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Sinare B, Desmae H, Nebié B, Konate D, John Eleblu, Miningou A, Traoré A, Ofori K, Zagre B. Diallel analysis, maternal effect and heritability in groundnut for yield components and oil content. Heliyon 2024; 10:e33379. [PMID: 39022008 PMCID: PMC11253538 DOI: 10.1016/j.heliyon.2024.e33379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 06/19/2024] [Accepted: 06/20/2024] [Indexed: 07/20/2024] Open
Abstract
Background Groundnut is one of the world's major food and oil crops. Being sources of nutrition and vegetable oil, rich in affordable and digestible protein, it is a strategic crop in Burkina Faso for food security, nutrition, and cash income. Understanding the nature of gene effect and genetic variation affecting yield and yield component traits will contribute to designing appropriate breeding methods for groundnut improvement and increase selection efficiency in Burkina Faso. Methods In 2018, a total of 30 F2 progenies were generated through a 6 x 6 full diallel mating using six different and contrasting varieties. In 2019, parents and progenies were evaluated in a lattice square design in 3 replications at ICRISAT-Mali experimental field to assess the general combining ability (GCA) and specific combining ability (SCA) effects, the inheritance and the maternal and reciprocal effects for yield component traits (YCT) and oil content (OC). Results Significant variabilities were observed among the parental genotypes and their F2 progenies for DTH, PSR, HPW, PL, PWD, SL, SWD, and OAC. Mean performance of the six parents were HPW (117.05g), HSW (57.24 g), PYH (1914.76), SYH (1312.73), PL (2.52), PWD (1,19), SL (1.38), SWD (0.83), OC (49.43), OAC (50.43) and LAC (33.61). Parent QH243C presented the highest value for SWD (1.02 cm) and OAC (60.76) while the parent ICGV09195 had the highest value of OC (50.36). Chalimbana presented the highest value of HPW (169.61 g), PL (2.98 cm), PWD (1. 41 cm), and SL (1.57 cm) while CG7 presented the highest value for HSW (75. 14 g), and SYH (1639.28 kg). Both YCT and OC are controlled by additive and non-additive gene effects with a predominance of additive gene action for HSW, SL, and SWD, whereas HPW, PL, PWD, and OAC were found to be more controlled by non-additive gene effects. Maternal effects as well as nuclear and cytoplasmic interaction effects were observed for both YCT and OC indicating that YCT and OC are influenced by a combination of genetic factors from both the maternal parent and the nuclear genome, as well as cytoplasmic factors such as mitochondrial DNA. Broad sense heritability ranged from 3.76 % to 91.56 %, and higher broad sense heritability values were recorded for pod length (91.56 %), hundred pod weight (83.71 %) and pod width (80.95 %). Conclusion The study yields valuable insights into the inheritance of YCT and OC. The parents, Chalimbana and CG7, showed promise as good combiners for both yield component traits and oil content when used as male parents while TE3, Sh470P and QH243C can be used as female for the oil content and its components (oleic and linoleic content).
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Affiliation(s)
- Boubacar Sinare
- West Africa Centre for Crop Improvement (WACCI), University of Ghana (UG), PMB 30, Legon, Accra, Ghana
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), BP 320, Bamako, Mali
- Institut National de l’Environnement et de Recherche Agricole (INERA), 04 BP 8645 04, Ouagadougou, Burkina Faso
| | - Haile Desmae
- International Maize and Wheat Improvement Center (CIMMYT-Senegal), Dakar, Senegal
| | - Baloua Nebié
- International Maize and Wheat Improvement Center (CIMMYT-Senegal), Dakar, Senegal
| | - Djeneba Konate
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), BP 320, Bamako, Mali
| | - John Eleblu
- West Africa Centre for Crop Improvement (WACCI), University of Ghana (UG), PMB 30, Legon, Accra, Ghana
| | - Amos Miningou
- Institut National de l’Environnement et de Recherche Agricole (INERA), 04 BP 8645 04, Ouagadougou, Burkina Faso
| | - Appolinaire Traoré
- Institut National de l’Environnement et de Recherche Agricole (INERA), 04 BP 8645 04, Ouagadougou, Burkina Faso
| | - Kwadwo Ofori
- West Africa Centre for Crop Improvement (WACCI), University of Ghana (UG), PMB 30, Legon, Accra, Ghana
| | - Bertin Zagre
- Institut National de l’Environnement et de Recherche Agricole (INERA), 04 BP 8645 04, Ouagadougou, Burkina Faso
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Miao P, Meng X, Li Z, Sun S, Chen CY, Yang X. Mapping Quantitative Trait Loci (QTLs) for Hundred-Pod and Hundred-Seed Weight under Seven Environments in a Recombinant Inbred Line Population of Cultivated Peanut ( Arachis hypogaea L.). Genes (Basel) 2023; 14:1792. [PMID: 37761932 PMCID: PMC10531390 DOI: 10.3390/genes14091792] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 09/06/2023] [Accepted: 09/08/2023] [Indexed: 09/29/2023] Open
Abstract
