species.
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Affiliation(s)
- Judith Burstin
- UMR1347, Agroecology, INRA, 17 rue de Sully, Dijon Cedex, 21065, France.
| | - Pauline Salloignon
- Clinical and Innovation Proteomic Platform (CLIPP), CHU Dijon, Université de Bourgogne, 1 rue du Professeur Marion, Dijon, 21000, France.
| | | | | | - Mathieu Siol
- UMR1347, Agroecology, INRA, 17 rue de Sully, Dijon Cedex, 21065, France.
| | - Françoise Jacquin
- UMR1347, Agroecology, INRA, 17 rue de Sully, Dijon Cedex, 21065, France.
| | - Aurélie Chauveau
- UMR1347, Agroecology, INRA, 17 rue de Sully, Dijon Cedex, 21065, France.
- Present address: US EPGV, IG-CEA, Centre National de Génotypage, 2 rue Gaston Crémieux, Evry Cedex, 91057, France.
| | - Caroline Pont
- UMR GDEC, Plateforme Gentyane, Clermont Ferrand, 63100, France.
| | - Grégoire Aubert
- UMR1347, Agroecology, INRA, 17 rue de Sully, Dijon Cedex, 21065, France.
| | - Catherine Delaitre
- UMR1347, Agroecology, INRA, 17 rue de Sully, Dijon Cedex, 21065, France.
| | - Caroline Truntzer
- Clinical and Innovation Proteomic Platform (CLIPP), CHU Dijon, Université de Bourgogne, 1 rue du Professeur Marion, Dijon, 21000, France.
| | - Gérard Duc
- UMR1347, Agroecology, INRA, 17 rue de Sully, Dijon Cedex, 21065, France.
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Jain S, Kumar A, Mamidi S, McPhee K. Genetic diversity and population structure among pea (Pisum sativum L.) cultivars as revealed by simple sequence repeat and novel genic markers. Mol Biotechnol 2014; 56:925-38. [PMID: 24894738 DOI: 10.1007/s12033-014-9772-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Field pea (Pisum sativum L.) is an important cool season legume crop widely grown around the world. This research provides a basis for selection of pea germplasm across geographical regions in current and future breeding and genetic mapping efforts for pea improvement. Eleven novel genic markers were developed from pea expressed sequence tag (EST) sequences having significant similarity with gene calls from Medicago truncatula spanning at least one intron. In this study, 96 cultivars widely grown or used in breeding programs in the USA and Canada were analyzed for genetic diversity using 31 microsatellite or simple sequence repeat (SSR) and 11 novel EST-derived genic markers. The polymorphic information content varied from 0.01-0.56 among SSR markers and 0.04-0.43 among genic markers. The results showed that SSR and EST-derived genic markers displayed one or more highly reproducible, multi-allelic, and easy to score loci ranging from 200 to 700 bp in size. Genetic diversity was assessed through unweighted neighbor-joining method, and 96 varieties were grouped into three main clusters based on the dissimilarity matrix. Four subpopulations were determined through STRUCTURE analysis with no significant geographic separation of the subpopulations. The findings of the present study can be used to select diverse genotypes to be used as parents of crosses aimed for breeding improved pea cultivars.
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Affiliation(s)
- Shalu Jain
- Department of Plant Sciences, North Dakota State University, Fargo, ND, 58108, USA
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Ali MN, Yeasmin L, Gantait S, Goswami R, Chakraborty S. Screening of rice landraces for salinity tolerance at seedling stage through morphological and molecular markers. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2014; 20:411-23. [PMID: 25320465 PMCID: PMC4185050 DOI: 10.1007/s12298-014-0250-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2014] [Revised: 05/29/2014] [Accepted: 06/24/2014] [Indexed: 05/24/2023]
Abstract
The present investigation was carried out to evaluate 33 rice landrace genotypes for assessment of their salt tolerance at seedling stage. Growth parameters like root length, shoot length and plant biomass were measured after 12 days of exposure to six different levels of saline solution (with electrical conductivity of 4, 6, 8, 10, 12 or 14 dS m (-1)). Genotypes showing significant interaction and differential response towards salinity were assessed at molecular level using 11 simple sequence repeats (SSR) markers, linked with salt tolerance quantitative trait loci. Shoot length, root length and plant biomass at seedling stage decreased with increasing salinity. However, relative salt tolerance in terms of these three parameters varied among genotypes. Out of the 11 SSR markers RM8094, RM336 and RM8046, the most competent descriptors to screen the salt tolerant genotypes with higher polymorphic information content coupled with higher marker index value, significantly distinguished the salt tolerant genotypes. Combining morphological and molecular assessment, four lanraces viz. Gheus, Ghunsi, Kuthiahara and Sholerpona were considered as true salt tolerant genotypes which may contribute in greater way in the development of salt tolerant genotypes in rice.
