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Kassie FC, Nguepjop JR, Ngalle HB, Assaha DVM, Gessese MK, Abtew WG, Tossim HA, Sambou A, Seye M, Rami JF, Fonceka D, Bell JM. An Overview of Mapping Quantitative Trait Loci in Peanut ( Arachis hypogaea L.). Genes (Basel) 2023; 14:1176. [PMID: 37372356 DOI: 10.3390/genes14061176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 05/24/2023] [Accepted: 05/25/2023] [Indexed: 06/29/2023] Open
Abstract
Quantitative Trait Loci (QTL) mapping has been thoroughly used in peanut genetics and breeding in spite of the narrow genetic diversity and the segmental tetraploid nature of the cultivated species. QTL mapping is helpful for identifying the genomic regions that contribute to traits, for estimating the extent of variation and the genetic action (i.e., additive, dominant, or epistatic) underlying this variation, and for pinpointing genetic correlations between traits. The aim of this paper is to review the recently published studies on QTL mapping with a particular emphasis on mapping populations used as well as traits related to kernel quality. We found that several populations have been used for QTL mapping including interspecific populations developed from crosses between synthetic tetraploids and elite varieties. Those populations allowed the broadening of the genetic base of cultivated peanut and helped with the mapping of QTL and identifying beneficial wild alleles for economically important traits. Furthermore, only a few studies reported QTL related to kernel quality. The main quality traits for which QTL have been mapped include oil and protein content as well as fatty acid compositions. QTL for other agronomic traits have also been reported. Among the 1261 QTL reported in this review, and extracted from the most relevant studies on QTL mapping in peanut, 413 (~33%) were related to kernel quality showing the importance of quality in peanut genetics and breeding. Exploiting the QTL information could accelerate breeding to develop highly nutritious superior cultivars in the face of climate change.
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Affiliation(s)
- Fentanesh C Kassie
- Department of Plant Biology and Physiology, Faculty of Sciences, University of Yaounde I, Yaounde P.O. Box 337, Cameroon
- Department of Plant Science, College of Agriculture, Wolaita Sodo University, Sodo P.O. Box 138, Ethiopia
| | - Joël R Nguepjop
- UMR AGAP, CIRAD, F-34398 Montpellier, France
- AGAP Institute, Institut Agro, CIRAD, INRAE, University of Montpellier, F-34060 Montpellier, France
- Centre d'Etudes Régional Pour l'Amélioration de l'Adaptation à la Sécheresse (CERAAS/ISRA), Route de Khombole, Thiès BP 3320, Senegal
- Dispositif de Recherche et de Formation en Partenariat, Innovation et Amélioration Variétale en Afrique de l'Ouest (IAVAO), CERAAS, Route de Khombole, Thiès BP 3320, Senegal
| | - Hermine B Ngalle
- Department of Plant Biology and Physiology, Faculty of Sciences, University of Yaounde I, Yaounde P.O. Box 337, Cameroon
| | - Dekoum V M Assaha
- Department of Agriculture, Higher Technical Teachers Training College, University of Buea, Kumba P.O. Box 249, Cameroon
| | - Mesfin K Gessese
- Department of Plant Science, College of Agriculture, Wolaita Sodo University, Sodo P.O. Box 138, Ethiopia
| | - Wosene G Abtew
- Department of Horticulture and Plant Science, College of Agriculture and Veterinary Medicine, Jimma University, Jimma P.O. Box 378, Ethiopia
| | - Hodo-Abalo Tossim
- Centre d'Etudes Régional Pour l'Amélioration de l'Adaptation à la Sécheresse (CERAAS/ISRA), Route de Khombole, Thiès BP 3320, Senegal
- Dispositif de Recherche et de Formation en Partenariat, Innovation et Amélioration Variétale en Afrique de l'Ouest (IAVAO), CERAAS, Route de Khombole, Thiès BP 3320, Senegal
| | - Aissatou Sambou
- Centre d'Etudes Régional Pour l'Amélioration de l'Adaptation à la Sécheresse (CERAAS/ISRA), Route de Khombole, Thiès BP 3320, Senegal
- Dispositif de Recherche et de Formation en Partenariat, Innovation et Amélioration Variétale en Afrique de l'Ouest (IAVAO), CERAAS, Route de Khombole, Thiès BP 3320, Senegal
| | - Maguette Seye
- Centre d'Etudes Régional Pour l'Amélioration de l'Adaptation à la Sécheresse (CERAAS/ISRA), Route de Khombole, Thiès BP 3320, Senegal
- Dispositif de Recherche et de Formation en Partenariat, Innovation et Amélioration Variétale en Afrique de l'Ouest (IAVAO), CERAAS, Route de Khombole, Thiès BP 3320, Senegal
| | - Jean-François Rami
- UMR AGAP, CIRAD, F-34398 Montpellier, France
- AGAP Institute, Institut Agro, CIRAD, INRAE, University of Montpellier, F-34060 Montpellier, France
- Dispositif de Recherche et de Formation en Partenariat, Innovation et Amélioration Variétale en Afrique de l'Ouest (IAVAO), CERAAS, Route de Khombole, Thiès BP 3320, Senegal
| | - Daniel Fonceka
- UMR AGAP, CIRAD, F-34398 Montpellier, France
- AGAP Institute, Institut Agro, CIRAD, INRAE, University of Montpellier, F-34060 Montpellier, France
- Centre d'Etudes Régional Pour l'Amélioration de l'Adaptation à la Sécheresse (CERAAS/ISRA), Route de Khombole, Thiès BP 3320, Senegal
- Dispositif de Recherche et de Formation en Partenariat, Innovation et Amélioration Variétale en Afrique de l'Ouest (IAVAO), CERAAS, Route de Khombole, Thiès BP 3320, Senegal
| | - Joseph M Bell
- Department of Plant Biology and Physiology, Faculty of Sciences, University of Yaounde I, Yaounde P.O. Box 337, Cameroon
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Nzepang DT, Gully D, Nguepjop JR, Zaiya Zazou A, Tossim HA, Sambou A, Rami JF, Hocher V, Fall S, Svistoonoff S, Fonceka D. Mapping of QTLs Associated with Biological Nitrogen Fixation Traits in Peanuts (Arachis hypogaea L.) Using an Interspecific Population Derived from the Cross between the Cultivated Species and Its Wild Ancestors. Genes (Basel) 2023; 14:genes14040797. [PMID: 37107555 PMCID: PMC10138160 DOI: 10.3390/genes14040797] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 03/16/2023] [Accepted: 03/22/2023] [Indexed: 03/29/2023] Open
Abstract
Peanuts (Arachis hypogaea L.) are an allotetraploid grain legume mainly cultivated by poor farmers in Africa, in degraded soil and with low input systems. Further understanding nodulation genetic mechanisms could be a relevant option to facilitate the improvement of yield and lift up soil without synthetic fertilizers. We used a subset of 83 chromosome segment substitution lines (CSSLs) derived from the cross between a wild synthetic tetraploid AiAd (Arachis ipaensis × Arachis duranensis)4× and the cultivated variety Fleur11, and evaluated them for traits related to BNF under shade-house conditions. Three treatments were tested: without nitrogen; with nitrogen; and without nitrogen, but with added0 Bradyrhizobium vignae strain ISRA400. The leaf chlorophyll content and total biomass were used as surrogate traits for BNF. We found significant variations for both traits specially linked to BNF, and four QTLs (quantitative trait loci) were consistently mapped. At all QTLs, the wild alleles decreased the value of the trait, indicating a negative effect on BNF. A detailed characterization of the lines carrying those QTLs in controlled conditions showed that the QTLs affected the nitrogen fixation efficiency, nodule colonization, and development. Our results provide new insights into peanut nodulation mechanisms and could be used to target BNF traits in peanut breeding programs.
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Affiliation(s)
- Darius T. Nzepang
- Centre d’Etudes Régional pour l’Amélioration de l’Adaptation à la Sécheresse, CERAAS-Route de Khombole, Thiès BP 3320, Senegal
- PHIM Plant Health Institute, Univ Montpellier, IRD, CIRAD, INRAE, Institut Agro, Montpellier, France
- Laboratoire Commun de Microbiologie (LCM) (IRD/ISRA/UCAD), Centre de Recherche de Bel Air, Dakar BP 1386, Senegal
- Laboratoire Mixte International Adaptation des Plantes et Microorganismes Associés aux Stress Environnementaux (LAPSE), Centre de Recherche de Bel Air, Dakar CP 18524, Senegal
- Dispositif de Recherche et de Formation en Partenariat, Innovation et Amélioration Variétale en Afrique de l’Ouest (IAVAO), CERAAS Route de Khombole, Thiès BP 3320, Senegal
| | - Djamel Gully
- PHIM Plant Health Institute, Univ Montpellier, IRD, CIRAD, INRAE, Institut Agro, Montpellier, France
- Laboratoire Mixte International Adaptation des Plantes et Microorganismes Associés aux Stress Environnementaux (LAPSE), Centre de Recherche de Bel Air, Dakar CP 18524, Senegal
| | - Joël R. Nguepjop
- Centre d’Etudes Régional pour l’Amélioration de l’Adaptation à la Sécheresse, CERAAS-Route de Khombole, Thiès BP 3320, Senegal
- Dispositif de Recherche et de Formation en Partenariat, Innovation et Amélioration Variétale en Afrique de l’Ouest (IAVAO), CERAAS Route de Khombole, Thiès BP 3320, Senegal
- CIRAD, UMR AGAP, F-34398 Montpellier, France
- AGAP, Univ Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Arlette Zaiya Zazou
- Institute of Agricultural Research for Development (IRAD) (IRAD), Maroua, Cameroon
| | - Hodo-Abalo Tossim
- Centre d’Etudes Régional pour l’Amélioration de l’Adaptation à la Sécheresse, CERAAS-Route de Khombole, Thiès BP 3320, Senegal
- Dispositif de Recherche et de Formation en Partenariat, Innovation et Amélioration Variétale en Afrique de l’Ouest (IAVAO), CERAAS Route de Khombole, Thiès BP 3320, Senegal
| | - Aissatou Sambou
- Centre d’Etudes Régional pour l’Amélioration de l’Adaptation à la Sécheresse, CERAAS-Route de Khombole, Thiès BP 3320, Senegal
- Dispositif de Recherche et de Formation en Partenariat, Innovation et Amélioration Variétale en Afrique de l’Ouest (IAVAO), CERAAS Route de Khombole, Thiès BP 3320, Senegal
| | - Jean-François Rami
- Dispositif de Recherche et de Formation en Partenariat, Innovation et Amélioration Variétale en Afrique de l’Ouest (IAVAO), CERAAS Route de Khombole, Thiès BP 3320, Senegal
- CIRAD, UMR AGAP, F-34398 Montpellier, France
- AGAP, Univ Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Valerie Hocher
- PHIM Plant Health Institute, Univ Montpellier, IRD, CIRAD, INRAE, Institut Agro, Montpellier, France
- Laboratoire Commun de Microbiologie (LCM) (IRD/ISRA/UCAD), Centre de Recherche de Bel Air, Dakar BP 1386, Senegal
- Laboratoire Mixte International Adaptation des Plantes et Microorganismes Associés aux Stress Environnementaux (LAPSE), Centre de Recherche de Bel Air, Dakar CP 18524, Senegal
| | - Saliou Fall
- Laboratoire Commun de Microbiologie (LCM) (IRD/ISRA/UCAD), Centre de Recherche de Bel Air, Dakar BP 1386, Senegal
- Laboratoire Mixte International Adaptation des Plantes et Microorganismes Associés aux Stress Environnementaux (LAPSE), Centre de Recherche de Bel Air, Dakar CP 18524, Senegal
| | - Sergio Svistoonoff
- PHIM Plant Health Institute, Univ Montpellier, IRD, CIRAD, INRAE, Institut Agro, Montpellier, France
- Laboratoire Mixte International Adaptation des Plantes et Microorganismes Associés aux Stress Environnementaux (LAPSE), Centre de Recherche de Bel Air, Dakar CP 18524, Senegal
| | - Daniel Fonceka
- Centre d’Etudes Régional pour l’Amélioration de l’Adaptation à la Sécheresse, CERAAS-Route de Khombole, Thiès BP 3320, Senegal
- Dispositif de Recherche et de Formation en Partenariat, Innovation et Amélioration Variétale en Afrique de l’Ouest (IAVAO), CERAAS Route de Khombole, Thiès BP 3320, Senegal
- CIRAD, UMR AGAP, F-34398 Montpellier, France
- AGAP, Univ Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
- Correspondence:
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Chu Y, Bertioli D, Levinson CM, Stalker HT, Holbrook CC, Ozias-Akins P. Homoeologous recombination is recurrent in the nascent synthetic allotetraploid Arachis ipaënsis × Arachis correntina4x and its derivatives. G3-GENES GENOMES GENETICS 2021; 11:6162164. [PMID: 33693764 PMCID: PMC8759810 DOI: 10.1093/g3journal/jkab066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Accepted: 02/21/2021] [Indexed: 11/13/2022]
Abstract
Genome instability in newly synthesized allotetraploids of peanut has breeding implications that have not been fully appreciated. Synthesis of wild species-derived neo-tetraploids offers the opportunity to broaden the gene pool of peanut; however, the dynamics among the newly merged genomes creates predictable and unpredictable variation. Selfed progenies from the neo-tetraploid Arachis ipaënsis × Arachis correntina (A. ipaënsis × A. correntina)4x and F1 hybrids and F2 progenies from crosses between A. hypogaea × [A. ipaënsis × A. correntina]4x were genotyped by the Axiom Arachis 48 K SNP array. Homoeologous recombination between the A. ipaënsis and A. correntina derived subgenomes was observed in the S0 generation. Among the S1 progenies, these recombined segments segregated and new events of homoeologous recombination emerged. The genomic regions undergoing homoeologous recombination segregated mostly disomically in the F2 progenies from A. hypogaea × [A. ipaënsis × A. correntina]4x crosses. New homoeologous recombination events also occurred in the F2 population, mostly found on chromosomes 03, 04, 05, and 06. From the breeding perspective, these phenomena offer both possibilities and perils; recombination between genomes increases genetic diversity, but genome instability could lead to instability of traits or even loss of viability within lineages.
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Affiliation(s)
- Ye Chu
- Horticulture Department, University of Georgia, Tifton, GA 31793, USA
| | - David Bertioli
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA 30602, USA.,Institute of Plant Breeding, Genetics and Genomics, University of Georgia, Athens, GA 30602, USA.,Department of Crop and Soil Science, University of Georgia, Athens, GA 30602, USA
| | - Chandler M Levinson
- Institute of Plant Breeding, Genetics and Genomics, University of Georgia, Athens, GA 30602, USA
| | - H Thomas Stalker
- Department of Crop and Soil Sciences, North Carolina State University, Raleigh, NC 27695, USA
| | - C Corley Holbrook
- USDA- Agricultural Research Service, Crop Genetics and Breeding Research Unit, Tifton, GA 31793, USA
| | - Peggy Ozias-Akins
- Horticulture Department, University of Georgia, Tifton, GA 31793, USA.,Institute of Plant Breeding, Genetics and Genomics, University of Georgia, Athens, GA 30602, USA
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Pereira L, Santo Domingo M, Argyris J, Mayobre C, Valverde L, Martín-Hernández AM, Pujol M, Garcia-Mas J. A novel introgression line collection to unravel the genetics of climacteric ripening and fruit quality in melon. Sci Rep 2021; 11:11364. [PMID: 34059766 PMCID: PMC8166866 DOI: 10.1038/s41598-021-90783-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Accepted: 05/18/2021] [Indexed: 11/09/2022] Open
Abstract
Introgression lines are valuable germplasm for scientists and breeders, since they ease genetic studies such as QTL interactions and positional cloning as well as the introduction of favorable alleles into elite varieties. We developed a novel introgression line collection in melon using two commercial European varieties with different ripening behavior, the climacteric cantalupensis 'Védrantais' as recurrent parent and the non-climacteric inodorus 'Piel de Sapo' as donor parent. The collection contains 34 introgression lines, covering 99% of the donor genome. The mean introgression size is 18.16 Mb and ~ 3 lines were obtained per chromosome, on average. The high segregation of these lines for multiple fruit quality traits allowed us to identify 27 QTLs that modified sugar content, altered fruit morphology or were involved in climacteric ripening. In addition, we confirmed the genomic location of five major genes previously described, which control mainly fruit appearance, such as mottled rind and external color. Most of the QTLs had been reported before in other populations sharing parental lines, while three QTLs (EAROQP11.3, ECDQP11.2 and FIRQP4.1) were newly detected in our work. These introgression lines would be useful to perform additional genetic studies, as fine mapping and gene pyramiding, especially for important complex traits such as fruit weight and climacteric ripening.