The cultivated peanut (Arachis hypogaea L.) is a significant oil and cash crop globally. Hundred-pod and -seed weight are important components for peanut yield. To unravel the genetic basis of hundred-pod weight (HPW) and hundred-seed weight (HSW), in the current study, a recombinant inbred line (RIL) population with 188 individuals was developed from a cross between JH5 (JH5, large pod and seed weight) and M130 (small pod and seed weight), and was utilized to identify QTLs for HPW and HSW. An integrated genetic linkage map was constructed by using SSR, AhTE, SRAP, TRAP and SNP markers. This map consisted of 3130 genetic markers, which were assigned to 20 chromosomes, and covered 1998.95 cM with an average distance 0.64 cM. On this basis, 31 QTLs for HPW and HSW were located on seven chromosomes, with each QTL accounting for 3.7-10.8% of phenotypic variance explained (PVE). Among these, seven QTLs were detected under multiple environments, and two major QTLs were found on B04 and B08. Notably, a QTL hotspot on chromosome A08 contained seven QTLs over a 2.74 cM genetic interval with an 0.36 Mb physical map, including 18 candidate genes. Of these, Arahy.D52S1Z, Arahy.IBM9RL, Arahy.W18Y25, Arahy.CPLC2W and Arahy.14EF4H might play a role in modulating peanut pod and seed weight. These findings could facilitate further research into the genetic mechanisms influencing pod and seed weight in cultivated peanut.
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Affiliation(s)
- Penghui Miao
- State Key Laboratory of North China for Crop Improvement and Regulation, North China Key Laboratory for Crop Germplasm Resources of Education Ministry, Key Laboratory of Crop Germplasm Resources of Hebei Province, Hebei Agricultural University, Baoding 071001, China
| | - Xinhao Meng
- State Key Laboratory of North China for Crop Improvement and Regulation, North China Key Laboratory for Crop Germplasm Resources of Education Ministry, Key Laboratory of Crop Germplasm Resources of Hebei Province, Hebei Agricultural University, Baoding 071001, China
| | - Zeren Li
- State Key Laboratory of North China for Crop Improvement and Regulation, North China Key Laboratory for Crop Germplasm Resources of Education Ministry, Key Laboratory of Crop Germplasm Resources of Hebei Province, Hebei Agricultural University, Baoding 071001, China
| | - Sainan Sun
- State Key Laboratory of North China for Crop Improvement and Regulation, North China Key Laboratory for Crop Germplasm Resources of Education Ministry, Key Laboratory of Crop Germplasm Resources of Hebei Province, Hebei Agricultural University, Baoding 071001, China
| | - Charles Y. Chen
- Department of Crop, Soil and Environmental Sciences, Auburn University, Auburn, AL 36849, USA
| | - Xinlei Yang
- State Key Laboratory of North China for Crop Improvement and Regulation, North China Key Laboratory for Crop Germplasm Resources of Education Ministry, Key Laboratory of Crop Germplasm Resources of Hebei Province, Hebei Agricultural University, Baoding 071001, China
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Katoch M, Mane RS, Chahota RK. Identification of QTLs Linked to Phenological and Morphological Traits in RILs Population of Horsegram ( Macrotyloma uniflorum). Front Genet 2022; 12:762604. [PMID: 35145543 PMCID: PMC8821879 DOI: 10.3389/fgene.2021.762604] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2021] [Accepted: 12/09/2021] [Indexed: 11/13/2022] Open
Abstract
Horsegram [Macrotyloma uniflorum (Lam.) Verdc.] is an important legume but understudied in terms of its genetic improvement. Genetic information on various phenological and morphological traits may help in the utilization of new genes for breeding in horsegram and thus affect agronomic practices and crop yield. A total of 162 recombinant inbred lines derived from intraspecific crosses between HPKM249 × HPK4 was used to construct a genetic linkage map and to identify quantitative trait loci (QTLs) associated with phenological and morphological traits. Of the total 2011 molecular markers, which were screened on parental lines for polymorphism survey, 493 markers were found to be polymorphic and used for genotyping of recombinant inbred line population. Out of 493 polymorphic markers, 295 were mapped on ten linkage groups at LOD 3.5 spanning a total distance of 1,541.7 cM with an average distance between markers of 5.20 cM. Phenotypic data of two years at two different locations were used to identify QTLs by composite interval mapping A total of four QTLs (LOD ≥2.5) for phenological traits (days to 50% flowering, reproductive period and days to maturity) and seven QTLs (LOD ≥2.5) for morphological traits (plant height, primary branches and secondary branches) were detected across different environments. The phenotypic variation explained by QTLs ranged from 6.36 to 47.53%. The present study will help to augment scanty genomic information in this orphan crop that would provide genomics tools to breeders for its genetic enhancement through molecular-assisted selection.