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Affiliation(s)
- Md. Nasim Ali
- />Department of Agricultural Biotechnology, Faculty Centre for Integrated Rural Development and Management, School of Agriculture and Rural Development, Ramakrishna Mission Ashrama, Narendrapur, Ramakrishna Mission Vivekananda University, Kolkata, 700103 India
| | - Lucina Yeasmin
- />Department of Agricultural Biotechnology, Faculty Centre for Integrated Rural Development and Management, School of Agriculture and Rural Development, Ramakrishna Mission Ashrama, Narendrapur, Ramakrishna Mission Vivekananda University, Kolkata, 700103 India
| | - Saikat Gantait
- />Department of Crop Science, Faculty of Agriculture, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia
- />Sasya Shyamala Krishi Vigyan Kendra, Ramakrishna Mission Vivekananda University, Arapanch, Sonarpur, Kolkata, 700150 India
| | - Rupak Goswami
- />Department of Agricultural Biotechnology, Faculty Centre for Integrated Rural Development and Management, School of Agriculture and Rural Development, Ramakrishna Mission Ashrama, Narendrapur, Ramakrishna Mission Vivekananda University, Kolkata, 700103 India
| | - Somsubhra Chakraborty
- />Department of Agricultural Biotechnology, Faculty Centre for Integrated Rural Development and Management, School of Agriculture and Rural Development, Ramakrishna Mission Ashrama, Narendrapur, Ramakrishna Mission Vivekananda University, Kolkata, 700103 India
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Dyachenko EA, Ryzhova NN, Vishnyakova MA, Kochieva EZ. Molecular genetic diversity of the pea (Pisum sativum L.) from the Vavilov Research Institute collection detected by the AFLP analysis. RUSS J GENET+ 2014. [DOI: 10.1134/s102279541409004x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Peng L, Ru M, Wang B, Wang Y, Li B, Yu J, Liang Z. Genetic diversity assessment of a germplasm collection of Salvia miltiorrhiza Bunge. based on morphology, ISSR and SRAP markers. BIOCHEM SYST ECOL 2014. [DOI: 10.1016/j.bse.2014.01.020] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Jing R, Ambrose MA, Knox MR, Smykal P, Hybl M, Ramos Á, Caminero C, Burstin J, Duc G, van Soest LJM, Święcicki WK, Pereira MG, Vishnyakova M, Davenport GF, Flavell AJ, Ellis THN. Genetic diversity in European Pisum germplasm collections. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2012; 125:367-80. [PMID: 22466957 PMCID: PMC3385700 DOI: 10.1007/s00122-012-1839-1] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2011] [Accepted: 02/29/2012] [Indexed: 05/21/2023]
Abstract
The distinctness of, and overlap between, pea genotypes held in several Pisum germplasm collections has been used to determine their relatedness and to test previous ideas about the genetic diversity of Pisum. Our characterisation of genetic diversity among 4,538 Pisum accessions held in 7 European Genebanks has identified sources of novel genetic variation, and both reinforces and refines previous interpretations of the overall structure of genetic diversity in Pisum. Molecular marker analysis was based upon the presence/absence of polymorphism of retrotransposon insertions scored by a high-throughput microarray and SSAP approaches. We conclude that the diversity of Pisum constitutes a broad continuum, with graded differentiation into sub-populations which display various degrees of distinctness. The most distinct genetic groups correspond to the named taxa while the cultivars and landraces of Pisum sativum can be divided into two broad types, one of which is strongly enriched for modern cultivars. The addition of germplasm sets from six European Genebanks, chosen to represent high diversity, to a single collection previously studied with these markers resulted in modest additions to the overall diversity observed, suggesting that the great majority of the total genetic diversity collected for the Pisum genus has now been described. Two interesting sources of novel genetic variation have been identified. Finally, we have proposed reference sets of core accessions with a range of sample sizes to represent Pisum diversity for the future study and exploitation by researchers and breeders.
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Affiliation(s)
- R. Jing
- Division of Plant Sciences, University of Dundee at JHI, Invergowrie, Dundee, DD2 5DA UK
- Present Address: Institut für Biochemie und Biologie, Universität Potsdam, Karl-Liebknecht-Str. 24-25, Haus 26, 14476 Potsdam-Golm, Germany
| | - M. A. Ambrose
- John Innes Centre, Norwich Research Park, Colney Lane, Norwich, NR4 7UH UK
| | - M. R. Knox
- John Innes Centre, Norwich Research Park, Colney Lane, Norwich, NR4 7UH UK
| | - P. Smykal
- Agritec Plant Research Ltd., Zemedelska 2520/16, 787 01 Sumperk, Czech Republic
- Department of Botany, Faculty of Sciences, Palacký University, Slechtitelu 11, 783 71 Olomouc, Czech Republic
| | - M. Hybl