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Affiliation(s)
- Lara Pereira
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Edifici CRAG, Campus UAB, 08193, Bellaterra, Barcelona, Spain
| | - Miguel Santo Domingo
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Edifici CRAG, Campus UAB, 08193, Bellaterra, Barcelona, Spain
| | - Jason Argyris
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Edifici CRAG, Campus UAB, 08193, Bellaterra, Barcelona, Spain.,Institut de Recerca i Tecnologia Agroalimentàries (IRTA), Edifici CRAG, Campus UAB, 08193, Bellaterra, Barcelona, Spain
| | - Carlos Mayobre
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Edifici CRAG, Campus UAB, 08193, Bellaterra, Barcelona, Spain
| | - Laura Valverde
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Edifici CRAG, Campus UAB, 08193, Bellaterra, Barcelona, Spain
| | - Ana Montserrat Martín-Hernández
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Edifici CRAG, Campus UAB, 08193, Bellaterra, Barcelona, Spain.,Institut de Recerca i Tecnologia Agroalimentàries (IRTA), Edifici CRAG, Campus UAB, 08193, Bellaterra, Barcelona, Spain
| | - Marta Pujol
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Edifici CRAG, Campus UAB, 08193, Bellaterra, Barcelona, Spain. .,Institut de Recerca i Tecnologia Agroalimentàries (IRTA), Edifici CRAG, Campus UAB, 08193, Bellaterra, Barcelona, Spain.
| | - Jordi Garcia-Mas
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Edifici CRAG, Campus UAB, 08193, Bellaterra, Barcelona, Spain. .,Institut de Recerca i Tecnologia Agroalimentàries (IRTA), Edifici CRAG, Campus UAB, 08193, Bellaterra, Barcelona, Spain.
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Fine-Mapping of a Wild Genomic Region Involved in Pod and Seed Size Reduction on Chromosome A07 in Peanut ( Arachis hypogaea L.). Genes (Basel) 2020; 11:genes11121402. [PMID: 33255801 PMCID: PMC7761091 DOI: 10.3390/genes11121402] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Revised: 11/20/2020] [Accepted: 11/24/2020] [Indexed: 01/24/2023] Open
Abstract
Fruit and seed size are important yield component traits that have been selected during crop domestication. In previous studies, Advanced Backcross Quantitative Trait Loci (AB-QTL) and Chromosome Segment Substitution Line (CSSL) populations were developed in peanut by crossing the cultivated variety Fleur11 and a synthetic wild allotetraploid (Arachis ipaensis × Arachis duranensis)4x. In the AB-QTL population, a major QTL for pod and seed size was detected in a ~5 Mb interval in the proximal region of chromosome A07. In the CSSL population, the line 12CS_091, which carries the QTL region and that produces smaller pods and seeds than Fleur11, was identified. In this study, we used a two-step strategy to fine-map the seed size QTL region on chromosome A07. We developed new SSR and SNP markers, as well as near-isogenic lines (NILs) in the target QTL region. We first located the QTL in ~1 Mb region between two SSR markers, thanks to the genotyping of a large F2 population of 2172 individuals and a single marker analysis approach. We then used nine new SNP markers evenly distributed in the refined QTL region to genotype 490 F3 plants derived from 88 F2, and we selected 10 NILs. The phenotyping of the NILs and marker/trait association allowed us to narrowing down the QTL region to a 168.37 kb chromosome segment, between the SNPs Aradu_A07_1148327 and Aradu_A07_1316694. This region contains 22 predicted genes. Among these genes, Aradu.DN3DB and Aradu.RLZ61, which encode a transcriptional regulator STERILE APETALA-like (SAP) and an F-box SNEEZY (SNE), respectively, were of particular interest. The function of these genes in regulating the variation of fruit and seed size is discussed. This study will contribute to a better knowledge of genes that have been targeted during peanut domestication.
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Liu Y, Zhu J, Sun S, Cui F, Han Y, Peng Z, Zhang X, Wan S, Li G. Defining the function of SUMO system in pod development and abiotic stresses in Peanut. BMC PLANT BIOLOGY 2019; 19:593. [PMID: 31884953 PMCID: PMC7194008 DOI: 10.1186/s12870-019-2136-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Accepted: 11/13/2019] [Indexed: 05/05/2023]
Abstract
BACKGROUND Posttranslational modification of proteins by small ubiquitin like modifier (SUMO) proteins play an important role during the developmental process and in response to abiotic stresses in plants. However, little is known about SUMOylation in peanut (Arachis hypogaea L.), one of the world's major food legume crops. In this study, we characterized the SUMOylation system from the diploid progenitor genomes of peanut, Arachis duranensis (AA) and Arachis ipaensis (BB). RESULTS Genome-wide analysis revealed the presence of 40 SUMO system genes in A. duranensis and A. ipaensis. Our results showed that peanut also encodes a novel class II isotype of the SCE1, which was previously reported to be uniquely present in cereals. RNA-seq data showed that the core components of the SUMOylation cascade SUMO1/2 and SCE1 genes exhibited pod-specific expression patterns, implying coordinated regulation during pod development. Furthermore, both transcripts and conjugate profiles revealed that SUMOylation has significant roles during the pod development. Moreover, dynamic changes in the SUMO conjugates were observed in response to abiotic stresses. CONCLUSIONS The identification and organization of peanut SUMO system revealed SUMOylation has important roles during stress defense and pod development. The present study will serve as a resource for providing new strategies to enhance agronomic yield and reveal the mechanism of peanut pod development.
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Affiliation(s)
- Yiyang Liu
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences; Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, China
- College of Life Science, Shandong Normal University, Jinan, China
| | - Jiao Zhu
- Shandong Key Laboratory of Greenhouse Vegetable Biology, Institute of Vegetables and Flowers, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Sheng Sun
- College of Teacher Education, Heze University, Heze, China
| | - Feng Cui
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences; Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, China
| | - Yan Han
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences; Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, China
- College of Life Science, Shandong Normal University, Jinan, China
| | - Zhenying Peng
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences; Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, China
| | - Xuejie Zhang
- College of Life Science, Shandong Normal University, Jinan, China
| | - Shubo Wan
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences; Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, China
| | - Guowei Li
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences; Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, China
- College of Life Science, Shandong Normal University, Jinan, China
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Desmae H, Janila P, Okori P, Pandey MK, Motagi BN, Monyo E, Mponda O, Okello D, Sako D, Echeckwu C, Oteng‐Frimpong R, Miningou A, Ojiewo C, Varshney RK. Genetics, genomics and breeding of groundnut ( Arachis hypogaea L.). PLANT BREEDING = ZEITSCHRIFT FUR PFLANZENZUCHTUNG 2019; 138:425-444. [PMID: 31598026 PMCID: PMC6774334 DOI: 10.1111/pbr.12645] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Revised: 04/10/2018] [Accepted: 07/13/2018] [Indexed: 05/04/2023]
Abstract
Groundnut is an important food and oil crop in the semiarid tropics, contributing to household food consumption and cash income. In Asia and Africa, yields are low attributed to various production constraints. This review paper highlights advances in genetics, genomics and breeding to improve the productivity of groundnut. Genetic studies concerning inheritance, genetic variability and heritability, combining ability and trait correlations have provided a better understanding of the crop's genetics to develop appropriate breeding strategies for target traits. Several improved lines and sources of variability have been identified or developed for various economically important traits through conventional breeding. Significant advances have also been made in groundnut genomics including genome sequencing, marker development and genetic and trait mapping. These advances have led to a better understanding of the groundnut genome, discovery of genes/variants for traits of interest and integration of marker-assisted breeding for selected traits. The integration of genomic tools into the breeding process accompanied with increased precision of yield trialing and phenotyping will increase the efficiency and enhance the genetic gain for release of improved groundnut varieties.
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Affiliation(s)
- Haile Desmae
- International Crop Research Institute for the Semi‐Arid Tropics (ICRISAT)BamakoMali
| | | | | | | | | | | | - Omari Mponda
- Division of Research and Development (DRD)Tanzania Agricultural Research Institute (TARI) ‐ NaliendeleMtwaraTanzania
| | - David Okello
- National Agricultural Research Organization (NARO)EntebbeUganda
| | | | | | | | - Amos Miningou
- Institut National d'Environnement et de Recherches Agricoles (INERA)OuagadougouBurkina Faso
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Wang L, Zhou X, Ren X, Huang L, Luo H, Chen Y, Chen W, Liu N, Liao B, Lei Y, Yan L, Shen J, Jiang H. A Major and Stable QTL for Bacterial Wilt Resistance on Chromosome B02 Identified Using a High-Density SNP-Based Genetic Linkage Map in Cultivated Peanut Yuanza 9102 Derived Population. Front Genet 2018; 9:652. [PMID: 30619474 PMCID: PMC6305283 DOI: 10.3389/fgene.2018.00652] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Accepted: 11/30/2018] [Indexed: 11/29/2022] Open
Abstract
Bacterial wilt (BW) is one of the important diseases limiting the production of peanut (Arachis hypogaea L.) worldwide. The sufficient precise information on the quantitative trait loci (QTL) for BW resistance is essential for facilitating gene mining and applying in molecular breeding. Cultivar Yuanza 9102 is BW resistant, bred from wide cross between cultivated peanut Baisha 1016 and a wild diploid peanut species A. chacoense with BW resistance. In this study, we aim to map the major QTLs related to BW-resistance in Yuanza 9102. A high density SNP-based genetic linkage map was constructed through double-digest restriction-site-associated DNA sequencing (ddRADseq) technique based on Yuanza 9102 derived recombinant inbred lines (RILs) population. The map contained 2,187 SNP markers distributed on 20 linkage groups (LGs) spanning 1566.10 cM, and showed good synteny with AA genome from A. duranensis and BB genome from A. ipaensis. Phenotypic frequencies of BW resistance among RIL population showed two-peak distribution in four environments. Four QTLs explaining 5.49 to 23.22% phenotypic variance were identified to be all located on chromosome B02. The major QTL, qBWB02.1 (12.17–23.33% phenotypic variation explained), was detected in three environments showing consistent and stable expression. Furthermore, there was positive additive effect among these major and minor QTLs. The major QTL region was mapped to a region covering 2.3 Mb of the pseudomolecule B02 of A. ipaensis which resides in 21 nucleotide-binding site -leucine-rich repeat (NBS-LRR) encoding genes. The result of the major stable QTL (qBWB02.1) not only offers good foundation for discovery of BW resistant gene but also provide opportunity for deployment of the QTL in marker-assisted breeding in peanut.
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Affiliation(s)
- Lifang Wang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China.,College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Xiaojing Zhou
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Xiaoping Ren
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Li Huang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Huaiyong Luo
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Yuning Chen
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Weigang Chen
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Nian Liu
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Boshou Liao
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Yong Lei
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Liying Yan
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Jinxiong Shen
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Huifang Jiang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
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9
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Khera P, Pandey MK, Mallikarjuna N, Sriswathi M, Roorkiwal M, Janila P, Sharma S, Shilpa K, Sudini H, Guo B, Varshney RK. Genetic imprints of domestication for disease resistance, oil quality, and yield component traits in groundnut (Arachis hypogaea L.). Mol Genet Genomics 2018; 294:365-378. [PMID: 30467595 DOI: 10.1007/s00438-018-1511-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2018] [Accepted: 11/08/2018] [Indexed: 11/29/2022]
Abstract
Ploidy difference between wild Arachis species and cultivated genotypes hinder transfer of useful alleles for agronomically important traits. To overcome this genetic barrier, two synthetic tetraploids, viz., ISATGR 1212 (A. duranensis ICG 8123 × A. ipaensis ICG 8206) and ISATGR 265-5A (A. kempff-mercadoi ICG 8164 × A. hoehnei ICG 8190), were used to generate two advanced backcross (AB) populations. The AB-populations, namely, AB-pop1 (ICGV 91114 × ISATGR 1212) and AB-pop2, (ICGV 87846 × ISATGR 265-5A) were genotyped with DArT and SSR markers. Genetic maps were constructed for AB-pop1 and AB-pop2 populations with 258 loci (1415.7 cM map length and map density of 5.5 cM/loci) and 1043 loci (1500.8 cM map length with map density of 1.4 cM/loci), respectively. Genetic analysis identified large number of wild segments in the population and provided a good source of diversity in these populations. Phenotyping of these two populations identified several introgression lines with good agronomic, oil quality, and disease resistance traits. Quantitative trait locus (QTL) analysis showed that the wild genomic segments contributed favourable alleles for foliar disease resistance while cultivated genomic segments mostly contributed favourable alleles for oil quality and yield component traits. These populations, after achieving higher stability, will be useful resource for genetic mapping and QTL discovery for wild species segments in addition to using population progenies in breeding program for diversifying the gene pool of cultivated groundnut.
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Affiliation(s)
- Pawan Khera
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Manish K Pandey
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Nalini Mallikarjuna
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Manda Sriswathi
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Manish Roorkiwal
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Pasupuleti Janila
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Shivali Sharma
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Krishna Shilpa
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Harikishan Sudini
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Baozhu Guo
- Crop Protection and Management Research Unit, US Department of Agriculture-Agricultural Research Service, Tifton, USA
| | - Rajeev K Varshney
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India.
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10
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Dutra WF, Guerra YL, Ramos JPC, Fernandes PD, Silva CRC, Bertioli DJ, Leal-Bertioli SCM, Santos RC. Introgression of wild alleles into the tetraploid peanut crop to improve water use efficiency, earliness and yield. PLoS One 2018; 13:e0198776. [PMID: 29889864 PMCID: PMC5995397 DOI: 10.1371/journal.pone.0198776] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Accepted: 05/24/2018] [Indexed: 11/19/2022] Open
Abstract
The introduction of genes from wild species is a practice little adopted by breeders for the improvement of commercial crops, although it represents an excellent opportunity to enrich the genetic basis and create new cultivars. In peanut, this practice is being increasingly adopted. In this study we present results of introgression of wild alleles from the wild species Arachis duranensis and A. batizocoi improving photosynthetic traits and yield in a set of lines derived from the cross of an induced allotetraploid and cultivated peanut with selection under water stress. The assays were carried out in greenhouse and field focusing on physiological and agronomic traits. A multivariate model (UPGMA) was adopted in order to classify drought tolerant lines. Several lines showed improved levels of tolerance, with values similar to or greater than the tolerant control. Two BC1F6 lines (53 P4 and 96 P9) were highlighted for good drought-related traits, earliness and pod yield, having better phenotypic profile to the drought tolerant elite commercial cultivar BR1. These lines are good candidates for the creation of peanut cultivars suitable for production in semiarid environments.