- Agritec Plant Research Ltd., Zemedelska 2520/16, 787 01 Sumperk, Czech Republic
| | - Á. Ramos
- Centro para la calidad de los alimentos, INIA, Campus universitario, 42004 Soria, Spain
| | - C. Caminero
- Instituto Tecnológico Agrario, Consejería de Agricultura y Ganadería de la Junta de Castilla y León, Ctra Burgos, km 119, 47071 Valladolid, Spain
| | - J. Burstin
- Institut National de la Recherche Agronomique (INRA), UMR LEG, 17 rue de Sully-Building B1, Office 110, BP 86510, 21065 Dijon Cédex, France
| | - G. Duc
- Institut National de la Recherche Agronomique (INRA), UMR LEG, 17 rue de Sully-Building B1, Office 110, BP 86510, 21065 Dijon Cédex, France
| | - L. J. M. van Soest
- Centre for Genetic Resources, The Netherlands (CGN), P. O. Box 16, 6700 AA Wageningen, The Netherlands
| | - W. K. Święcicki
- Institute of Plant Genetics, Polish Academy of Sciences, ul. Strzeszyńska 34, 60-479 Poznan, Poland
| | - M. G. Pereira
- Instituto Nacional de Investigação Agrária, Apartado 6, 7350-951 Elvas, Portugal
| | - M. Vishnyakova
- N.I. Vavilov Institute of Plant Industry (VIR), Bolshaya Morskaya Street 42-44, 190000 St. Petersburg, Russian Federation
| | - G. F. Davenport
- Crop Informatics, 211 Malecon Armenariz, Miraflores, Lima, Peru
| | - A. J. Flavell
- Division of Plant Sciences, University of Dundee at JHI, Invergowrie, Dundee, DD2 5DA UK
| | - T. H. N. Ellis
- John Innes Centre, Norwich Research Park, Colney Lane, Norwich, NR4 7UH UK
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Gogerddan, Aberystwyth, SY23 3EB UK
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Kwon SJ, Brown AF, Hu J, McGee R, Watt C, Kisha T, Timmerman-Vaughan G, Grusak M, McPhee KE, Coyne CJ. Genetic diversity, population structure and genome-wide marker-trait association analysis emphasizing seed nutrients of the USDA pea (Pisum sativum L.) core collection. Genes Genomics 2012. [DOI: 10.1007/s13258-011-0213-z] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Kaur S, Pembleton LW, Cogan NOI, Savin KW, Leonforte T, Paull J, Materne M, Forster JW. Transcriptome sequencing of field pea and faba bean for discovery and validation of SSR genetic markers. BMC Genomics 2012; 13:104. [PMID: 22433453 PMCID: PMC3352077 DOI: 10.1186/1471-2164-13-104] [Citation(s) in RCA: 130] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2011] [Accepted: 03/20/2012] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Field pea (Pisum sativum L.) and faba bean (Vicia faba L.) are cool-season grain legume species that provide rich sources of food for humans and fodder for livestock. To date, both species have been relative 'genomic orphans' due to limited availability of genetic and genomic information. A significant enrichment of genomic resources is consequently required in order to understand the genetic architecture of important agronomic traits, and to support germplasm enhancement, genetic diversity, population structure and demographic studies. RESULTS cDNA samples obtained from various tissue types of specific field pea and faba bean genotypes were sequenced using 454 Roche GS FLX Titanium technology. A total of 720,324 and 304,680 reads for field pea and faba bean, respectively, were de novo assembled to generate sets of 70,682 and 60,440 unigenes. Consensus sequences were compared against the genome of the model legume species Medicago truncatula Gaertn., as well as that of the more distantly related, but better-characterised genome of Arabidopsis thaliana L.. In comparison to M. truncatula coding sequences, 11,737 and 10,179 unique hits were obtained from field pea and faba bean. Totals of 22,057 field pea and 18,052 faba bean unigenes were subsequently annotated from GenBank. Comparison to the genome of soybean (Glycine max L.) resulted in 19,451 unique hits for field pea and 16,497 unique hits for faba bean, corresponding to c. 35% and 30% of the known gene space, respectively. Simple sequence repeat (SSR)-containing expressed sequence tags (ESTs) were identified from consensus sequences, and totals of 2,397 and 802 primer pairs were designed for field pea and faba bean. Subsets of 96 EST-SSR markers were screened for validation across modest panels of field pea and faba bean cultivars, as well as related non-domesticated species. For field pea, 86 primer pairs successfully obtained amplification products from one or more template genotypes, of which 59% revealed polymorphism between 6 genotypes. In the case of faba bean, 81 primer pairs displayed successful amplification, of which 48% detected polymorphism. CONCLUSIONS The generation of EST datasets for field pea and faba bean has permitted effective unigene identification and functional sequence annotation. EST-SSR loci were detected at incidences of 14-17%, permitting design of comprehensive sets of primer pairs. The subsets from these primer pairs proved highly useful for polymorphism detection within Pisum and Vicia germplasm.