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Affiliation(s)
- Wellison F. Dutra
- Federal University of Paraíba, Agronomy Pos-Graduation, Rodovia PB 079, km 12, CEP, Areia, PB, Brazil
| | - Yrlânia L. Guerra
- State University of Paraíba, Pró-Reitoria de Pós-Graduação e Pesquisa, Rua Baraúnas, n° 351, Universitário, CEP, Campina Grande, PB, Brazil
| | - Jean P. C. Ramos
- Federal University of Paraíba, Agronomy Pos-Graduation, Rodovia PB 079, km 12, CEP, Areia, PB, Brazil
| | - Pedro D. Fernandes
- State University of Paraíba, Pró-Reitoria de Pós-Graduação e Pesquisa, Rua Baraúnas, n° 351, Universitário, CEP, Campina Grande, PB, Brazil
| | - Carliane R. C. Silva
- Laboratory of Biotechnology, Embrapa Cotton, Rua Osvaldo Cruz, n° 1143, Centenário, CEP, Campina Grande, PB, Brazil
| | - David J. Bertioli
- Crop and Soil Science Department/Center for Applied Genetic Technologies, University of Georgia, Athens, GA, United States of America
| | - Soraya C. M. Leal-Bertioli
- Plant Pathology Department/Center for Applied Genetic Technologies, University of Georgia, Athens, GA, United States of America
- * E-mail:
| | - Roseane C. Santos
- State University of Paraíba, Pró-Reitoria de Pós-Graduação e Pesquisa, Rua Baraúnas, n° 351, Universitário, CEP, Campina Grande, PB, Brazil
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11
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Leal-Bertioli SCM, Godoy IJ, Santos JF, Doyle JJ, Guimarães PM, Abernathy BL, Jackson SA, Moretzsohn MC, Bertioli DJ. Segmental allopolyploidy in action: Increasing diversity through polyploid hybridization and homoeologous recombination. AMERICAN JOURNAL OF BOTANY 2018; 105:1053-1066. [PMID: 29985538 DOI: 10.1002/ajb2.1112] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Accepted: 04/18/2018] [Indexed: 05/05/2023]
Abstract
PREMISE OF THE STUDY The genetic bottleneck of polyploid formation can be mitigated by multiple origins, gene flow, and recombination among different lineages. In crop plants with limited origins, efforts to increase genetic diversity have limitations. Here we used lineage recombination to increase genetic diversity in peanut, an allotetraploid likely of single origin, by crossing with a novel allopolyploid genotype and selecting improved lines. METHODS Single backcross progeny from cultivated peanut × wild species-derived allotetraploid cross were studied over successive generations. Using genetic assumptions that encompass segmental allotetraploidy, we used single nucleotide polymorphisms and whole-genome sequence data to infer genome structures. KEY RESULTS Selected lines, despite a high proportion of wild alleles, are agronomically adapted, productive, and with improved disease resistances. Wild alleles mostly substituted homologous segments of the peanut genome. Regions of dispersed wild alleles, characteristic of gene conversion, also occurred. However, wild chromosome segments sometimes replaced cultivated peanut's homeologous subgenome; A. ipaënsis B sometimes replaced A. hypogaea A subgenome (~0.6%), and A. duranensis replaced A. hypogaea B subgenome segments (~2%). Furthermore, some subgenome regions historically lost in cultivated peanut were "recovered" by wild chromosome segments (effectively reversing the "polyploid ratchet"). These processes resulted in lines with new genome structure variations. CONCLUSIONS Genetic diversity was introduced by wild allele introgression, and by introducing new genome structure variations. These results highlight the special possibilities of segmental allotetraploidy and of using lineage recombination to increase genetic diversity in peanut, likely mirroring what occurs in natural segmental allopolyploids with multiple origins.
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Affiliation(s)
- Soraya C M Leal-Bertioli
- University of Georgia, Center for Applied Genetic Technologies, 111 Riverbend Road, Athens, GA, 30602-6810, USA
| | - Ignácio J Godoy
- Campinas Agronomical Institute, Avenida Barão de Itapura, 1.481, Campinas, SP, 13020-902, Brazil
| | - João F Santos
- Campinas Agronomical Institute, Avenida Barão de Itapura, 1.481, Campinas, SP, 13020-902, Brazil
| | - Jeff J Doyle
- Cornell University, School of Integrative Plant Science, Plant Breeding & Genetics Section, Ithaca, NY, 14853, USA
| | - Patrícia M Guimarães
- Embrapa Genetic Resources and Biotechnology, PqEB, W5 Norte Final, Brasília, DF, 70770-917, Brazil
| | - Brian L Abernathy
- University of Georgia, Center for Applied Genetic Technologies, 111 Riverbend Road, Athens, GA, 30602-6810, USA
| | - Scott A Jackson
- University of Georgia, Center for Applied Genetic Technologies, 111 Riverbend Road, Athens, GA, 30602-6810, USA
| | - Márcio C Moretzsohn
- Embrapa Genetic Resources and Biotechnology, PqEB, W5 Norte Final, Brasília, DF, 70770-917, Brazil
| | - David J Bertioli
- University of Georgia, Center for Applied Genetic Technologies, 111 Riverbend Road, Athens, GA, 30602-6810, USA
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12
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Hu XH, Zhang SZ, Miao HR, Cui FG, Shen Y, Yang WQ, Xu TT, Chen N, Chi XY, Zhang ZM, Chen J. High-Density Genetic Map Construction and Identification of QTLs Controlling Oleic and Linoleic Acid in Peanut using SLAF-seq and SSRs. Sci Rep 2018; 8:5479. [PMID: 29615772 PMCID: PMC5883025 DOI: 10.1038/s41598-018-23873-7] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Accepted: 03/20/2018] [Indexed: 11/08/2022] Open
Abstract
The cultivated peanut, A. hypogaea L., is an important oil and food crop globally.High-density genetic linkage mapping is a valuable and effective method for exploring complex quantitative traits. In this context, a recombinant inbred line (RIL) of 146 lines was developed by crossing Huayu28 and P76. We developed 433,679 high-quality SLAFs, of which 29,075 were polymorphic. 4,817 SLAFs were encoded and grouped into different segregation patterns. A high-resolution genetic map containing 2,334 markers (68 SSRs and 2,266 SNPs) on 20 linkage groups (LGs) spanning 2586.37 cM was constructed for peanut. The average distance between adjacent markers was 2.25 cM. Based on phenotyping in seven environments, QTLs for oleic acid (C18:1), linoleic acid (C18:2) and the ratio of oleic acid to linoleic acid (O/L) were identified and positioned on linkage groups A03, A04, A09, B09 and B10. Marker2575339 and Marker2379598 in B09 were associated with C18:1, C18:2 and O/L in seven environments, Marker4391589 and Marker4463600 in A09 were associated with C18:1, C18:2 and O/L in six environments. This map exhibits high resolution and accuracy, which will facilitate QTL discovery for essential agronomic traits in peanut.
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Affiliation(s)
- X H Hu
- Shandong Peanut Research Institute, Qingdao, 266100, P.R. China
| | - S Z Zhang
- Shandong Peanut Research Institute, Qingdao, 266100, P.R. China
| | - H R Miao
- Shandong Peanut Research Institute, Qingdao, 266100, P.R. China
| | - F G Cui
- Shandong Peanut Research Institute, Qingdao, 266100, P.R. China
| | - Y Shen
- Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, P.R. China
| | - W Q Yang
- Shandong Peanut Research Institute, Qingdao, 266100, P.R. China
| | - T T Xu
- Shandong Peanut Research Institute, Qingdao, 266100, P.R. China
| | - N Chen
- Shandong Peanut Research Institute, Qingdao, 266100, P.R. China
| | - X Y Chi
- Shandong Peanut Research Institute, Qingdao, 266100, P.R. China
| | - Z M Zhang
- Shandong Peanut Research Institute, Qingdao, 266100, P.R. China
| | - J Chen
- Shandong Peanut Research Institute, Qingdao, 266100, P.R. China.
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13
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do Nascimento EFDMB, Dos Santos BV, Marques LOC, Guimarães PM, Brasileiro ACM, Leal-Bertioli SCM, Bertioli DJ, Araujo ACG. The genome structure of Arachis hypogaea (Linnaeus, 1753) and an induced Arachis allotetraploid revealed by molecular cytogenetics. COMPARATIVE CYTOGENETICS 2018; 12:111-140. [PMID: 29675140 PMCID: PMC5904367 DOI: 10.3897/compcytogen.v12i1.20334] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Accepted: 01/23/2018] [Indexed: 05/03/2023]
Abstract
Peanut, Arachis hypogaea (Linnaeus, 1753) is an allotetraploid cultivated plant with two subgenomes derived from the hybridization between two diploid wild species, A. duranensis (Krapovickas & W. C. Gregory, 1994) and A. ipaensis (Krapovickas & W. C. Gregory, 1994), followed by spontaneous chromosomal duplication. To understand genome changes following polyploidy, the chromosomes of A. hypogaea, IpaDur1, an induced allotetraploid (A. ipaensis × A. duranensis)4x and the diploid progenitor species were cytogenetically compared. The karyotypes of the allotetraploids share the number and general morphology of chromosomes; DAPI+ bands pattern and number of 5S rDNA loci. However, one 5S rDNA locus presents a heteromorphic FISH signal in both allotetraploids, relative to corresponding progenitor. Whilst for A. hypogaea the number of 45S rDNA loci was equivalent to the sum of those present in the diploid species, in IpaDur1, two loci have not been detected. Overall distribution of repetitive DNA sequences was similar in both allotetraploids, although A. hypogaea had additional CMA3+ bands and few slight differences in the LTR-retrotransposons distribution compared to IpaDur1. GISH showed that the chromosomes of both allotetraploids had preferential hybridization to their corresponding diploid genomes. Nevertheless, at least one pair of IpaDur1 chromosomes had a clear mosaic hybridization pattern indicating recombination between the subgenomes, clear evidence that the genome of IpaDur1 shows some instability comparing to the genome of A. hypogaea that shows no mosaic of subgenomes, although both allotetraploids derive from the same progenitor species. For some reasons, the chromosome structure of A. hypogaea is inherently more stable, or, it has been at least, partially stabilized through genetic changes and selection.
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Affiliation(s)
- Eliza F de M B do Nascimento
- University of Brasilia, Institute of Biological Sciences, Campus Darcy Ribeiro, CEP 70.910-900, Brasília, DF, Brazil
- Embrapa Genetic Resources and Biotechnology, PqEB W5 Norte Final, CP 02372, CEP 70.770-917, Brasília, DF, Brazil
| | - Bruna V Dos Santos
- Embrapa Genetic Resources and Biotechnology, PqEB W5 Norte Final, CP 02372, CEP 70.770-917, Brasília, DF, Brazil
| | - Lara O C Marques
- Embrapa Genetic Resources and Biotechnology, PqEB W5 Norte Final, CP 02372, CEP 70.770-917, Brasília, DF, Brazil
- Catholic University of Brasilia, Campus I, CEP 71966-700, Brasília, DF, Brazil
| | - Patricia M Guimarães
- Embrapa Genetic Resources and Biotechnology, PqEB W5 Norte Final, CP 02372, CEP 70.770-917, Brasília, DF, Brazil
| | - Ana C M Brasileiro
- Embrapa Genetic Resources and Biotechnology, PqEB W5 Norte Final, CP 02372, CEP 70.770-917, Brasília, DF, Brazil
| | - Soraya C M Leal-Bertioli
- Center for Applied Genetic Technologies, University of Georgia, 111 Riverbend Road, 30602-6810, Athens, Georgia, USA
| | - David J Bertioli
- Center for Applied Genetic Technologies, University of Georgia, 111 Riverbend Road, 30602-6810, Athens, Georgia, USA
| | - Ana C G Araujo
- Embrapa Genetic Resources and Biotechnology, PqEB W5 Norte Final, CP 02372, CEP 70.770-917, Brasília, DF, Brazil
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14
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Classical and Molecular Approaches for Mapping of Genes and Quantitative Trait Loci in Peanut. ACTA ACUST UNITED AC 2017. [DOI: 10.1007/978-3-319-63935-2_7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/15/2023]
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15
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Clevenger J, Chu Y, Chavarro C, Agarwal G, Bertioli DJ, Leal-Bertioli SCM, Pandey MK, Vaughn J, Abernathy B, Barkley NA, Hovav R, Burow M, Nayak SN, Chitikineni A, Isleib TG, Holbrook CC, Jackson SA, Varshney RK, Ozias-Akins P. Genome-wide SNP Genotyping Resolves Signatures of Selection and Tetrasomic Recombination in Peanut. MOLECULAR PLANT 2017; 10:309-322. [PMID: 27993622 PMCID: PMC5315502 DOI: 10.1016/j.molp.2016.11.015] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2016] [Revised: 11/07/2016] [Accepted: 11/21/2016] [Indexed: 05/19/2023]
Abstract
Peanut (Arachis hypogaea; 2n = 4x = 40) is a nutritious food and a good source of vitamins, minerals, and healthy fats. Expansion of genetic and genomic resources for genetic enhancement of cultivated peanut has gained momentum from the sequenced genomes of the diploid ancestors of cultivated peanut. To facilitate high-throughput genotyping of Arachis species, 20 genotypes were re-sequenced and genome-wide single nucleotide polymorphisms (SNPs) were selected to develop a large-scale SNP genotyping array. For flexibility in genotyping applications, SNPs polymorphic between tetraploid and diploid species were included for use in cultivated and interspecific populations. A set of 384 accessions was used to test the array resulting in 54 564 markers that produced high-quality polymorphic clusters between diploid species, 47 116 polymorphic markers between cultivated and interspecific hybrids, and 15 897 polymorphic markers within A. hypogaea germplasm. An additional 1193 markers were identified that illuminated genomic regions exhibiting tetrasomic recombination. Furthermore, a set of elite cultivars that make up the pedigree of US runner germplasm were genotyped and used to identify genomic regions that have undergone positive selection. These observations provide key insights on the inclusion of new genetic diversity in cultivated peanut and will inform the development of high-resolution mapping populations. Due to its efficiency, scope, and flexibility, the newly developed SNP array will be very useful for further genetic and breeding applications in Arachis.
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Affiliation(s)
- Josh Clevenger
- Department of Horticulture and Institute of Plant Breeding, Genetics & Genomics, The University of Georgia, 2356 Rainwater Road, Tifton, GA 31793, USA
| | - Ye Chu
- Department of Horticulture and Institute of Plant Breeding, Genetics & Genomics, The University of Georgia, 2356 Rainwater Road, Tifton, GA 31793, USA
| | - Carolina Chavarro
- Center for Applied Genetic Technologies and Institute of Plant Breeding, Genetics & Genomics, The University of Georgia, Athens, GA 30602, USA
| | - Gaurav Agarwal
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad 502324, India
| | - David J Bertioli
- Center for Applied Genetic Technologies and Institute of Plant Breeding, Genetics & Genomics, The University of Georgia, Athens, GA 30602, USA; University of Brasília, Institute of Biological Sciences, Campus Darcy Ribeiro, 70910-900 Brasília, DF, Brazil
| | - Soraya C M Leal-Bertioli
- Center for Applied Genetic Technologies and Institute of Plant Breeding, Genetics & Genomics, The University of Georgia, Athens, GA 30602, USA; Embrapa Genetic Resources and Biotechnology, 70770-917 Brasília, DF, Brazil
| | - Manish K Pandey
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad 502324, India
| | - Justin Vaughn
- Center for Applied Genetic Technologies and Institute of Plant Breeding, Genetics & Genomics, The University of Georgia, Athens, GA 30602, USA
| | - Brian Abernathy
- Center for Applied Genetic Technologies and Institute of Plant Breeding, Genetics & Genomics, The University of Georgia, Athens, GA 30602, USA
| | | | - Ran Hovav
- Agricultural Research Organization, Plant Sciences Institute, 7528809 Rishon LeZion, Israel
| | - Mark Burow
- Department of Plant and Soil Science, Texas Tech University, Lubbock, TX 79409-2122, USA
| | - Spurthi N Nayak
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad 502324, India
| | - Annapurna Chitikineni
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad 502324, India
| | - Thomas G Isleib
- Department of Crop and Soil Sciences, North Carolina State University, Box 7629, Raleigh, NC 28695-7629, USA
| | | | - Scott A Jackson
- Center for Applied Genetic Technologies and Institute of Plant Breeding, Genetics & Genomics, The University of Georgia, Athens, GA 30602, USA
| | - Rajeev K Varshney
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad 502324, India
| | - Peggy Ozias-Akins
- Department of Horticulture and Institute of Plant Breeding, Genetics & Genomics, The University of Georgia, 2356 Rainwater Road, Tifton, GA 31793, USA.
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16
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Nguepjop JR, Tossim HA, Bell JM, Rami JF, Sharma S, Courtois B, Mallikarjuna N, Sane D, Fonceka D. Evidence of Genomic Exchanges between Homeologous Chromosomes in a Cross of Peanut with Newly Synthetized Allotetraploid Hybrids. FRONTIERS IN PLANT SCIENCE 2016; 7:1635. [PMID: 27847512 PMCID: PMC5088615 DOI: 10.3389/fpls.2016.01635] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2016] [Accepted: 10/17/2016] [Indexed: 05/02/2023]
Abstract
Cultivated peanut and synthetics are allotetraploids (2n = 4x = 40) with two homeologous sets of chromosomes. Meiosis in allotetraploid peanut is generally thought to show diploid-like behavior. However, a recent study pointed out the occurrence of recombination between homeologous chromosomes, especially when synthetic allotetraploids are used, challenging the view of disomic inheritance in peanut. In this study, we investigated the meiotic behavior of allotetraploid peanut using 380 SSR markers and 90 F2 progeny derived from the cross between Arachis hypogaea cv Fleur 11 (AABB) and ISATGR278-18 (AAKK), a synthetic allotetraploid that harbors a K-genome that was reported to pair with the cultivated B-genome during meiosis. Segregation analysis of SSR markers showed 42 codominant SSRs with unexpected null bands among some progeny. Chi-square tests for these loci deviate from the expected 1:2:1 Mendelian ratio under disomic inheritance. A linkage map of 357 codominant loci aligned on 20 linkage groups (LGs) with a total length of 1728 cM, averaging 5.1 cM between markers, was developed. Among the 10 homeologous sets of LGs, one set consisted of markers that all segregated in a polysomic-like pattern, six in a likely disomic pattern and the three remaining in a mixed pattern with disomic and polysomic loci clustered on the same LG. Moreover, we reported a substitution of homeologous chromosomes in some progeny. Our results suggest that the homeologous recombination events occurred between the A and K genomes in the newly synthesized allotetraploid and have been highlighted in the progeny. Homeologous exchanges are rarely observed in tetraploid peanut and have not yet been reported for AAKK and AABB genomes. The implications of these results on peanut breeding are discussed.
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Affiliation(s)
- Joel R. Nguepjop
- Centre d’Etudes Régional pour I’Amélioration de I’Adaptation à la SécheresseThies, Senegal
| | - Hodo-Abalo Tossim
- Centre d’Etudes Régional pour I’Amélioration de I’Adaptation à la SécheresseThies, Senegal
| | - Joseph M. Bell
- Département de Biologie et Physiologie Végétales, Université de Yaoundé IYaoundé, Cameroon
| | - Jean-François Rami
- UMR AGAP, Centre de Coopération Internationale en Recherche Agronomique pour le DéveloppementMontpellier, France
| | - Shivali Sharma
- International Crops Research Institute for the Semi-Arid TropicsPatancheru, India
| | - Brigitte Courtois
- Centre d’Etudes Régional pour I’Amélioration de I’Adaptation à la SécheresseThies, Senegal
| | - Nalini Mallikarjuna
- International Crops Research Institute for the Semi-Arid TropicsPatancheru, India
| | - Djibril Sane
- Département de Biologie Végétale, Université Cheikh Anta DiopDakar, Senegal
| | - Daniel Fonceka
- Centre d’Etudes Régional pour I’Amélioration de I’Adaptation à la SécheresseThies, Senegal
- UMR AGAP, Centre de Coopération Internationale en Recherche Agronomique pour le DéveloppementMontpellier, France
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Janila P, Variath MT, Pandey MK, Desmae H, Motagi BN, Okori P, Manohar SS, Rathnakumar AL, Radhakrishnan T, Liao B, Varshney RK. Genomic Tools in Groundnut Breeding Program: Status and Perspectives. FRONTIERS IN PLANT SCIENCE 2016; 7:289. [PMID: 27014312 PMCID: PMC4794498 DOI: 10.3389/fpls.2016.00289] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2015] [Accepted: 02/23/2016] [Indexed: 05/20/2023]
Abstract
Groundnut, a nutrient-rich food legume, is cultivated world over. It is valued for its good quality cooking oil, energy and protein rich food, and nutrient-rich fodder. Globally, groundnut improvement programs have developed varieties to meet the preferences of farmers, traders, processors, and consumers. Enhanced yield, tolerance to biotic and abiotic stresses and quality parameters have been the target traits. Spurt in genetic information of groundnut was facilitated by development of molecular markers, genetic, and physical maps, generation of expressed sequence tags (EST), discovery of genes, and identification of quantitative trait loci (QTL) for some important biotic and abiotic stresses and quality traits. The first groundnut variety developed using marker assisted breeding (MAB) was registered in 2003. Since then, USA, China, Japan, and India have begun to use genomic tools in routine groundnut improvement programs. Introgression lines that combine foliar fungal disease resistance and early maturity were developed using MAB. Establishment of marker-trait associations (MTA) paved way to integrate genomic tools in groundnut breeding for accelerated genetic gain. Genomic Selection (GS) tools are employed to improve drought tolerance and pod yield, governed by several minor effect QTLs. Draft genome sequence and low cost genotyping tools such as genotyping by sequencing (GBS) are expected to accelerate use of genomic tools to enhance genetic gains for target traits in groundnut.
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Affiliation(s)
- P. Janila
- International Crops Research Institute for Semi-Arid TropicsPatancheru, India
| | - Murali T. Variath
- International Crops Research Institute for Semi-Arid TropicsPatancheru, India
| | - Manish K. Pandey
- International Crops Research Institute for Semi-Arid TropicsPatancheru, India
| | - Haile Desmae
- International Crops Research Institute for Semi-Arid TropicsBamako, Mali
| | - Babu N. Motagi
- International Crops Research Institute for Semi-Arid TropicsKano, Nigeria
| | - Patrick Okori
- International Crops Research Institute for Semi-Arid TropicsLilongwe, Malawi
| | - Surendra S. Manohar
- International Crops Research Institute for Semi-Arid TropicsPatancheru, India
| | | | | | - Boshou Liao
- Oil Crops Research Institute Chinese Academy of Agricultural SciencesWuhan, China
| | - Rajeev K. Varshney
- International Crops Research Institute for Semi-Arid TropicsPatancheru, India
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18
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The genome sequences of Arachis duranensis and Arachis ipaensis, the diploid ancestors of cultivated peanut. Nat Genet 2016; 48:438-46. [PMID: 26901068 DOI: 10.1038/ng.3517] [Citation(s) in RCA: 469] [Impact Index Per Article: 58.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Accepted: 01/29/2016] [Indexed: 12/20/2022]
Abstract
Cultivated peanut (Arachis hypogaea) is an allotetraploid with closely related subgenomes of a total size of ∼2.7 Gb. This makes the assembly of chromosomal pseudomolecules very challenging. As a foundation to understanding the genome of cultivated peanut, we report the genome sequences of its diploid ancestors (Arachis duranensis and Arachis ipaensis). We show that these genomes are similar to cultivated peanut's A and B subgenomes and use them to identify candidate disease resistance genes, to guide tetraploid transcript assemblies and to detect genetic exchange between cultivated peanut's subgenomes. On the basis of remarkably high DNA identity of the A. ipaensis genome and the B subgenome of cultivated peanut and biogeographic evidence, we conclude that A. ipaensis may be a direct descendant of the same population that contributed the B subgenome to cultivated peanut.
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Zhou X, Xia Y, Ren X, Chen Y, Huang L, Huang S, Liao B, Lei Y, Yan L, Jiang H. Construction of a SNP-based genetic linkage map in cultivated peanut based on large scale marker development using next-generation double-digest restriction-site-associated DNA sequencing (ddRADseq). BMC Genomics 2014; 15:351. [PMID: 24885639 PMCID: PMC4035077 DOI: 10.1186/1471-2164-15-351] [Citation(s) in RCA: 115] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2013] [Accepted: 04/21/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Cultivated peanut, or groundnut (Arachis hypogaea L.), is an important oilseed crop with an allotetraploid genome (AABB, 2n=4x=40). In recent years, many efforts have been made to construct linkage maps in cultivated peanut, but almost all of these maps were constructed using low-throughput molecular markers, and most show a low density, directly influencing the value of their applications. With advances in next-generation sequencing (NGS) technology, the construction of high-density genetic maps has become more achievable in a cost-effective and rapid manner. The objective of this study was to establish a high-density single nucleotide polymorphism (SNP)-based genetic map for cultivated peanut by analyzing next-generation double-digest restriction-site-associated DNA sequencing (ddRADseq) reads. RESULTS We constructed reduced representation libraries (RRLs) for two A. hypogaea lines and 166 of their recombinant inbred line (RIL) progenies using the ddRADseq technique. Approximately 175 gigabases of data containing 952,679,665 paired-end reads were obtained following Solexa sequencing. Mining this dataset, 53,257 SNPs were detected between the parents, of which 14,663 SNPs were also detected in the population, and 1,765 of the obtained polymorphic markers met the requirements for use in the construction of a genetic map. Among 50 randomly selected in silico SNPs, 47 were able to be successfully validated. One linkage map was constructed, which was comprised of 1,685 marker loci, including 1,621 SNPs and 64 simple sequence repeat (SSR) markers. The map displayed a distribution of the markers into 20 linkage groups (LGs A01-A10 and B01-B10), spanning a distance of 1,446.7 cM. The alignment of the LGs from this map was shown in comparison with a previously integrated consensus map from peanut. CONCLUSIONS This study showed that the ddRAD library combined with NGS allowed the rapid discovery of a large number of SNPs in the cultivated peanut. The first high density SNP-based linkage map for A. hypogaea was generated that can serve as a reference map for cultivated Arachis species and will be useful in genetic mapping. Our results contribute to the available molecular marker resources and to the assembly of a reference genome sequence for the peanut.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Huifang Jiang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan 430062, Hubei, People's Republic of China.
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20
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Kumari V, Gowda M, Tasiwal V, Pandey MK, Bhat RS, Mallikarjuna N, Upadhyaya HD, Varshney RK. Diversification of primary gene pool through introgression of resistance to foliar diseases from synthetic amphidiploids to cultivated groundnut (Arachis hypogaea L.). ACTA ACUST UNITED AC 2014. [DOI: 10.1016/j.cj.2014.03.002] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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21
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Abstract
Single nucleotide polymorphic markers (SNPs) are attractive for use in genetic mapping and marker-assisted breeding because they can be scored in parallel assays at favorable costs. However, scoring SNP markers in polyploid plants like the peanut is problematic because of interfering signal generated from the DNA bases that are homeologous to those being assayed. The present study used a previously constructed 1536 GoldenGate SNP assay developed using SNPs identified between two A. duranensis accessions. In this study, the performance of this assay was tested on two RIL mapping populations, one diploid (A. duranensis × A. stenosperma) and one tetraploid [A. hypogaea cv. Runner IAC 886 × synthetic tetraploid (A. ipaënsis × A. duranensis)4×]. The scoring was performed using the software GenomeStudio version 2011.1. For the diploid, polymorphic markers provided excellent genotyping scores with default software parameters. In the tetraploid, as expected, most of the polymorphic markers provided signal intensity plots that were distorted compared to diploid patterns and that were incorrectly scored using default parameters. However, these scorings were easily corrected using the GenomeStudio software. The degree of distortion was highly variable. Of the polymorphic markers, approximately 10% showed no distortion at all behaving as expected for single-dose markers, and another 30% showed low distortion and could be considered high-quality. The genotyped markers were incorporated into diploid and tetraploid genetic maps of Arachis and, in the latter case, were located almost entirely on A genome linkage groups.
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22
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Sharma S, Upadhyaya HD, Varshney RK, Gowda CLL. Pre-breeding for diversification of primary gene pool and genetic enhancement of grain legumes. FRONTIERS IN PLANT SCIENCE 2013; 4:309. [PMID: 23970889 PMCID: PMC3747629 DOI: 10.3389/fpls.2013.00309] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2013] [Accepted: 07/23/2013] [Indexed: 05/18/2023]
Abstract
The narrow genetic base of cultivars coupled with low utilization of genetic resources are the major factors limiting grain legume production and productivity globally. Exploitation of new and diverse sources of variation is needed for the genetic enhancement of grain legumes. Wild relatives with enhanced levels of resistance/tolerance to multiple stresses provide important sources of genetic diversity for crop improvement. However, their exploitation for cultivar improvement is limited by cross-incompatibility barriers and linkage drags. Pre-breeding provides a unique opportunity, through the introgression of desirable genes from wild germplasm into genetic backgrounds readily used by the breeders with minimum linkage drag, to overcome this. Pre-breeding activities using promising landraces, wild relatives, and popular cultivars have been initiated at International Crops Research Institute for the Semi-Arid Tropics (ICRISAT) to develop new gene pools in chickpea, pigeonpea, and groundnut with a high frequency of useful genes, wider adaptability, and a broad genetic base. The availability of molecular markers will greatly assist in reducing linkage drags and increasing the efficiency of introgression in pre-breeding programs.
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Affiliation(s)
- Shivali Sharma
- International Crops Research Institute for the Semi-Arid TropicsHyderabad, India
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23
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Stalker HT, Tallury SP, Ozias-Akins P, Bertioli D, Bertioli SCL. The Value of Diploid Peanut Relatives for Breeding and Genomics. ACTA ACUST UNITED AC 2013. [DOI: 10.3146/ps13-6.1] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
ABSTRACT
Collection, evaluation, and introgression research has been conducted with Arachis species for more than 60 years. Eighty species in the genus have been described and additional species will be named in the future. Extremely high levels of disease and insect resistances to immunity have been observed in many species of the genus as compared to the cultivated peanut, which makes them extremely important for crop improvement. Many thousands of interspecific hybrids have been produced in the genus, but introgression has been slow because of genomic incompatibilities and sterility of hybrids. Genomics research was initiated during the late 1980s to characterize species relationships and investigate more efficient methods to introgress genes from wild species to A. hypogaea. Relatively low density genetic maps have been created from inter- and intra-specific crosses, several of which have placed disease resistance genes into limited linkage groups. Of particular interest is associating molecular markers with traits of interest to enhance breeding for disease and insect resistances. Only recently have sufficiently large numbers of markers become available to effectively conduct marker assisted breeding in peanut. Future analyses of the diploid ancestors of the cultivated peanut, A. duranensis and A. ipaensis, will allow more detailed characterization of peanut genetics and the effects of Arachis species alleles on agronomic traits. Extensive efforts are being made to create populations for genomic analyses of peanut, and introgression of genes from wild to cultivated genotypes should become more efficient in the near future.
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Affiliation(s)
- H. T. Stalker
- Department of Crop Science, North Carolina State University, Raleigh, NC 27695
| | - S. P. Tallury
- Department of Crop Science, North Carolina State University, Raleigh, NC 27695
| | - P. Ozias-Akins
- Department of Horticulture, The University of Georgia, Tifton, GA, 31973
| | - D. Bertioli
- Department of Gentics and Morphology, University of Brasilia, Campus Darcy Ribeiro, Brasília, DF. Brazil
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24
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Guo B, Pandey MK, He G, Zhang X, Liao B, Culbreath A, Varshney RK, Nwosu V, Wilson RF, Stalker HT. Recent Advances in Molecular Genetic Linkage Maps of Cultivated Peanut. ACTA ACUST UNITED AC 2013. [DOI: 10.3146/ps13-03.1] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
ABSTRACT
The competitiveness of peanuts in domestic and global markets has been threatened by losses in productivity and quality that are attributed to diseases, pests, environmental stresses and allergy or food safety issues. Narrow genetic diversity and a deficiency of polymorphic DNA markers severely hindered construction of dense genetic maps and quantitative trait loci (QTL) mapping in order to deploy linked markers in marker-assisted peanut improvement. The U.S. Peanut Genome Initiative (PGI) was launched in 2004, and expanded to a global effort in 2006 to address these issues through coordination of international efforts in genome research beginning with molecular marker development and improvement of map resolution and coverage. Ultimately, a peanut genome sequencing project was launched in 2012 by the Peanut Genome Consortium (PGC). We reviewed the progress for accelerated development of peanut genomic resources in peanut, such as generation of expressed sequenced tags (ESTs) (252,832 ESTs as December 2012 in the public NCBI EST database), development of molecular markers (over 15,518 SSRs), and construction of peanut genetic linkage maps, in particular for cultivated peanut. Several consensus genetic maps have been constructed, and there are examples of recent international efforts to develop high density maps. An international reference consensus genetic map was developed recently with 897 marker loci based on 11 published mapping populations. Furthermore, a high-density integrated consensus map of cultivated peanut and wild diploid relatives also has been developed, which was enriched further with 3693 marker loci on a single map by adding information from five new genetic mapping populations to the published reference consensus map.