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Affiliation(s)
- Sukhjiwan Kaur
- Department of Primary Industries, Biosciences Research Division, Victorian AgriBiosciences Centre, 1 Park Drive, La Trobe University Research and Development Park, Bundoora, Victoria 3083, Australia
| | - Luke W Pembleton
- Department of Primary Industries, Biosciences Research Division, Victorian AgriBiosciences Centre, 1 Park Drive, La Trobe University Research and Development Park, Bundoora, Victoria 3083, Australia
| | - Noel OI Cogan
- Department of Primary Industries, Biosciences Research Division, Victorian AgriBiosciences Centre, 1 Park Drive, La Trobe University Research and Development Park, Bundoora, Victoria 3083, Australia
| | - Keith W Savin
- Department of Primary Industries, Biosciences Research Division, Victorian AgriBiosciences Centre, 1 Park Drive, La Trobe University Research and Development Park, Bundoora, Victoria 3083, Australia
| | - Tony Leonforte
- Department of Primary Industries, Biosciences Research Division, Grains Innovation Park, Horsham, Victoria 3401, Australia
| | - Jeffrey Paull
- School of Agriculture, Food and Wine, The University of Adelaide, Waite Campus, Glen Osmond, South Australia 5064, Australia
| | - Michael Materne
- Department of Primary Industries, Biosciences Research Division, Grains Innovation Park, Horsham, Victoria 3401, Australia
| | - John W Forster
- Department of Primary Industries, Biosciences Research Division, Victorian AgriBiosciences Centre, 1 Park Drive, La Trobe University Research and Development Park, Bundoora, Victoria 3083, Australia
- La Trobe University, Bundoora, Victoria 3086, Australia
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Hood-Niefer SD, Warkentin TD, Chibbar RN, Vandenberg A, Tyler RT. Effect of genotype and environment on the concentrations of starch and protein in, and the physicochemical properties of starch from, field pea and fababean. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2012; 92:141-50. [PMID: 21780131 DOI: 10.1002/jsfa.4552] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2010] [Revised: 05/31/2011] [Accepted: 06/06/2011] [Indexed: 05/31/2023]
Abstract
BACKGROUND The effects of genotype and environment and their interaction on the concentrations of starch and protein in, and the amylose content and thermal and pasting properties of starch from, pea and fababean are not well known. RESULTS Differences due to genotype were observed in the concentrations of starch and protein in pea and fababean, in the onset temperature (To) and peak temperature (Tp) of gelatinization of fababean starch, and in the pasting, trough, cooling and final viscosities of pea starch and fababean starch. Significant two-way interactions (location × genotype) were observed for the concentration of starch in fababean and the amylose content, To, endothermic enthalpy of gelatinization (ΔH) and trough viscosity of fababean starch. Significant three-way interactions (location × year × genotype) were observed for the concentration of starch in pea and the pasting, trough, cooling and final viscosities of pea starch. CONCLUSION Differences observed in the concentrations of starch and protein in pea and fababean were sufficient to be of practical significance to end-users, but the relatively small differences in amylose content and physicochemical properties of starch from pea and fababean were not.
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Affiliation(s)
- Shannon D Hood-Niefer
- Department of Food and Bioproduct Sciences, University of Saskatchewan, Saskatoon, SK S7N 5A8, Canada.
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Li L, Fan XZ, Liu W, Xiao Y, Bian YB. Comparative analysis on the diversity of Auricularia auricula-judae by physiological characteristics, somatic incompatibility and TRAP fingerprinting. World J Microbiol Biotechnol 2011. [DOI: 10.1007/s11274-011-0671-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Tucak M, Popović S, Čupić T, Grljušić S, Meglič V, Jurković Z. Efficiency of phenotypic and DNA markers for a genetic diversity study of alfalfa. RUSS J GENET+ 2010. [DOI: 10.1134/s1022795410110062] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Deulvot C, Charrel H, Marty A, Jacquin F, Donnadieu C, Lejeune-Hénaut I, Burstin J, Aubert G. Highly-multiplexed SNP genotyping for genetic mapping and germplasm diversity studies in pea. BMC Genomics 2010; 11:468. [PMID: 20701750 PMCID: PMC3091664 DOI: 10.1186/1471-2164-11-468] [Citation(s) in RCA: 75] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2009] [Accepted: 08/11/2010] [Indexed: 11/12/2022] Open
Abstract
BACKGROUND Single Nucleotide Polymorphisms (SNPs) can be used as genetic markers for applications such as genetic diversity studies or genetic mapping. New technologies now allow genotyping hundreds to thousands of SNPs in a single reaction.In order to evaluate the potential of these technologies in pea, we selected a custom 384-SNP set using SNPs discovered in Pisum through the resequencing of gene fragments in different genotypes and by compiling genomic sequence data present in databases. We then designed an Illumina GoldenGate assay to genotype both a Pisum germplasm collection and a genetic mapping population with the SNP set. RESULTS We obtained clear allelic data for more than 92% of the SNPs (356 out of 384). Interestingly, the technique was successful for all the genotypes present in the germplasm collection, including those from species or subspecies different from the P. sativum ssp sativum used to generate sequences. By genotyping the mapping population with the SNP set, we obtained a genetic map and map positions for 37 new gene markers. CONCLUSION Our results show that the Illumina GoldenGate assay can be used successfully for high-throughput SNP genotyping of diverse germplasm in pea. This genotyping approach will simplify genotyping procedures for association mapping or diversity studies purposes and open new perspectives in legume genomics.
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Affiliation(s)
| | | | - Amandine Marty
- GENOTOUL Platform, INRA chemin de Borde-Rouge BP52627 31326 Auzeville, France
- Euralis semences, Domaine de Sandreau, 31700 Mondonville, France
| | | | - Cécile Donnadieu
- GENOTOUL Platform, INRA chemin de Borde-Rouge BP52627 31326 Auzeville, France
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Sarikamiş G, Yanmaz R, Ermiş S, Bakir M, Yüksel C. Genetic characterization of pea (Pisum sativum) germplasm from Turkey using morphological and SSR markers. GENETICS AND MOLECULAR RESEARCH 2010; 9:591-600. [PMID: 20391343 DOI: 10.4238/vol9-1gmr762] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2023]
Abstract
The need for the conservation of plant genetic resources has been widely accepted. Germplasm characterization and evaluation yield information for more efficient utilization of these valuable resources. The aim of the present study was to characterize the pea germplasm conserved at the Aegean Agricultural Research Institute of Turkey using morphological and simple sequence repeat (SSR)-based molecular approaches. Genetic characterization of 30 pea genotypes collected from different regions of Turkey and 10 commercial pea cultivars was performed using the criteria of the International Union for the Protection of New Varieties of Plants (UPOV) (TG 7/9 Pisum sativum), and with 10 SSR markers. We originally tested 15 SSR markers; 10 of these markers were selected on the basis of high polymorphism information content in the molecular assays. Sixty-one alleles were detected at the 10 loci. The number of alleles per SSR locus ranged from 3 (PVSBE2) to 12 (AB53), with a mean of 6.1 alleles. The most informative loci were AB53 (12 alleles), AA355 (9 alleles), AD270 (8 alleles), A9 (7 alleles), AD61 (7 alleles), and AB25 (6 alleles). The UPGMA dendrogram defined by SSR markers revealed genetic relatedness of the pea genotypes. These findings can be used to guide future breeding studies and germplasm management of these pea genotypes.