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Affiliation(s)
- Baozhu Guo
- USDA- Agricultural Research Service, Crop Protection and Management Research Unit, Tifton, GA 31793
| | - Manish K. Pandey
- Department of Plant Pathology, University of Georgia, Athens, GA 30602
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad 502324, India
| | - Guohao He
- Department of Agricultural and Environmental Sciences, Tuskegee University, Tuskegee, AL 36088
| | - Xinyou Zhang
- Henan Academy of Agricultural Sciences, Zhengzhou 450002, China
| | - Boshou Liao
- Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Albert Culbreath
- Department of Plant Pathology, University of Georgia, Athens, GA 30602
| | - Rajeev K. Varshney
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad 502324, India
| | - Victor Nwosu
- Plant Science Program, Global Chocolate Science & Technology, Mars Chocolate North America, Hackettstown, NJ 07840
| | - Richard F. Wilson
- Oilseeds & Bioscience Consulting, 5517 Hickory Leaf Drive, Raleigh, NC 27606
| | - H. Thomas Stalker
- Department of Crop Science, North Carolina State University, Raleigh, NC 27695
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25
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Shirasawa K, Bertioli DJ, Varshney RK, Moretzsohn MC, Leal-Bertioli SCM, Thudi M, Pandey MK, Rami JF, Foncéka D, Gowda MVC, Qin H, Guo B, Hong Y, Liang X, Hirakawa H, Tabata S, Isobe S. Integrated consensus map of cultivated peanut and wild relatives reveals structures of the A and B genomes of Arachis and divergence of the legume genomes. DNA Res 2013; 20:173-84. [PMID: 23315685 PMCID: PMC3628447 DOI: 10.1093/dnares/dss042] [Citation(s) in RCA: 98] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2012] [Accepted: 12/21/2012] [Indexed: 02/02/2023] Open
Abstract
The complex, tetraploid genome structure of peanut (Arachis hypogaea) has obstructed advances in genetics and genomics in the species. The aim of this study is to understand the genome structure of Arachis by developing a high-density integrated consensus map. Three recombinant inbred line populations derived from crosses between the A genome diploid species, Arachis duranensis and Arachis stenosperma; the B genome diploid species, Arachis ipaënsis and Arachis magna; and between the AB genome tetraploids, A. hypogaea and an artificial amphidiploid (A. ipaënsis × A. duranensis)(4×), were used to construct genetic linkage maps: 10 linkage groups (LGs) of 544 cM with 597 loci for the A genome; 10 LGs of 461 cM with 798 loci for the B genome; and 20 LGs of 1442 cM with 1469 loci for the AB genome. The resultant maps plus 13 published maps were integrated into a consensus map covering 2651 cM with 3693 marker loci which was anchored to 20 consensus LGs corresponding to the A and B genomes. The comparative genomics with genome sequences of Cajanus cajan, Glycine max, Lotus japonicus, and Medicago truncatula revealed that the Arachis genome has segmented synteny relationship to the other legumes. The comparative maps in legumes, integrated tetraploid consensus maps, and genome-specific diploid maps will increase the genetic and genomic understanding of Arachis and should facilitate molecular breeding.
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Janila P, Nigam SN, Pandey MK, Nagesh P, Varshney RK. Groundnut improvement: use of genetic and genomic tools. FRONTIERS IN PLANT SCIENCE 2013; 4:23. [PMID: 23443056 PMCID: PMC3580887 DOI: 10.3389/fpls.2013.00023] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2012] [Accepted: 02/02/2013] [Indexed: 05/04/2023]
Abstract
Groundnut (Arachis hypogaea L.), a self-pollinated legume is an important crop cultivated in 24 million ha world over for extraction of edible oil and food uses. The kernels are rich in oil (48-50%) and protein (25-28%), and are source of several vitamins, minerals, antioxidants, biologically active polyphenols, flavonoids, and isoflavones. Improved varieties of groundnut with high yield potential were developed and released for cultivation world over. The improved varieties belong to different maturity durations and possess resistance to diseases, tolerance to drought, enhanced oil content, and improved quality traits for food uses. Conventional breeding procedures along with the tools for phenotyping were largely used in groundnut improvement programs. Mutations were used to induce variability and wide hybridization was attempted to tap variability from wild species. Low genetic variability has been a bottleneck for groundnut improvement. The vast potential of wild species, reservoir of new alleles remains under-utilized. Development of linkage maps of groundnut during the last decade was followed by identification of markers and quantitative trait loci for the target traits. Consequently, the last decade has witnessed the deployment of molecular breeding approaches to complement the ongoing groundnut improvement programs in USA, China, India, and Japan. The other potential advantages of molecular breeding are the feasibility to target multiple traits for improvement and provide tools to tap new alleles from wild species. The first groundnut variety developed through marker-assisted back-crossing is a root-knot nematode-resistant variety, NemaTAM in USA. The uptake of molecular breeding approaches in groundnut improvement programs by NARS partners in India and many African countries is slow or needs to be initiated in part due to inadequate infrastructure, high genotyping costs, and human capacities. Availability of draft genome sequence for diploid (AA and BB) and tetraploid, AABB genome species of Arachis in coming years is expected to bring low-cost genotyping to the groundnut community that will facilitate use of modern genetics and breeding approaches such as genome-wide association studies for trait mapping and genomic selection for crop improvement.
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Affiliation(s)
- Pasupuleti Janila
- International Crops Research Institute for the Semi-Arid TropicsPatancheru, Andhra Pradesh, India
| | - S. N. Nigam
- International Crops Research Institute for the Semi-Arid TropicsPatancheru, Andhra Pradesh, India
| | - Manish K. Pandey
- International Crops Research Institute for the Semi-Arid TropicsPatancheru, Andhra Pradesh, India
| | - P. Nagesh
- International Crops Research Institute for the Semi-Arid TropicsPatancheru, Andhra Pradesh, India
| | - Rajeev K. Varshney
- International Crops Research Institute for the Semi-Arid TropicsPatancheru, Andhra Pradesh, India
- Generation Challenge Programme, c/o Centro Internacional de Mejoramiento de Maíz y TrigoMexico DF, Mexico
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27
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Varshney RK, Mohan SM, Gaur PM, Gangarao NVPR, Pandey MK, Bohra A, Sawargaonkar SL, Chitikineni A, Kimurto PK, Janila P, Saxena KB, Fikre A, Sharma M, Rathore A, Pratap A, Tripathi S, Datta S, Chaturvedi SK, Mallikarjuna N, Anuradha G, Babbar A, Choudhary AK, Mhase MB, Bharadwaj C, Mannur DM, Harer PN, Guo B, Liang X, Nadarajan N, Gowda CLL. Achievements and prospects of genomics-assisted breeding in three legume crops of the semi-arid tropics. Biotechnol Adv 2013; 31:1120-34. [PMID: 23313999 DOI: 10.1016/j.biotechadv.2013.01.001] [Citation(s) in RCA: 157] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2012] [Revised: 12/16/2012] [Accepted: 01/03/2013] [Indexed: 10/27/2022]
Abstract
Advances in next-generation sequencing and genotyping technologies have enabled generation of large-scale genomic resources such as molecular markers, transcript reads and BAC-end sequences (BESs) in chickpea, pigeonpea and groundnut, three major legume crops of the semi-arid tropics. Comprehensive transcriptome assemblies and genome sequences have either been developed or underway in these crops. Based on these resources, dense genetic maps, QTL maps as well as physical maps for these legume species have also been developed. As a result, these crops have graduated from 'orphan' or 'less-studied' crops to 'genomic resources rich' crops. This article summarizes the above-mentioned advances in genomics and genomics-assisted breeding applications in the form of marker-assisted selection (MAS) for hybrid purity assessment in pigeonpea; marker-assisted backcrossing (MABC) for introgressing QTL region for drought-tolerance related traits, Fusarium wilt (FW) resistance and Ascochyta blight (AB) resistance in chickpea; late leaf spot (LLS), leaf rust and nematode resistance in groundnut. We critically present the case of use of other modern breeding approaches like marker-assisted recurrent selection (MARS) and genomic selection (GS) to utilize the full potential of genomics-assisted breeding for developing superior cultivars with enhanced tolerance to various environmental stresses. In addition, this article recommends the use of advanced-backcross (AB-backcross) breeding and development of specialized populations such as multi-parents advanced generation intercross (MAGIC) for creating new variations that will help in developing superior lines with broadened genetic base. In summary, we propose the use of integrated genomics and breeding approach in these legume crops to enhance crop productivity in marginal environments ensuring food security in developing countries.
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Affiliation(s)
- Rajeev K Varshney
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad 502324, India; CGIAR Generation Challenge Programme (GCP), c/o CIMMYT, DF 06600, Mexico; The University of Western Australia, Crawley 6009, Australia; Crops Research Institute, Guangdong Academy of Agricultural Sciences (GAAS), Guangzhou 510640, China.
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28
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Fonceka D, Tossim HA, Rivallan R, Vignes H, Lacut E, de Bellis F, Faye I, Ndoye O, Leal-Bertioli SCM, Valls JFM, Bertioli DJ, Glaszmann JC, Courtois B, Rami JF. Construction of chromosome segment substitution lines in peanut (Arachis hypogaea L.) using a wild synthetic and QTL mapping for plant morphology. PLoS One 2012; 7:e48642. [PMID: 23185268 PMCID: PMC3501512 DOI: 10.1371/journal.pone.0048642] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2012] [Accepted: 09/28/2012] [Indexed: 11/22/2022] Open
Abstract
Chromosome segment substitution lines (CSSLs) are powerful QTL mapping populations that have been used to elucidate the molecular basis of interesting traits of wild species. Cultivated peanut is an allotetraploid with limited genetic diversity. Capturing the genetic diversity from peanut wild relatives is an important objective in many peanut breeding programs. In this study, we used a marker-assisted backcrossing strategy to produce a population of 122 CSSLs from the cross between the wild synthetic allotetraploid (A. ipaënsis×A. duranensis)(4x) and the cultivated Fleur11 variety. The 122 CSSLs offered a broad coverage of the peanut genome, with target wild chromosome segments averaging 39.2 cM in length. As a demonstration of the utility of these lines, four traits were evaluated in a subset of 80 CSSLs. A total of 28 lines showed significant differences from Fleur11. The line×trait significant associations were assigned to 42 QTLs: 14 for plant growth habit, 15 for height of the main stem, 12 for plant spread and one for flower color. Among the 42 QTLs, 37 were assigned to genomic regions and three QTL positions were considered putative. One important finding arising from this QTL analysis is that peanut growth habit is a complex trait that is governed by several QTLs with different effects. The CSSL population developed in this study has proved efficient for deciphering the molecular basis of trait variations and will be useful to the peanut scientific community for future QTL mapping studies.
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Affiliation(s)
| | | | | | | | | | | | - Issa Faye
- ISRA, Centre National de Recherche Agronomique, Bambey, Sénégal
| | | | | | - José F. M. Valls
- Embrapa Recursos Genéticos e Biotecnologia, Brasilia, Distrito Federal, Brazil
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Guo Y, Khanal S, Tang S, Bowers JE, Heesacker AF, Khalilian N, Nagy ED, Zhang D, Taylor CA, Stalker HT, Ozias-Akins P, Knapp SJ. Comparative mapping in intraspecific populations uncovers a high degree of macrosynteny between A- and B-genome diploid species of peanut. BMC Genomics 2012; 13:608. [PMID: 23140574 PMCID: PMC3532320 DOI: 10.1186/1471-2164-13-608] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2012] [Accepted: 10/31/2012] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Cultivated peanut or groundnut (Arachis hypogaea L.) is an important oilseed crop with an allotetraploid genome (AABB, 2n = 4x = 40). Both the low level of genetic variation within the cultivated gene pool and its polyploid nature limit the utilization of molecular markers to explore genome structure and facilitate genetic improvement. Nevertheless, a wealth of genetic diversity exists in diploid Arachis species (2n = 2x = 20), which represent a valuable gene pool for cultivated peanut improvement. Interspecific populations have been used widely for genetic mapping in diploid species of Arachis. However, an intraspecific mapping strategy was essential to detect chromosomal rearrangements among species that could be obscured by mapping in interspecific populations. To develop intraspecific reference linkage maps and gain insights into karyotypic evolution within the genus, we comparatively mapped the A- and B-genome diploid species using intraspecific F2 populations. Exploring genome organization among diploid peanut species by comparative mapping will enhance our understanding of the cultivated tetraploid peanut genome. Moreover, new sources of molecular markers that are highly transferable between species and developed from expressed genes will be required to construct saturated genetic maps for peanut. RESULTS A total of 2,138 EST-SSR (expressed sequence tag-simple sequence repeat) markers were developed by mining a tetraploid peanut EST assembly including 101,132 unigenes (37,916 contigs and 63,216 singletons) derived from 70,771 long-read (Sanger) and 270,957 short-read (454) sequences. A set of 97 SSR markers were also developed by mining 9,517 genomic survey sequences of Arachis. An SSR-based intraspecific linkage map was constructed using an F2 population derived from a cross between K 9484 (PI 298639) and GKBSPSc 30081 (PI 468327) in the B-genome species A. batizocoi. A high degree of macrosynteny was observed when comparing the homoeologous linkage groups between A (A. duranensis) and B (A. batizocoi) genomes. Comparison of the A- and B-genome genetic linkage maps also showed a total of five inversions and one major reciprocal translocation between two pairs of chromosomes under our current mapping resolution. CONCLUSIONS Our findings will contribute to understanding tetraploid peanut genome origin and evolution and eventually promote its genetic improvement. The newly developed EST-SSR markers will enrich current molecular marker resources in peanut.
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Affiliation(s)
- Yufang Guo
- Institute of Plant Breeding, Genetics, and Genomics, 111 Riverbend Road, The University of Georgia, Athens, GA, 30602, USA
- Department of Horticulture, The University of Georgia, Tifton, GA, 31973, USA
| | - Sameer Khanal
- Institute of Plant Breeding, Genetics, and Genomics, 111 Riverbend Road, The University of Georgia, Athens, GA, 30602, USA
| | - Shunxue Tang
- Institute of Plant Breeding, Genetics, and Genomics, 111 Riverbend Road, The University of Georgia, Athens, GA, 30602, USA
| | - John E Bowers
- Institute of Plant Breeding, Genetics, and Genomics, 111 Riverbend Road, The University of Georgia, Athens, GA, 30602, USA
| | - Adam F Heesacker
- Institute of Plant Breeding, Genetics, and Genomics, 111 Riverbend Road, The University of Georgia, Athens, GA, 30602, USA
| | - Nelly Khalilian
- Institute of Plant Breeding, Genetics, and Genomics, 111 Riverbend Road, The University of Georgia, Athens, GA, 30602, USA
| | - Ervin D Nagy
- Institute of Plant Breeding, Genetics, and Genomics, 111 Riverbend Road, The University of Georgia, Athens, GA, 30602, USA
| | - Dong Zhang
- Institute of Plant Breeding, Genetics, and Genomics, 111 Riverbend Road, The University of Georgia, Athens, GA, 30602, USA
| | - Christopher A Taylor
- Institute of Plant Breeding, Genetics, and Genomics, 111 Riverbend Road, The University of Georgia, Athens, GA, 30602, USA
| | - H Thomas Stalker
- Department of Crop Science, North Carolina State University, Raleigh, NC, 27695, USA
| | - Peggy Ozias-Akins
- Department of Horticulture, The University of Georgia, Tifton, GA, 31973, USA
| | - Steven J Knapp
- Institute of Plant Breeding, Genetics, and Genomics, 111 Riverbend Road, The University of Georgia, Athens, GA, 30602, USA
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Nagy ED, Guo Y, Tang S, Bowers JE, Okashah RA, Taylor CA, Zhang D, Khanal S, Heesacker AF, Khalilian N, Farmer AD, Carrasquilla-Garcia N, Penmetsa RV, Cook D, Stalker HT, Nielsen N, Ozias-Akins P, Knapp SJ. A high-density genetic map of Arachis duranensis, a diploid ancestor of cultivated peanut. BMC Genomics 2012; 13:469. [PMID: 22967170 PMCID: PMC3542255 DOI: 10.1186/1471-2164-13-469] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2011] [Accepted: 08/30/2012] [Indexed: 01/06/2023] Open
Abstract
Background Cultivated peanut (Arachis hypogaea) is an allotetraploid species whose ancestral genomes are most likely derived from the A-genome species, A. duranensis, and the B-genome species, A. ipaensis. The very recent (several millennia) evolutionary origin of A. hypogaea has imposed a bottleneck for allelic and phenotypic diversity within the cultigen. However, wild diploid relatives are a rich source of alleles that could be used for crop improvement and their simpler genomes can be more easily analyzed while providing insight into the structure of the allotetraploid peanut genome. The objective of this research was to establish a high-density genetic map of the diploid species A. duranensis based on de novo generated EST databases. Arachis duranensis was chosen for mapping because it is the A-genome progenitor of cultivated peanut and also in order to circumvent the confounding effects of gene duplication associated with allopolyploidy in A. hypogaea. Results More than one million expressed sequence tag (EST) sequences generated from normalized cDNA libraries of A. duranensis were assembled into 81,116 unique transcripts. Mining this dataset, 1236 EST-SNP markers were developed between two A. duranensis accessions, PI 475887 and Grif 15036. An additional 300 SNP markers also were developed from genomic sequences representing conserved legume orthologs. Of the 1536 SNP markers, 1054 were placed on a genetic map. In addition, 598 EST-SSR markers identified in A. hypogaea assemblies were included in the map along with 37 disease resistance gene candidate (RGC) and 35 other previously published markers. In total, 1724 markers spanning 1081.3 cM over 10 linkage groups were mapped. Gene sequences that provided mapped markers were annotated using similarity searches in three different databases, and gene ontology descriptions were determined using the Medicago Gene Atlas and TAIR databases. Synteny analysis between A. duranensis, Medicago and Glycine revealed significant stretches of conserved gene clusters spread across the peanut genome. A higher level of colinearity was detected between A. duranensis and Glycine than with Medicago. Conclusions The first high-density, gene-based linkage map for A. duranensis was generated that can serve as a reference map for both wild and cultivated Arachis species. The markers developed here are valuable resources for the peanut, and more broadly, to the legume research community. The A-genome map will have utility for fine mapping in other peanut species and has already had application for mapping a nematode resistance gene that was introgressed into A. hypogaea from A. cardenasii.
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Affiliation(s)
- Ervin D Nagy
- Institute of Plant Breeding, Genetics and Genomics, University of Georgia,111 Riverbend Rd, Athens, GA 30605, USA
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Sujay V, Gowda MVC, Pandey MK, Bhat RS, Khedikar YP, Nadaf HL, Gautami B, Sarvamangala C, Lingaraju S, Radhakrishan T, Knapp SJ, Varshney RK. Quantitative trait locus analysis and construction of consensus genetic map for foliar disease resistance based on two recombinant inbred line populations in cultivated groundnut (Arachis hypogaea L.). MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2012; 30:773-788. [PMID: 22924018 PMCID: PMC3410029 DOI: 10.1007/s11032-011-9661-z] [Citation(s) in RCA: 76] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2011] [Accepted: 10/17/2011] [Indexed: 05/20/2023]
Abstract
Late leaf spot (LLS) and rust have the greatest impact on yield losses worldwide in groundnut (Arachis hypogaea L.). With the objective of identifying tightly linked markers to these diseases, a total of 3,097 simple sequence repeats (SSRs) were screened on the parents of two recombinant inbred line (RIL) populations, namely TAG 24 × GPBD 4 (RIL-4) and TG 26 × GPBD 4 (RIL-5), and segregation data were obtained for 209 marker loci for each of the mapping populations. Linkage map analysis of the 209 loci resulted in the mapping of 188 and 181 loci in RIL-4 and RIL-5 respectively. Using 143 markers common to the two maps, a consensus map with 225 SSR loci and total map distance of 1,152.9 cM was developed. Comprehensive quantitative trait locus (QTL) analysis detected a total of 28 QTL for LLS and 15 QTL for rust. A major QTL for LLS, namely QTL(LLS)01 (GM1573/GM1009-pPGPseq8D09), with 10.27-62.34% phenotypic variance explained (PVE) was detected in all the six environments in the RIL-4 population. In the case of rust resistance, in addition to marker IPAHM103 identified earlier, four new markers (GM2009, GM1536, GM2301 and GM2079) showed significant association with the major QTL (82.96% PVE). Localization of 42 QTL for LLS and rust on the consensus map identified two candidate genomic regions conferring resistance to LLS and rust. One region present on linkage group AhXV contained three QTL each for LLS (up to 67.98% PVE) and rust (up to 82.96% PVE). The second candidate genomic region contained the major QTL with up to 62.34% PVE for LLS. Molecular markers associated with the major QTL for resistance to LLS and rust can be deployed in molecular breeding for developing groundnut varieties with enhanced resistance to foliar diseases. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1007/s11032-011-9661-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- V. Sujay
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, 502 324 India
- Department of Genetics and Plant Breeding, University of Agricultural Sciences, Dharwad, 580 005 India
| | - M. V. C. Gowda
- Department of Genetics and Plant Breeding, University of Agricultural Sciences, Dharwad, 580 005 India
| | - M. K. Pandey
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, 502 324 India
| | - R. S. Bhat
- Department of Biotechnology, University of Agricultural Sciences, Dharwad, 580 005 India
| | - Y. P. Khedikar
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, 502 324 India
- Department of Genetics and Plant Breeding, University of Agricultural Sciences, Dharwad, 580 005 India
| | - H. L. Nadaf
- Department of Genetics and Plant Breeding, University of Agricultural Sciences, Dharwad, 580 005 India
| | - B. Gautami
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, 502 324 India
| | - C. Sarvamangala
- Department of Genetics and Plant Breeding, University of Agricultural Sciences, Dharwad, 580 005 India
| | - S. Lingaraju
- Department of Plant Pathology, University of Agricultural Sciences, Dharwad, 580 005 India
| | - T. Radhakrishan
- Directorate of Groundnut Research (DGR), Junagadh, 362 001 India
| | - S. J. Knapp
- The University of Georgia, Athens, GA 30602 USA
| | - R. K. Varshney
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, 502 324 India
- CGIAR-Generation Challenge Programme (GCP), c/o CIMMYT, Mexico, DF 06600 Mexico
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Zhao Y, Prakash CS, He G. Characterization and compilation of polymorphic simple sequence repeat (SSR) markers of peanut from public database. BMC Res Notes 2012; 5:362. [PMID: 22818284 PMCID: PMC3500262 DOI: 10.1186/1756-0500-5-362] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2012] [Accepted: 06/25/2012] [Indexed: 12/22/2022] Open
Abstract
Background There are several reports describing thousands of SSR markers in the peanut (Arachis hypogaea L.) genome. There is a need to integrate various research reports of peanut DNA polymorphism into a single platform. Further, because of lack of uniformity in the labeling of these markers across the publications, there is some confusion on the identities of many markers. We describe below an effort to develop a central comprehensive database of polymorphic SSR markers in peanut. Findings We compiled 1,343 SSR markers as detecting polymorphism (14.5%) within a total of 9,274 markers. Amongst all polymorphic SSRs examined, we found that AG motif (36.5%) was the most abundant followed by AAG (12.1%), AAT (10.9%), and AT (10.3%).The mean length of SSR repeats in dinucleotide SSRs was significantly longer than that in trinucleotide SSRs. Dinucleotide SSRs showed higher polymorphism frequency for genomic SSRs when compared to trinucleotide SSRs, while for EST-SSRs, the frequency of polymorphic SSRs was higher in trinucleotide SSRs than in dinucleotide SSRs. The correlation of the length of SSR and the frequency of polymorphism revealed that the frequency of polymorphism was decreased as motif repeat number increased. Conclusions The assembled polymorphic SSRs would enhance the density of the existing genetic maps of peanut, which could also be a useful source of DNA markers suitable for high-throughput QTL mapping and marker-assisted selection in peanut improvement and thus would be of value to breeders.
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Affiliation(s)
- Yongli Zhao
- Department of Agricultural and Environmental Sciences, Tuskegee University, Tuskegee, AL 36088, USA
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Gautami B, Foncéka D, Pandey MK, Moretzsohn MC, Sujay V, Qin H, Hong Y, Faye I, Chen X, BhanuPrakash A, Shah TM, Gowda MVC, Nigam SN, Liang X, Hoisington DA, Guo B, Bertioli DJ, Rami JF, Varshney RK. An international reference consensus genetic map with 897 marker loci based on 11 mapping populations for tetraploid groundnut (Arachis hypogaea L.). PLoS One 2012; 7:e41213. [PMID: 22815973 PMCID: PMC3399818 DOI: 10.1371/journal.pone.0041213] [Citation(s) in RCA: 83] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2012] [Accepted: 06/18/2012] [Indexed: 01/21/2023] Open
Abstract
Only a few genetic maps based on recombinant inbred line (RIL) and backcross (BC) populations have been developed for tetraploid groundnut. The marker density, however, is not very satisfactory especially in the context of large genome size (2800 Mb/1C) and 20 linkage groups (LGs). Therefore, using marker segregation data for 10 RILs and one BC population from the international groundnut community, with the help of common markers across different populations, a reference consensus genetic map has been developed. This map is comprised of 897 marker loci including 895 simple sequence repeat (SSR) and 2 cleaved amplified polymorphic sequence (CAPS) loci distributed on 20 LGs (a01-a10 and b01-b10) spanning a map distance of 3, 863.6 cM with an average map density of 4.4 cM. The highest numbers of markers (70) were integrated on a01 and the least number of markers (21) on b09. The marker density, however, was lowest (6.4 cM) on a08 and highest (2.5 cM) on a01. The reference consensus map has been divided into 20 cM long 203 BINs. These BINs carry 1 (a10_02, a10_08 and a10_09) to 20 (a10_04) loci with an average of 4 marker loci per BIN. Although the polymorphism information content (PIC) value was available for 526 markers in 190 BINs, 36 and 111 BINs have at least one marker with >0.70 and >0.50 PIC values, respectively. This information will be useful for selecting highly informative and uniformly distributed markers for developing new genetic maps, background selection and diversity analysis. Most importantly, this reference consensus map will serve as a reliable reference for aligning new genetic and physical maps, performing QTL analysis in a multi-populations design, evaluating the genetic background effect on QTL expression, and serving other genetic and molecular breeding activities in groundnut.
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Affiliation(s)
- Bhimana Gautami
- Center of Excellence in Genomics, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India
| | - Daniel Foncéka
- UMR Développement et Amélioration des plantes, Centre de coopération Internationale en Recherche Agronomique pour le Développement (CIRAD), Montpellier, France
| | - Manish K. Pandey
- Center of Excellence in Genomics, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India
- Department of Plant Pathology, University of Georgia (UGA), Tifton, Georgia, United States of America
- Crop Protection and Management Research Unit, USDA-Agricultural Research Service, Tifton, Georgia, United States of America
| | - Márcio C. Moretzsohn
- Plant Genetics Lab, EMBRAPA Genetic Resources and Biotechnology, Brasilia, Brazil
| | - Venkataswamy Sujay
- Center of Excellence in Genomics, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India
- Department of Genetics and Plant Breeding, University of Agricultural Sciences (UAS-D), Dharwad, India
| | - Hongde Qin
- Department of Plant Pathology, University of Georgia (UGA), Tifton, Georgia, United States of America
- Cash Crop Research Institute, Hubei Academy of Agricultural Sciences (HAAS), Wuhan, Hubei, China
| | - Yanbin Hong
- Crops Research Institute, Guangdong Academy of Agricultural Sciences (GAAS), Guangzhou, Guangdong, China
| | - Issa Faye
- Centre National de Recherche Agronomique (CNRA), Institut Sénégalais de Recherches Agricoles (ISRA), Bambey, Sénégal
| | - Xiaoping Chen
- Crops Research Institute, Guangdong Academy of Agricultural Sciences (GAAS), Guangzhou, Guangdong, China
| | - Amindala BhanuPrakash
- Center of Excellence in Genomics, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India
| | - Trushar M. Shah
- Center of Excellence in Genomics, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India
| | - Makanahally V. C. Gowda
- Department of Genetics and Plant Breeding, University of Agricultural Sciences (UAS-D), Dharwad, India
| | - Shyam N. Nigam
- Center of Excellence in Genomics, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India
| | - Xuanqiang Liang
- Crops Research Institute, Guangdong Academy of Agricultural Sciences (GAAS), Guangzhou, Guangdong, China
| | - Dave A. Hoisington
- Center of Excellence in Genomics, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India
| | - Baozhu Guo
- Crop Protection and Management Research Unit, USDA-Agricultural Research Service, Tifton, Georgia, United States of America
| | | | - Jean-Francois Rami
- UMR Développement et Amélioration des plantes, Centre de coopération Internationale en Recherche Agronomique pour le Développement (CIRAD), Montpellier, France
| | - Rajeev K. Varshney
- Center of Excellence in Genomics, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India
- Crops Research Institute, Guangdong Academy of Agricultural Sciences (GAAS), Guangzhou, Guangdong, China
- Theme- Comparative and Applied Genomics, CGIAR Generation Challenge Programme (GCP), CIMMYT, Mexico, Mexico
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Peanut (Arachis hypogaea) Expressed Sequence Tag Project: Progress and Application. Comp Funct Genomics 2012; 2012:373768. [PMID: 22745594 PMCID: PMC3382957 DOI: 10.1155/2012/373768] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2012] [Accepted: 04/26/2012] [Indexed: 12/12/2022] Open
Abstract
Many plant ESTs have been sequenced as an alternative to whole genome sequences, including peanut because of the genome size and complexity. The US peanut research community had the historic 2004 Atlanta Genomics Workshop and named the EST project as a main priority. As of August 2011, the peanut research community had deposited 252,832 ESTs in the public NCBI EST database, and this resource has been providing the community valuable tools and core foundations for various genome-scale experiments before the whole genome sequencing project. These EST resources have been used for marker development, gene cloning, microarray gene expression and genetic map construction. Certainly, the peanut EST sequence resources have been shown to have a wide range of applications and accomplished its essential role at the time of need. Then the EST project contributes to the second historic event, the Peanut Genome Project 2010 Inaugural Meeting also held in Atlanta where it was decided to sequence the entire peanut genome. After the completion of peanut whole genome sequencing, ESTs or transcriptome will continue to play an important role to fill in knowledge gaps, to identify particular genes and to explore gene function.
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Shirasawa K, Koilkonda P, Aoki K, Hirakawa H, Tabata S, Watanabe M, Hasegawa M, Kiyoshima H, Suzuki S, Kuwata C, Naito Y, Kuboyama T, Nakaya A, Sasamoto S, Watanabe A, Kato M, Kawashima K, Kishida Y, Kohara M, Kurabayashi A, Takahashi C, Tsuruoka H, Wada T, Isobe S. In silico polymorphism analysis for the development of simple sequence repeat and transposon markers and construction of linkage map in cultivated peanut. BMC PLANT BIOLOGY 2012; 12:80. [PMID: 22672714 PMCID: PMC3404960 DOI: 10.1186/1471-2229-12-80] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2012] [Accepted: 06/06/2012] [Indexed: 05/18/2023]
Abstract
BACKGROUND Peanut (Arachis hypogaea) is an autogamous allotetraploid legume (2n = 4x = 40) that is widely cultivated as a food and oil crop. More than 6,000 DNA markers have been developed in Arachis spp., but high-density linkage maps useful for genetics, genomics, and breeding have not been constructed due to extremely low genetic diversity. Polymorphic marker loci are useful for the construction of such high-density linkage maps. The present study used in silico analysis to develop simple sequence repeat-based and transposon-based markers. RESULTS The use of in silico analysis increased the efficiency of polymorphic marker development by more than 3-fold. In total, 926 (34.2%) of 2,702 markers showed polymorphisms between parental lines of the mapping population. Linkage analysis of the 926 markers along with 253 polymorphic markers selected from 4,449 published markers generated 21 linkage groups covering 2,166.4 cM with 1,114 loci. Based on the map thus produced, 23 quantitative trait loci (QTLs) for 15 agronomical traits were detected. Another linkage map with 326 loci was also constructed and revealed a relationship between the genotypes of the FAD2 genes and the ratio of oleic/linoleic acid in peanut seed. CONCLUSIONS In silico analysis of polymorphisms increased the efficiency of polymorphic marker development, and contributed to the construction of high-density linkage maps in cultivated peanut. The resultant maps were applicable to QTL analysis. Marker subsets and linkage maps developed in this study should be useful for genetics, genomics, and breeding in Arachis. The data are available at the Kazusa DNA Marker Database (http://marker.kazusa.or.jp).