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Affiliation(s)
- G Sarikamiş
- Department of Horticulture, Faculty of Agriculture, Ankara University, Ankara, Turkey.
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Jing R, Vershinin A, Grzebyta J, Shaw P, Smýkal P, Marshall D, Ambrose MJ, Ellis THN, Flavell AJ. The genetic diversity and evolution of field pea (Pisum) studied by high throughput retrotransposon based insertion polymorphism (RBIP) marker analysis. BMC Evol Biol 2010; 10:44. [PMID: 20156342 PMCID: PMC2834689 DOI: 10.1186/1471-2148-10-44] [Citation(s) in RCA: 80] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2009] [Accepted: 02/15/2010] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND The genetic diversity of crop species is the result of natural selection on the wild progenitor and human intervention by ancient and modern farmers and breeders. The genomes of modern cultivars, old cultivated landraces, ecotypes and wild relatives reflect the effects of these forces and provide insights into germplasm structural diversity, the geographical dimension to species diversity and the process of domestication of wild organisms. This issue is also of great practical importance for crop improvement because wild germplasm represents a rich potential source of useful under-exploited alleles or allele combinations. The aim of the present study was to analyse a major Pisum germplasm collection to gain a broad understanding of the diversity and evolution of Pisum and provide a new rational framework for designing germplasm core collections of the genus. RESULTS 3020 Pisum germplasm samples from the John Innes Pisum germplasm collection were genotyped for 45 retrotransposon based insertion polymorphism (RBIP) markers by the Tagged Array Marker (TAM) method. The data set was stored in a purpose-built Germinate relational database and analysed by both principal coordinate analysis and a nested application of the Structure program which yielded substantially similar but complementary views of the diversity of the genus Pisum. Structure revealed three Groups (1-3) corresponding approximately to landrace, cultivar and wild Pisum respectively, which were resolved by nested Structure analysis into 14 Sub-Groups, many of which correlate with taxonomic sub-divisions of Pisum, domestication related phenotypic traits and/or restricted geographical locations. Genetic distances calculated between these Sub-Groups are broadly supported by principal coordinate analysis and these, together with the trait and geographical data, were used to infer a detailed model for the domestication of Pisum. CONCLUSIONS These data provide a clear picture of the major distinct gene pools into which the genus Pisum is partitioned and their geographical distribution. The data strongly support the model of independent domestications for P. sativum ssp abyssinicum and P. sativum. The relationships between these two cultivated germplasms and the various sub-divisions of wild Pisum have been clarified and the most likely ancestral wild gene pools for domesticated P. sativum identified. Lastly, this study provides a framework for defining global Pisum germplasm which will be useful for designing core collections.
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Affiliation(s)
- Runchun Jing
- Division of Plant Sciences, University of Dundee at SCRI, Invergowrie, DUNDEE 5DA, UK
- Current address: School of Biological Sciences, University of East Anglia, Norwich, NR4 7TJ, UK
| | - Alexander Vershinin
- John Innes Centre, Colney, Norwich, NR4 7UH, UK
- Current address: Institute of Cytology and Genetics, Novosibirsk, Russia
| | - Jacek Grzebyta
- Division of Plant Sciences, University of Dundee at SCRI, Invergowrie, DUNDEE 5DA, UK
- Current address: Rothamstead Research, Harpenden, Herts, UK
| | - Paul Shaw
- Scottish Crop Research Institute, Invergowrie, Dundee, DD2 5DA, UK
| | - Petr Smýkal
- Agritec Plant Research Ltd, Plant Biotechnology Department, Zemědělská 2520/16, CZ-787 01 Šumperk, Czech Republic
| | - David Marshall
- Scottish Crop Research Institute, Invergowrie, Dundee, DD2 5DA, UK
| | | | | | - Andrew J Flavell
- Division of Plant Sciences, University of Dundee at SCRI, Invergowrie, DUNDEE 5DA, UK
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Kesari V, Madurai Sathyanarayana V, Parida A, Rangan L. Molecular marker-based characterization in candidate plus trees of Pongamia pinnata, a potential biodiesel legume. AOB PLANTS 2010; 2010:plq017. [PMID: 22476075 PMCID: PMC2997655 DOI: 10.1093/aobpla/plq017] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2010] [Revised: 09/14/2010] [Accepted: 10/05/2010] [Indexed: 05/22/2023]
Abstract
BACKGROUND AND AIMS Pongamia pinnata, a legume tree, has many traditional uses and is a potential biodiesel plant. Despite its importance and the availability of appropriate molecular genetic tools, the full potential of Pongamia is yet to be realized. The objective of this study was to assess genetic diversity among 10 systematically characterized candidate plus trees (CPTs) of P. pinnata from North Guwahati. METHODOLOGY The application and informativeness of polymerase chain reaction-based molecular markers [random amplified polymorphic DNA (RAPD), inter-simple sequence repeat (ISSR) and amplified fragment length polymorphism (AFLP)] to assess the genetic variability and relatedness among 10 CPTs of P. pinnata were investigated. PRINCIPAL RESULTS Polymorphism rates of 10.48, 10.08 and 100 % were achieved using 18 RAPD, 12 ISSR and 4 AFLP primer combinations, respectively. Polymorphic information content (PIC) varied in the range 0.33-0.49, 0.18-0.49 and 0.26-0.34 for RAPD, ISSR and AFLP markers, respectively, whereas the corresponding average marker index (MI) values for the above markers were 7.48, 6.69 and 30.75. Based on Nei's gene diversity and Shannon's information index, inter-population diversity (h(sp)) was highest when compared with intra-population diversity (h(pop)) and the gene flow (N(m)) ranged from a moderate value of 0.607 to a high value of 6.287 for the three DNA markers. Clustering of individuals was not similar when RAPD- and ISSR-derived dendrogram analyses were compared with that of AFLP. The Mantel test cophenetic correlation coefficient was higher for AFLP (r = 0.98) than for ISSR (r = 0.73) and RAPD (r = 0.84). Molecular markers discriminated the individuals efficiently and generated a high similarity in dendrogram topologies derived using unweighted pair-group arithmetic average, although some differences were observed. The three-dimensional scaling by principal coordinate analysis supported the result of clustering. CONCLUSIONS Comparing the results obtained with the three DNA markers, AFLP indicated higher efficiency for estimating the levels of genetic diversity and proved to be reliable for fingerprinting, mapping and diversity studies in Pongamia in view of their suitability for energy production purposes.
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Affiliation(s)
- Vigya Kesari
- Department of Biotechnology, Indian Institute of Technology, Guwahati, Assam 781039, India
| | | | - Ajay Parida
- M S Swaminathan Research Foundation, 3rd Cross Street, Institutional Area, Taramani, Chennai 600113, India
| | - Latha Rangan
- Department of Biotechnology, Indian Institute of Technology, Guwahati, Assam 781039, India
- Corresponding author's e-mail address:
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Identification and Analysis of Genetic Diversity Structure Within Pisum Genus Based on Microsatellite Markers. ACTA ACUST UNITED AC 2009. [DOI: 10.1016/s1671-2927(08)60208-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Ramos-Gómez S, López-Enríquez L, Caminero C, Hernández M. Pea detection in food and feed samples by a real-time PCR method based on a specific legumin gene that allows diversity analysis. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2008; 56:11098-104. [PMID: 18986147 DOI: 10.1021/jf8023968] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Real-time polymerase chain reaction is currently being used for the identification and quantification of plant and animal species as well as microorganisms in food or feed samples based on the amplification of specific sequences of low copy genes. We report here the development of a new real-time PCR method for the detection and quantification of the pea (Pisum sativum) based on the amplification of a specific region of the legS gene. The specificity was evaluated in a wide range of plant species (51 varieties of Pisum sp., and 32 other plant species and varieties taxonomically related or nonrelated). The method allows the detection and quantification of as low as 21.6 pg of DNA, which corresponds to 5 haploid genome copies. The system has been shown to be sensitive, reproducible and 100% specific for the rapid detection and quantification of pea DNA in processed food and feed samples, being therefore suitable for high-throughput analysis.
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Affiliation(s)
- Sonia Ramos-Gómez
- Department of Plant Production and Agronomy, Instituto Tecnológico Agrario de Castilla y León, Valladolid, Spain
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ZONG XX, GUAN JP, WANG SM, LIU QC, REDDEN RR, FORD R. Genetic Diversity and Core Collection of Alien Pisum sativum L. Germplasm. ACTA ACUST UNITED AC 2008. [DOI: 10.1016/s1875-2780(09)60003-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Smýkal P, Hýbl M, Corander J, Jarkovský J, Flavell AJ, Griga M. Genetic diversity and population structure of pea (Pisum sativum L.) varieties derived from combined retrotransposon, microsatellite and morphological marker analysis. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2008; 117:413-24. [PMID: 18504543 DOI: 10.1007/s00122-008-0785-4] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2007] [Accepted: 05/02/2008] [Indexed: 05/18/2023]
Abstract
One hundred and sixty-four accessions representing Czech and Slovak pea (Pisum sativum L.) varieties bred over the last 50 years were evaluated for genetic diversity using morphological, simple sequence repeat (SSR) and retrotransposon-based insertion polymorphism (RBIP) markers. Polymorphic information content (PIC) values of 10 SSR loci and 31 RBIP markers were on average high at 0.89 and 0.73, respectively. The silhouette method after the Ward clustering produced the most probable cluster estimate, identifying nine clusters from molecular data and five to seven clusters from morphological characters. Principal component analysis of nine qualitative and eight quantitative morphological parameters explain over 90 and 93% of total variability, respectively, in the first three axes. Multidimensional scaling of molecular data revealed a continuous structure for the set. To enable integration and evaluation of all data types, a Bayesian method for clustering was applied. Three clusters identified using morphology data, with clear separation of fodder, dry seed and afila types, were resolved by DNA data into 17, 12 and five sub-clusters, respectively. A core collection of 34 samples was derived from the complete collection by BAPS Bayesian analysis. Values for average gene diversity and allelic richness for molecular marker loci and diversity indexes of phenotypic data were found to be similar between the two collections, showing that this is a useful approach for representative core selection.