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Affiliation(s)
- Kenta Shirasawa
- Kazusa DNA Research Institute, 2-6-7 Kazusa-Kamatari, Kisarazu, Chiba, 292-0818, Japan
| | - Padmalatha Koilkonda
- Kazusa DNA Research Institute, 2-6-7 Kazusa-Kamatari, Kisarazu, Chiba, 292-0818, Japan
| | - Koh Aoki
- Kazusa DNA Research Institute, 2-6-7 Kazusa-Kamatari, Kisarazu, Chiba, 292-0818, Japan
- Graduate School of Life & Environmental Sciences, Osaka Prefecture University, 1-1 Gakuencho, Naka, Sakai, Osaka, 599-8531, Japan
| | - Hideki Hirakawa
- Kazusa DNA Research Institute, 2-6-7 Kazusa-Kamatari, Kisarazu, Chiba, 292-0818, Japan
| | - Satoshi Tabata
- Kazusa DNA Research Institute, 2-6-7 Kazusa-Kamatari, Kisarazu, Chiba, 292-0818, Japan
| | - Manabu Watanabe
- Chiba Prefectural Agriculture and Forestry Research Center, 808 Daizennocho, Midori, Chiba, 266-0006, Japan
| | - Makoto Hasegawa
- Chiba Prefectural Agriculture and Forestry Research Center, 808 Daizennocho, Midori, Chiba, 266-0006, Japan
| | - Hiroyuki Kiyoshima
- Chiba Prefectural Agriculture and Forestry Research Center, 808 Daizennocho, Midori, Chiba, 266-0006, Japan
| | - Shigeru Suzuki
- Chiba Prefectural Agriculture and Forestry Research Center, 808 Daizennocho, Midori, Chiba, 266-0006, Japan
| | - Chikara Kuwata
- Chiba Prefectural Agriculture and Forestry Research Center, 808 Daizennocho, Midori, Chiba, 266-0006, Japan
| | - Yoshiki Naito
- Mitsubishi Chemical Medience Corporation, 4-25-11 Azusawa, Itabashi, Tokyo, 174-0051, Japan
| | - Tsutomu Kuboyama
- College of Agriculture, Ibaraki University, 3-21-1 Chuo, Ami, Ibaraki, 300-0393, Japan
| | - Akihiro Nakaya
- Center for Transdisciplinary Research, Niigata University, 1-757 Asahimachidori, Chuo, Niigata, 951-8585, Japan
| | - Shigemi Sasamoto
- Kazusa DNA Research Institute, 2-6-7 Kazusa-Kamatari, Kisarazu, Chiba, 292-0818, Japan
| | - Akiko Watanabe
- Kazusa DNA Research Institute, 2-6-7 Kazusa-Kamatari, Kisarazu, Chiba, 292-0818, Japan
| | - Midori Kato
- Kazusa DNA Research Institute, 2-6-7 Kazusa-Kamatari, Kisarazu, Chiba, 292-0818, Japan
| | - Kumiko Kawashima
- Kazusa DNA Research Institute, 2-6-7 Kazusa-Kamatari, Kisarazu, Chiba, 292-0818, Japan
| | - Yoshie Kishida
- Kazusa DNA Research Institute, 2-6-7 Kazusa-Kamatari, Kisarazu, Chiba, 292-0818, Japan
| | - Mitsuyo Kohara
- Kazusa DNA Research Institute, 2-6-7 Kazusa-Kamatari, Kisarazu, Chiba, 292-0818, Japan
| | - Atsushi Kurabayashi
- Kazusa DNA Research Institute, 2-6-7 Kazusa-Kamatari, Kisarazu, Chiba, 292-0818, Japan
| | - Chika Takahashi
- Kazusa DNA Research Institute, 2-6-7 Kazusa-Kamatari, Kisarazu, Chiba, 292-0818, Japan
| | - Hisano Tsuruoka
- Kazusa DNA Research Institute, 2-6-7 Kazusa-Kamatari, Kisarazu, Chiba, 292-0818, Japan
| | - Tsuyuko Wada
- Kazusa DNA Research Institute, 2-6-7 Kazusa-Kamatari, Kisarazu, Chiba, 292-0818, Japan
| | - Sachiko Isobe
- Kazusa DNA Research Institute, 2-6-7 Kazusa-Kamatari, Kisarazu, Chiba, 292-0818, Japan
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Koilkonda P, Sato S, Tabata S, Shirasawa K, Hirakawa H, Sakai H, Sasamoto S, Watanabe A, Wada T, Kishida Y, Tsuruoka H, Fujishiro T, Yamada M, Kohara M, Suzuki S, Hasegawa M, Kiyoshima H, Isobe S. Large-scale development of expressed sequence tag-derived simple sequence repeat markers and diversity analysis in Arachis spp. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2012; 30:125-138. [PMID: 22707912 PMCID: PMC3362703 DOI: 10.1007/s11032-011-9604-8] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2011] [Accepted: 06/07/2011] [Indexed: 05/20/2023]
Abstract
Large-scale development of expressed sequence tag simple sequence repeat (EST-SSR) markers was performed in peanut (Arachis hypogaea L.) to obtain more informative genetic markers. A total of 10,102 potential non-redundant EST sequences, including 3,445 contigs and 6,657 singletons, were generated from cDNA libraries of the gynophore, roots, leaves and seedlings. A total of 3,187 primer pairs were designed on flanking regions of SSRs, some of which allowed one and two base mismatches. Among the 3,187 markers generated, 2,540 (80%) were trinucleotide repeats, 302 (9%) were dinucleotide repeats, and 345 (11%) were tetranucleotide repeats. Pre-polymorphic analyses of 24 Arachis accessions were performed using 10% polyacrylamide gels. A total of 1,571 EST-SSR markers showing clear polymorphisms were selected for further polymorphic analysis with a Fluoro-fragment Analyzer. The 16 Arachis accessions examined included cultivated peanut varieties as well as diploid species with the A or B genome. Altogether 1,281 (81.5%) of the 1,571 markers were polymorphic among the 16 accessions, and 366 (23.3%) were polymorphic among the 12 cultivated varieties. Diversity analysis was performed and the genotypes of all 16 Arachis accessions showed similarity coefficients ranging from 0.37 to 0.97. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1007/s11032-011-9604-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Padmalatha Koilkonda
- Kazusa DNA Research Institute, 2-6-7 Kazusa-Kamatari, Kisarazu, Chiba 292-0818 Japan
| | - Shusei Sato
- Kazusa DNA Research Institute, 2-6-7 Kazusa-Kamatari, Kisarazu, Chiba 292-0818 Japan
| | - Satoshi Tabata
- Kazusa DNA Research Institute, 2-6-7 Kazusa-Kamatari, Kisarazu, Chiba 292-0818 Japan
| | - Kenta Shirasawa
- Kazusa DNA Research Institute, 2-6-7 Kazusa-Kamatari, Kisarazu, Chiba 292-0818 Japan
| | - Hideki Hirakawa
- Kazusa DNA Research Institute, 2-6-7 Kazusa-Kamatari, Kisarazu, Chiba 292-0818 Japan
| | - Hiroe Sakai
- Kazusa DNA Research Institute, 2-6-7 Kazusa-Kamatari, Kisarazu, Chiba 292-0818 Japan
| | - Shigemi Sasamoto
- Kazusa DNA Research Institute, 2-6-7 Kazusa-Kamatari, Kisarazu, Chiba 292-0818 Japan
| | - Akiko Watanabe
- Kazusa DNA Research Institute, 2-6-7 Kazusa-Kamatari, Kisarazu, Chiba 292-0818 Japan
| | - Tsuyuko Wada
- Kazusa DNA Research Institute, 2-6-7 Kazusa-Kamatari, Kisarazu, Chiba 292-0818 Japan
| | - Yoshie Kishida
- Kazusa DNA Research Institute, 2-6-7 Kazusa-Kamatari, Kisarazu, Chiba 292-0818 Japan
| | - Hisano Tsuruoka
- Kazusa DNA Research Institute, 2-6-7 Kazusa-Kamatari, Kisarazu, Chiba 292-0818 Japan
| | - Tsunakazu Fujishiro
- Kazusa DNA Research Institute, 2-6-7 Kazusa-Kamatari, Kisarazu, Chiba 292-0818 Japan
| | - Manabu Yamada
- Kazusa DNA Research Institute, 2-6-7 Kazusa-Kamatari, Kisarazu, Chiba 292-0818 Japan
| | - Mitsuyo Kohara
- Kazusa DNA Research Institute, 2-6-7 Kazusa-Kamatari, Kisarazu, Chiba 292-0818 Japan
| | - Shigeru Suzuki
- Chiba Prefectural Agriculture and Forestry Research Center, Daizenno-cyou 808, Midori, Chiba 266-0006 Japan
| | - Makoto Hasegawa
- Chiba Prefectural Agriculture and Forestry Research Center, Daizenno-cyou 808, Midori, Chiba 266-0006 Japan
| | - Hiroyuki Kiyoshima
- Chiba Prefectural Agriculture and Forestry Research Center, Daizenno-cyou 808, Midori, Chiba 266-0006 Japan
| | - Sachiko Isobe
- Kazusa DNA Research Institute, 2-6-7 Kazusa-Kamatari, Kisarazu, Chiba 292-0818 Japan
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Qin H, Feng S, Chen C, Guo Y, Knapp S, Culbreath A, He G, Wang ML, Zhang X, Holbrook CC, Ozias-Akins P, Guo B. An integrated genetic linkage map of cultivated peanut (Arachis hypogaea L.) constructed from two RIL populations. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2012; 124:653-64. [PMID: 22072100 DOI: 10.1007/s00122-011-1737-y] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2011] [Accepted: 10/14/2011] [Indexed: 05/18/2023]
Abstract
Construction and improvement of a genetic map for peanut (Arachis hypogaea L.) continues to be an important task in order to facilitate quantitative trait locus (QTL) analysis and the development of tools for marker-assisted breeding. The objective of this study was to develop a comparative integrated map from two cultivated × cultivated recombinant inbred line (RIL) mapping populations and to apply in mapping Tomato spotted wilt virus (TSWV) resistance trait in peanut. A total of 4,576 simple sequence repeat (SSR) markers from three sources: published SSR markers, newly developed SSR markers from expressed sequence tags (EST) and from bacterial artificial chromosome end-sequences were used for screening polymorphisms. Two cleaved amplified polymorphic sequence markers were also included to differentiate ahFAD2A alleles and ahFAD2B alleles. A total of 324 markers were anchored on this integrated map covering 1,352.1 cM with 21 linkage groups (LGs). Combining information from duplicated loci between LGs and comparing with published diploid maps, seven homoeologous groups were defined and 17 LGs (A1-A10, B1-B4, B7, B8, and B9) were aligned to corresponding A-subgenome or B-subgenome of diploid progenitors. One reciprocal translocation was confirmed in the tetraploid-cultivated peanut genome. Several chromosomal rearrangements were observed by comparing with published cultivated peanut maps. High consistency with cultivated peanut maps derived from different populations may support this integrated map as a reliable reference map for peanut whole genome sequencing assembling. Further two major QTLs for TSWV resistance were identified for each RILs, which illustrated the application of this map.
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Affiliation(s)
- Hongde Qin
- Department of Plant Pathology, University of Georgia, Tifton, GA, USA
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Fonceka D, Tossim HA, Rivallan R, Vignes H, Faye I, Ndoye O, Moretzsohn MC, Bertioli DJ, Glaszmann JC, Courtois B, Rami JF. Fostered and left behind alleles in peanut: interspecific QTL mapping reveals footprints of domestication and useful natural variation for breeding. BMC PLANT BIOLOGY 2012; 12:26. [PMID: 22340522 PMCID: PMC3312858 DOI: 10.1186/1471-2229-12-26] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2011] [Accepted: 02/17/2012] [Indexed: 05/18/2023]
Abstract
BACKGROUND Polyploidy can result in genetic bottlenecks, especially for species of monophyletic origin. Cultivated peanut is an allotetraploid harbouring limited genetic diversity, likely resulting from the combined effects of its single origin and domestication. Peanut wild relatives represent an important source of novel alleles that could be used to broaden the genetic basis of the cultigen. Using an advanced backcross population developed with a synthetic amphidiploid as donor of wild alleles, under two water regimes, we conducted a detailed QTL study for several traits involved in peanut productivity and adaptation as well as domestication. RESULTS A total of 95 QTLs were mapped in the two water treatments. About half of the QTL positive effects were associated with alleles of the wild parent and several QTLs involved in yield components were specific to the water-limited treatment. QTLs detected for the same trait mapped to non-homeologous genomic regions, suggesting differential control in subgenomes as a consequence of polyploidization. The noteworthy clustering of QTLs for traits involved in seed and pod size and in plant and pod morphology suggests, as in many crops, that a small number of loci have contributed to peanut domestication. CONCLUSION In our study, we have identified QTLs that differentiated cultivated peanut from its wild relatives as well as wild alleles that contributed positive variation to several traits involved in peanut productivity and adaptation. These findings offer novel opportunities for peanut improvement using wild relatives.
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Affiliation(s)
- Daniel Fonceka
- Cirad, UMR AGAP, TA A108/3, Avenue Agropolis, Montpellier F-34398, France
| | | | - Ronan Rivallan
- Cirad, UMR AGAP, TA A108/3, Avenue Agropolis, Montpellier F-34398, France
| | - Hélène Vignes
- Cirad, UMR AGAP, TA A108/3, Avenue Agropolis, Montpellier F-34398, France
| | - Issa Faye
- ISRA/Ceraas, Route de Khombole, BP 3320, Thiès Escale, Senegal
| | - Ousmane Ndoye
- ISRA/Ceraas, Route de Khombole, BP 3320, Thiès Escale, Senegal
| | - Márcio C Moretzsohn
- Embrapa Recursos Genéticos e Biotecnologia, C.P. 02372, CEP 70.770-900 Brasilia, DF, Brazil
| | - David J Bertioli
- Universidade de Brasília, Campus Universitário, CEP 70.910-900 Brasília, DF, Brazil
| | | | - Brigitte Courtois
- Cirad, UMR AGAP, TA A108/3, Avenue Agropolis, Montpellier F-34398, France
| | - Jean-François Rami
- Cirad, UMR AGAP, TA A108/3, Avenue Agropolis, Montpellier F-34398, France
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Macedo SE, Moretzsohn MC, M Leal-Bertioli SC, Alves DM, Gouvea EG, Azevedo VC, Bertioli DJ. Development and characterization of highly polymorphic long TC repeat microsatellite markers for genetic analysis of peanut. BMC Res Notes 2012; 5:86. [PMID: 22305491 PMCID: PMC3296580 DOI: 10.1186/1756-0500-5-86] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2011] [Accepted: 02/03/2012] [Indexed: 11/12/2022] Open
Abstract
Background Peanut (Arachis hypogaea L.) is a crop of economic and social importance, mainly in tropical areas, and developing countries. Its molecular breeding has been hindered by a shortage of polymorphic genetic markers due to a very narrow genetic base. Microsatellites (SSRs) are markers of choice in peanut because they are co-dominant, highly transferrable between species and easily applicable in the allotetraploid genome. In spite of substantial effort over the last few years by a number of research groups, the number of SSRs that are polymorphic for A. hypogaea is still limiting for routine application, creating the demand for the discovery of more markers polymorphic within cultivated germplasm. Findings A plasmid genomic library enriched for TC/AG repeats was constructed and 1401 clones sequenced. From the sequences obtained 146 primer pairs flanking mostly TC microsatellites were developed. The average number of repeat motifs amplified was 23. These 146 markers were characterized on 22 genotypes of cultivated peanut. In total 78 of the markers were polymorphic within cultivated germplasm. Most of those 78 markers were highly informative with an average of 5.4 alleles per locus being amplified. Average gene diversity index (GD) was 0.6, and 66 markers showed a GD of more than 0.5. Genetic relationship analysis was performed and corroborated the current taxonomical classification of A. hypogaea subspecies and varieties. Conclusions The microsatellite markers described here are a useful resource for genetics and genomics in Arachis. In particular, the 66 markers that are highly polymorphic in cultivated peanut are a significant step towards routine genetic mapping and marker-assisted selection for the crop.
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Affiliation(s)
- Selma E Macedo
- Institute of Biological Sciences, Campus Darcy Ribeiro, University of Brasilia, CEP 70,910-900 Brasília, DF, Brazil.