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Affiliation(s)
- Petr Smýkal
- Plant Biotechnology Department, Agritec Plant Research Ltd., Zemedelská 2520/16, Czech Republic.
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Zhao H, Bughrara SS. Isolation and characterization of cold-regulated transcriptional activator LpCBF3 gene from perennial ryegrass (Lolium perenne L.). Mol Genet Genomics 2008; 279:585-94. [PMID: 18351391 DOI: 10.1007/s00438-008-0335-4] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2006] [Accepted: 02/27/2008] [Indexed: 11/29/2022]
Abstract
In plants, low temperatures can activate the CBF cold response pathway playing a prominent role in cold acclimation by triggering a set of cold-related gene expressions. CBF homologous gene, designated as LpCBF3, from a cold-tolerant perennial ryegrass (Lolium perenne L.) accession was identified. It carries the sequences for nuclear localization signal (NLS), AP2 DNA-binding domains and an acidic activation present in most of the plant CBF proteins. Southern analysis indicated the presence of three homologs of LpCBF3 gene in perennial ryegrass genome, and only one amino acid variation in LpCBF3 protein between cold-tolerant and -sensitive perennial ryegrass accessions. In their putative promoter regions, some differential regions were found. Northern blotting and RT-PCR analysis found that LpCBF3 reached the highest expression after 1.5 h of cold treatment (4 degrees C). The COR homologous gene, a downstream gene of CBF, can be expressed in the plant stem of cold-tolerant perennial ryegrass accessions without cold treatment. Without cold treatment, the COR gene cannot be activated in cold-sensitive perennial ryegrass accessions. Cold treatment can prompt expression levels of COR homologous genes in both perennial ryegrass accessions. In transgenic Arabidopsis, the overexpression of LpCBF3 with the 35S promoter resulted in dwarf-like plants, later flowering and greater freezing tolerance.
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Affiliation(s)
- Han Zhao
- Department of Crop and Soil Sciences, Michigan State University, East Lansing, MI 48824, USA
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Jing R, Johnson R, Seres A, Kiss G, Ambrose MJ, Knox MR, Ellis THN, Flavell AJ. Gene-based sequence diversity analysis of field pea (Pisum). Genetics 2007; 177:2263-75. [PMID: 18073431 PMCID: PMC2219474 DOI: 10.1534/genetics.107.081323] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2007] [Accepted: 10/11/2007] [Indexed: 11/18/2022] Open
Abstract
Sequence diversity of 39 dispersed gene loci was analyzed in 48 diverse individuals representative of the genus Pisum. The different genes show large variation in diversity parameters, suggesting widely differing levels of selection and a high overall diversity level for the species. The data set yields a genetic diversity tree whose deep branches, involving wild samples, are preserved in a tree derived from a polymorphic retrotransposon insertions in an identical sample set. Thus, gene regions and intergenic "junk DNA" share a consistent picture for the genomic diversity of Pisum, despite low linkage disequilibrium in wild and landrace germplasm, which might be expected to allow independent evolution of these very different DNA classes. Additional lines of evidence indicate that recombination has shuffled gene haplotypes efficiently within Pisum, despite its high level of inbreeding and widespread geographic distribution. Trees derived from individual gene loci show marked differences from each other, and genetic distance values between sample pairs show high standard deviations. Sequence mosaic analysis of aligned sequences identifies nine loci showing evidence for intragenic recombination. Lastly, phylogenetic network analysis confirms the non-treelike structure of Pisum diversity and indicates the major germplasm classes involved. Overall, these data emphasize the artificiality of simple tree structures for representing genomic sequence variation within Pisum and emphasize the need for fine structure haplotype analysis to accurately define the genetic structure of the species.
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Affiliation(s)
- Runchun Jing
- Plant Research Unit, University of Dundee at Scotish Crop Research Institute, United Kingdom
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Abril AB, Bucher EH. Genetic diversity of fungi occurring in nests of three Acromyrmex leaf-cutting ant species from Córdoba, Argentina. MICROBIAL ECOLOGY 2007; 54:417-23. [PMID: 17468962 DOI: 10.1007/s00248-007-9252-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2007] [Revised: 03/06/2007] [Accepted: 03/27/2007] [Indexed: 05/15/2023]
Abstract
It is assumed in current literature that the fungus garden cultivated by leaf-cutting ants consists of a single fungus species, the putative mutualistic fungus. However, most studies report a very high rate of fungi contamination (fungi isolated from fungus gardens that are considered not to be the mutualistic fungus). In this article, we report a genetic similarity analysis of all fungi (regardless of their mutualistic condition) isolated from 16 fungus gardens of three Acromyrmex species in Córdoba, Argentina, using intersimple sequence repeat (ISSR) as genetic markers. We isolated 60 clones, of which the three primers employed yielded 53 loci. The patterns revealed a high interclone polymorphism, with a few bands shared by the clones. Of all possible pairwise comparisons, 99% showed a genetic similarity (S) lower than 0.5, the threshold level assumed for fungus Operational Taxonomy Unit (OTU). We found more than one fungus OTU in all studied nests (range 2-11). Cumulative number of OTUs increased linearly with the number of nests sampled. The number of fungus OTUs common to both ant species and sites was very small. We did not find a core group composed of few very common OTUs, as expected if a set of truly mutualistic OTU was present. A simple explanation for the high number of OTUs found is that they are regular components of the fungus garden, which may be used as food source by the ants.