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Wang H, Penmetsa RV, Yuan M, Gong L, Zhao Y, Guo B, Farmer AD, Rosen BD, Gao J, Isobe S, Bertioli DJ, Varshney RK, Cook DR, He G. Development and characterization of BAC-end sequence derived SSRs, and their incorporation into a new higher density genetic map for cultivated peanut (Arachis hypogaea L.). BMC PLANT BIOLOGY 2012; 12:10. [PMID: 22260238 PMCID: PMC3298471 DOI: 10.1186/1471-2229-12-10] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2011] [Accepted: 01/19/2012] [Indexed: 05/18/2023]
Abstract
BACKGROUND Cultivated peanut (Arachis hypogaea L.) is an important crop worldwide, valued for its edible oil and digestible protein. It has a very narrow genetic base that may well derive from a relatively recent single polyploidization event. Accordingly molecular markers have low levels of polymorphism and the number of polymorphic molecular markers available for cultivated peanut is still limiting. RESULTS Here, we report a large set of BAC-end sequences (BES), use them for developing SSR (BES-SSR) markers, and apply them in genetic linkage mapping. The majority of BESs had no detectable homology to known genes (49.5%) followed by sequences with similarity to known genes (44.3%), and miscellaneous sequences (6.2%) such as transposable element, retroelement, and organelle sequences. A total of 1,424 SSRs were identified from 36,435 BESs. Among these identified SSRs, dinucleotide (47.4%) and trinucleotide (37.1%) SSRs were predominant. The new set of 1,152 SSRs as well as about 4,000 published or unpublished SSRs were screened against two parents of a mapping population, generating 385 polymorphic loci. A genetic linkage map was constructed, consisting of 318 loci onto 21 linkage groups and covering a total of 1,674.4 cM, with an average distance of 5.3 cM between adjacent loci. Two markers related to resistance gene homologs (RGH) were mapped to two different groups, thus anchoring 1 RGH-BAC contig and 1 singleton. CONCLUSIONS The SSRs mined from BESs will be of use in further molecular analysis of the peanut genome, providing a novel set of markers, genetically anchoring BAC clones, and incorporating gene sequences into a linkage map. This will aid in the identification of markers linked to genes of interest and map-based cloning.
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Affiliation(s)
- Hui Wang
- Shandong Peanut Research Institute, Qingdao, China
- Fujian Agricultural and Forestry University, Fuzhou, China
| | | | - Mei Yuan
- Shandong Peanut Research Institute, Qingdao, China
| | - Limin Gong
- Tuskegee University, Tuskegee, AL 36088, USA
| | - Yongli Zhao
- Fujian Agricultural and Forestry University, Fuzhou, China
| | | | - Andrew D Farmer
- National Center of Genome Resources (NCGR), Santa Fe, NM 87505, USA
| | | | | | | | | | - Rajeev K Varshney
- Intenational Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India
| | | | - Guohao He
- Tuskegee University, Tuskegee, AL 36088, USA
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Matita, a new retroelement from peanut: characterization and evolutionary context in the light of the Arachis A-B genome divergence. Mol Genet Genomics 2011; 287:21-38. [PMID: 22120641 DOI: 10.1007/s00438-011-0656-6] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2011] [Accepted: 10/20/2011] [Indexed: 12/16/2022]
Abstract
Cultivated peanut is an allotetraploid with an AB-genome. In order to learn more of the genomic structure of peanut, we characterized and studied the evolution of a retrotransposon originally isolated from a resistance gene analog (RGA)-containing bacterial artificial chromosome (BAC) clone. It is a moderate copy number Ty1-copia retrotransposon from the Bianca lineage and we named it Matita. Fluorescent in situ hybridization (FISH) experiments showed that Matita is mainly located on the distal regions of chromosome arms and is of approximately equal frequency on both A- and B-chromosomes. Its chromosome-specific hybridization pattern facilitates the identification of individual chromosomes, a useful cytogenetic tool considering that chromosomes in peanut are mostly metacentric and of similar size. Phylogenetic analysis of Matita elements, molecular dating of transposition events, and an estimation of the evolutionary divergence of the most probable A- and B-donor species suggest that Matita underwent its last major burst of transposition activity at around the same time of the A- and B-genome divergence about 3.5 million years ago. By probing BAC libraries with overgos probes for Matita, resistance gene analogues, and single- or low-copy genes, it was demonstrated that Matita is not randomly distributed in the genome but exhibits a significant tendency of being more abundant near resistance gene homologues than near single-copy genes. The described work is a further step towards broadening the knowledge on genomic and chromosomal structure of peanut and on its evolution.
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Pandey MK, Monyo E, Ozias-Akins P, Liang X, Guimarães P, Nigam SN, Upadhyaya HD, Janila P, Zhang X, Guo B, Cook DR, Bertioli DJ, Michelmore R, Varshney RK. Advances in Arachis genomics for peanut improvement. Biotechnol Adv 2011; 30:639-51. [PMID: 22094114 DOI: 10.1016/j.biotechadv.2011.11.001] [Citation(s) in RCA: 191] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2011] [Revised: 10/24/2011] [Accepted: 11/01/2011] [Indexed: 01/01/2023]
Abstract
Peanut genomics is very challenging due to its inherent problem of genetic architecture. Blockage of gene flow from diploid wild relatives to the tetraploid; cultivated peanut, recent polyploidization combined with self pollination, and the narrow genetic base of the primary genepool have resulted in low genetic diversity that has remained a major bottleneck for genetic improvement of peanut. Harnessing the rich source of wild relatives has been negligible due to differences in ploidy level as well as genetic drag and undesirable alleles for low yield. Lack of appropriate genomic resources has severely hampered molecular breeding activities, and this crop remains among the less-studied crops. The last five years, however, have witnessed accelerated development of genomic resources such as development of molecular markers, genetic and physical maps, generation of expressed sequenced tags (ESTs), development of mutant resources, and functional genomics platforms that facilitate the identification of QTLs and discovery of genes associated with tolerance/resistance to abiotic and biotic stresses and agronomic traits. Molecular breeding has been initiated for several traits for development of superior genotypes. The genome or at least gene space sequence is expected to be available in near future and this will further accelerate use of biotechnological approaches for peanut improvement.
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Affiliation(s)
- Manish K Pandey
- International Crops Research Institute for the Semi-Arid Tropics, Patancheru 502324, India
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Belamkar V, Selvaraj MG, Ayers JL, Payton PR, Puppala N, Burow MD. A first insight into population structure and linkage disequilibrium in the US peanut minicore collection. Genetica 2011; 139:411-29. [PMID: 21442404 DOI: 10.1007/s10709-011-9556-2] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2010] [Accepted: 01/25/2011] [Indexed: 12/13/2022]
Abstract
Knowledge of genetic diversity, population structure, and degree of linkage disequilibrium (LD) in target association mapping populations is of great importance and is a prerequisite for LD-based mapping. In the present study, 96 genotypes comprising 92 accessions of the US peanut minicore collection, a component line of the tetraploid variety Florunner, diploid progenitors A. duranensis (AA) and A. ipaënsis (BB), and synthetic amphidiploid accession TxAG-6 were investigated with 392 simple sequence repeat (SSR) marker bands amplified using 32 highly-polymorphic SSR primer pairs. Both distance- and model-based (Bayesian) cluster analysis revealed the presence of structured diversity. In general, the wild-species accessions and the synthetic amphidiploid grouped separately from most minicore accessions except for COC155, and were eliminated from most subsequent analyses. UPGMA analysis divided the population into four subgroups, two major subgroups representing subspecies fastigiata and hypogaea, a third group containing individuals from each subspecies or possibly of mixed ancestry, and a fourth group, either consisting of COC155 alone if wild species were excluded, or of COC155, the diploid species, and the synthetic amphidiploid. Model-based clustering identified four subgroups- one each for fastigiata and hypogaea subspecies, a third consisting of individuals of both subspecies or of mixed ancestry predominantly from Africa or Asia, and a fourth group, consisting of individuals predominantly of var fastigiata, peruviana, and aequatoriana accessions from South America, including COC155. Analysis of molecular variance (AMOVA) revealed statistically-significant (P < 0.0001) genetic variance of 16.87% among subgroups. A total of 4.85% of SSR marker pairs revealed significant LD (at r(2) ≥ 0.1). Of the syntenic marker pairs separated by distances < 10 cM, 11-20 cM, 21-50 cM, and > 50 cM, 19.33, 5.19, 6.25 and 5.29% of marker pairs were found in strong LD (P ≤ 0.01), in accord with LD extending to great distances in self pollinated crops. A threshold value of r(2) > 0.035 was found to distinguish mean r(2) values of linkage distance groups statistically from the mean r(2) values of unlinked markers; LD was found to extend to 10 cM over the entire minicore collection by this criterion. However, there were large differences in r(2) values among marker pairs even among tightly-linked markers. The implications of these findings with regard to the possibility of using association mapping for detection of genome-wide SSR marker-phenotype association are discussed.
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Affiliation(s)
- Vikas Belamkar
- Center for Biotechnology and Genomics, Texas Tech University, Lubbock, TX 79409, USA
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Xiong F, Zhong R, Han Z, Jiang J, He L, Zhuang W, Tang R. Start codon targeted polymorphism for evaluation of functional genetic variation and relationships in cultivated peanut (Arachis hypogaea L.) genotypes. Mol Biol Rep 2010; 38:3487-94. [DOI: 10.1007/s11033-010-0459-6] [Citation(s) in RCA: 85] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2009] [Accepted: 11/09/2010] [Indexed: 10/18/2022]
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Varshney RK, Glaszmann JC, Leung H, Ribaut JM. More genomic resources for less-studied crops. Trends Biotechnol 2010; 28:452-60. [PMID: 20692061 DOI: 10.1016/j.tibtech.2010.06.007] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2010] [Revised: 06/23/2010] [Accepted: 06/27/2010] [Indexed: 01/14/2023]
Abstract
Many of the crop species considered to be minor on a global scale, yet are important locally for food security in the developing world, have remained less-studied crops. Recent years have witnessed the development of large-scale genomic and genetic resources, including simple sequence repeat, single nucleotide polymorphism and diversity array technology markers, expressed sequence tags or transcript reads, bacterial artificial chromosome libraries, genetic and physical maps, and genetic stocks with rich genetic diversity, such as core reference sets and introgression lines in these crops. These resources have the potential to accelerate gene discovery and initiate molecular breeding in these crops, thereby enhancing crop productivity to ensure food security in developing countries.
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Affiliation(s)
- Rajeev K Varshney
- International Crops Research Institute for the Semi-Arid Tropics, Patancheru 502324, A.P., India.
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FIDEL-a retrovirus-like retrotransposon and its distinct evolutionary histories in the A- and B-genome components of cultivated peanut. Chromosome Res 2010; 18:227-46. [PMID: 20127167 PMCID: PMC2844528 DOI: 10.1007/s10577-009-9109-z] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2009] [Accepted: 12/16/2009] [Indexed: 12/26/2022]
Abstract
In this paper, we describe a Ty3-gypsy retrotransposon from allotetraploid peanut (Arachis hypogaea) and its putative diploid ancestors Arachis duranensis (A-genome) and Arachis ipaënsis (B-genome). The consensus sequence is 11,223 bp. The element, named FIDEL (Fairly long Inter-Dispersed Euchromatic LTR retrotransposon), is more frequent in the A- than in the B-genome, with copy numbers of about 3,000 (±950, A. duranensis), 820 (±480, A. ipaënsis), and 3,900 (±1,500, A. hypogaea) per haploid genome. Phylogenetic analysis of reverse transcriptase sequences showed distinct evolution of FIDEL in the ancestor species. Fluorescent in situ hybridization revealed disperse distribution in euchromatin and absence from centromeres, telomeric regions, and the nucleolar organizer region. Using paired sequences from bacterial artificial chromosomes, we showed that elements appear less likely to insert near conserved ancestral genes than near the fast evolving disease resistance gene homologs. Within the Ty3-gypsy elements, FIDEL is most closely related with the Athila/Calypso group of retrovirus-like retrotransposons. Putative transmembrane domains were identified, supporting the presence of a vestigial envelope gene. The results emphasize the importance of FIDEL in the evolution and divergence of different Arachis genomes and also may serve as an example of the role of retrotransposons in the evolution of legume genomes in general.
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Hong Y, Chen X, Liang X, Liu H, Zhou G, Li S, Wen S, Holbrook CC, Guo B. A SSR-based composite genetic linkage map for the cultivated peanut (Arachis hypogaea L.) genome. BMC PLANT BIOLOGY 2010; 10:17. [PMID: 20105299 PMCID: PMC2835713 DOI: 10.1186/1471-2229-10-17] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2009] [Accepted: 01/27/2010] [Indexed: 05/18/2023]
Abstract
BACKGROUND The construction of genetic linkage maps for cultivated peanut (Arachis hypogaea L.) has and continues to be an important research goal to facilitate quantitative trait locus (QTL) analysis and gene tagging for use in a marker-assisted selection in breeding. Even though a few maps have been developed, they were constructed using diploid or interspecific tetraploid populations. The most recently published intra-specific map was constructed from the cross of cultivated peanuts, in which only 135 simple sequence repeat (SSR) markers were sparsely populated in 22 linkage groups. The more detailed linkage map with sufficient markers is necessary to be feasible for QTL identification and marker-assisted selection. The objective of this study was to construct a genetic linkage map of cultivated peanut using simple sequence repeat (SSR) markers derived primarily from peanut genomic sequences, expressed sequence tags (ESTs), and by "data mining" sequences released in GenBank. RESULTS Three recombinant inbred lines (RILs) populations were constructed from three crosses with one common female parental line Yueyou 13, a high yielding Spanish market type. The four parents were screened with 1044 primer pairs designed to amplify SSRs and 901 primer pairs produced clear PCR products. Of the 901 primer pairs, 146, 124 and 64 primer pairs (markers) were polymorphic in these populations, respectively, and used in genotyping these RIL populations. Individual linkage maps were constructed from each of the three populations and a composite map based on 93 common loci were created using JoinMap. The composite linkage maps consist of 22 composite linkage groups (LG) with 175 SSR markers (including 47 SSRs on the published AA genome maps), representing the 20 chromosomes of A. hypogaea. The total composite map length is 885.4 cM, with an average marker density of 5.8 cM. Segregation distortion in the 3 populations was 23.0%, 13.5% and 7.8% of the markers, respectively. These distorted loci tended to cluster on LG1, LG3, LG4 and LG5. There were only 15 EST-SSR markers mapped due to low polymorphism. By comparison, there were potential synteny, collinear order of some markers and conservation of collinear linkage groups among the maps and with the AA genome but not fully conservative. CONCLUSION A composite linkage map was constructed from three individual mapping populations with 175 SSR markers in 22 composite linkage groups. This composite genetic linkage map is among the first "true" tetraploid peanut maps produced. This map also consists of 47 SSRs that have been used in the published AA genome maps, and could be used in comparative mapping studies. The primers described in this study are PCR-based markers, which are easy to share for genetic mapping in peanuts. All 1044 primer pairs are provided as additional files and the three RIL populations will be made available to public upon request for quantitative trait loci (QTL) analysis and linkage map improvement.
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Affiliation(s)
- Yanbin Hong
- Guangdong Academy of Agricultural Sciences, Crops Research Institute, Guangzhou, PR China
| | - Xiaoping Chen
- Guangdong Academy of Agricultural Sciences, Crops Research Institute, Guangzhou, PR China
- US Department of Agriculture, Agricultural Research Service, Crop Protection and Management Research Unit, Tifton, GA 31793, USA
- University of Georgia, Department of Plant Pathology, Tifton, GA 31793, USA
| | - Xuanqiang Liang
- Guangdong Academy of Agricultural Sciences, Crops Research Institute, Guangzhou, PR China
| | - Haiyan Liu
- Guangdong Academy of Agricultural Sciences, Crops Research Institute, Guangzhou, PR China
| | - Guiyuan Zhou
- Guangdong Academy of Agricultural Sciences, Crops Research Institute, Guangzhou, PR China
| | - Shaoxiong Li
- Guangdong Academy of Agricultural Sciences, Crops Research Institute, Guangzhou, PR China
| | - Shijie Wen
- Guangdong Academy of Agricultural Sciences, Crops Research Institute, Guangzhou, PR China
| | - C Corley Holbrook
- US Department of Agriculture, Agricultural Research Service, Crop Genetics and Breeding Research Unit, Tifton, GA 31793, USA
| | - Baozhu Guo
- US Department of Agriculture, Agricultural Research Service, Crop Protection and Management Research Unit, Tifton, GA 31793, USA
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