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Affiliation(s)
- A B Abril
- Departamento de Recursos Naturales, Facultad de Ciencias Agropecuarias, Universidad Nacional de Córdoba, C.C. 509, 5000, Córdoba, Argentina.
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Choudhury PR, Tanveer H, Dixit GP. Identification and detection of genetic relatedness among important varieties of pea (Pisum sativum L.) grown in India. Genetica 2007; 130:183-91. [PMID: 16909333 DOI: 10.1007/s10709-006-9005-9] [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: 01/05/2006] [Accepted: 07/13/2006] [Indexed: 10/24/2022]
Abstract
Among the cool season legume crops grown in India and the Indian sub-continent, peas are very popular and preferred by the growers as well as consumers for various uses. The third largest area in pea cultivation is occupied by India after Canada and Russia. Among the important and popular varieties of peas that are grown in India, several are from exotic background. But very little work has been done to carry out the genetic diversity present in the widely adapted Indian pea varieties using DNA markers. Twenty-four most popular and widely adapted varieties were subjected to RAPD analysis to find out the genetic relatedness among them using 60 decamer primers. All the primers used in our study were found to be polymorphic and seven of them showed 100% polymorphism. Out of 579 amplified products, 433 showed polymorphism (74.8%). On an average, 9.65 bands were amplified per primer. Cluster analysis based on Jaccard's similarity coefficient using UPGMA grouped all the tall type varieties together, whereas, dwarf types formed two different clusters based upon their pedigree. The arithmetic mean heterozygosity (Hav) value and marker index (MI) was found to be 0.496 and 4.787, respectively, thus this indicated the efficiency of RAPD as a marker system. Moreover, the calculated value of probability of identical match by chance suggested that about 10(53) genotypes can be unambiguously distinguish by employing 60 RAPD primers.
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Affiliation(s)
- P Ray Choudhury
- Biotechnology Unit, Indian Institute of Pulses Research, Type 4/9, IIPR Campus, Kalyanpur, Kanpur, Uttar Pradesh, 208 024, India.
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Smýkal P. Development of an efficient retrotransposon-based fingerprinting method for rapid pea variety identification. J Appl Genet 2006; 47:221-30. [PMID: 16877800 DOI: 10.1007/bf03194627] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Fast and efficient DNA fingerprinting of crop cultivars and individuals is frequently used in both theoretical population genetics and in practical breeding. Numerous DNA marker technologies exist and the ratio of speed, cost and accuracy are of importance. Therefore even in species where highly accurate and polymorphic marker systems are available, such as microsatellite SSR (simple sequence repeats), also alternative methods may be of interest. Thanks to their high abundance and ubiquity, temporary mobile retrotransposable elements come into recent focus. Their properties, such as genome wide distribution and well-defined origin of individual insertions by descent, predetermine them for use as molecular markers. In this study, several Ty3-gypsy type retrotransposons have been developed and adopted for the inter-retrotransposon amplified polymorphism (IRAP) method, which is suitable for fast and efficient pea cultivar fingerprinting. The method can easily distinguish even between genetically closely related pea cultivars and provide high polymorphic information content (PIC) in a single PCR analysis.
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Affiliation(s)
- Petr Smýkal
- AGRITEC Plant Research Ltd., Plant Biotechnology Department, Czech Republic.
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Loridon K, McPhee K, Morin J, Dubreuil P, Pilet-Nayel ML, Aubert G, Rameau C, Baranger A, Coyne C, Lejeune-Hènaut I, Burstin J. Microsatellite marker polymorphism and mapping in pea (Pisum sativum L.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2005; 111:1022-31. [PMID: 16133320 DOI: 10.1007/s00122-005-0014-3] [Citation(s) in RCA: 108] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2005] [Accepted: 06/09/2005] [Indexed: 05/03/2023]
Abstract
This paper aims at providing reliable and cost effective genotyping conditions, level of polymorphism in a range of genotypes and map position of newly developed microsatellite markers in order to promote broad application of these markers as a common set for genetic studies in pea. Optimal PCR conditions were determined for 340 microsatellite markers based on amplification in eight genotypes. Levels of polymorphism were determined for 309 of these markers. Compared to data obtained for other species, levels of polymorphism detected in a panel of eight genotypes were high with a mean number of 3.8 alleles per polymorphic locus and an average PIC value of 0.62, indicating that pea represents a rather polymorphic autogamous species. One of our main objectives was to locate a maximum number of microsatellite markers on the pea genetic map. Data obtained from three different crosses were used to build a composite genetic map of 1,430 cM (Haldane) comprising 239 microsatellite markers. These include 216 anonymous SSRs developed from enriched genomic libraries and 13 SSRs located in genes. The markers are quite evenly distributed throughout the seven linkage groups of the map, with 85% of intervals between the adjacent SSR markers being smaller than 10 cM. There was a good conservation of marker order and linkage group assignment across the three populations. In conclusion, we hope this report will promote wide application of these markers and will allow information obtained by different laboratories worldwide in diverse fields of pea genetics, such as QTL mapping studies and genetic resource surveys, to be easily aligned.
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Affiliation(s)
- K Loridon
- INRA URLEG, Domaine d'Epoisses, 21110 Bretenières, France
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