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Affiliation(s)
- Megha Katoch
- Department of Agricultural Biotechnology, College of Agriculture, CSK HP Krishi Vishvavidyalaya, Himachal Pradesh, India
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Genetic diversity, population structure and relationship of Ethiopian barley (Hordeum vulgare L.) landraces as revealed by SSR markers. J Genet 2022. [DOI: 10.1007/s12041-021-01346-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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Paliwal R, Adegboyega TT, Abberton M, Faloye B, Oyatomi O. Potential of genomics for the improvement of underutilized legumes in sub‐Saharan Africa. LEGUME SCIENCE 2021; 3. [PMID: 0 DOI: 10.1002/leg3.69] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Affiliation(s)
- Rajneesh Paliwal
- Genetic Resources Center International Institute of Tropical Agriculture Ibadan Nigeria
| | | | - Michael Abberton
- Genetic Resources Center International Institute of Tropical Agriculture Ibadan Nigeria
| | - Ben Faloye
- Genetic Resources Center International Institute of Tropical Agriculture Ibadan Nigeria
| | - Olaniyi Oyatomi
- Genetic Resources Center International Institute of Tropical Agriculture Ibadan Nigeria
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Identification of novel QTLs for late leaf spot resistance and validation of a major rust QTL in peanut ( Arachis hypogaea L.). 3 Biotech 2020; 10:458. [PMID: 33088655 DOI: 10.1007/s13205-020-02446-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Accepted: 09/21/2020] [Indexed: 10/23/2022] Open
Abstract
Co-occurrence of two devastating foliar-fungal diseases of peanut, viz., late leaf spot (LLS), and rust may cause heavy yield loss besides adversely affecting the quality of kernel and fodder. This study reports the mapping of seven novel stress-related candidate EST-SSRs in a region having major QTLs for LLS and rust diseases using an F2 mapping population (GJG17 × GPBD4) consisting of 328 individuals. The parental polymorphism using 1311 SSRs revealed 84 SSRs (6.4%) as polymorphic and of these 70 SSRs could be mapped on 14 linkage groups (LG). QTL analysis has identified a common QTL (LLSQTL1/RustQTL) for LLS and rust diseases in the map interval of 1.41 cM on A03 chromosome, explaining 47.45% and 70.52% phenotypic variations, respectively. Another major QTL for LLS (LLSQTL1), explaining a 29.06% phenotypic variation was also found on LG_A03. A major rust QTL has been validated which was found harboring R-gene and resistance-related genes having a role in inducing hypersensitive response (HR). Further, 23 linked SSRs including seven novel EST-SSRs were also validated in 177 diverse Indian groundnut genotypes. Twelve genotypes resistant to both LLS and rust were found carrying the common (rust and LLS) QTL region, LLS QTL region, and surrounding regions. These identified and validated candidate EST-SSR markers would be of great use for the peanut breeding groups working for the improvement of foliar-fungal disease resistance.
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Kumar A, Saripalli G, Jan I, Kumar K, Sharma PK, Balyan HS, Gupta PK. Meta-QTL analysis and identification of candidate genes for drought tolerance in bread wheat ( Triticum aestivum L.). PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2020; 26:1713-1725. [PMID: 32801498 PMCID: PMC7415061 DOI: 10.1007/s12298-020-00847-6] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Revised: 06/30/2020] [Accepted: 07/03/2020] [Indexed: 05/18/2023]
Abstract
Meta-QTL (MQTL) analysis for drought tolerance was undertaken in bread wheat to identify consensus and robust MQTLs using 340 known QTLs from 11 earlier studies; 13 MQTLs located on 6 chromosomes (1D, 3B, 5A, 6D, 7A and 7D) were identified, with maximum of 4 MQTLs on chromosome 5A. Mean confidence intervals for MQTLs were much narrower (mean, 6.01 cM; range 2.07-19.46 cM), relative to those in original QTLs (mean, 13.6 cM; range, 1.0-119.1 cM). Two MQTLs, namely MQTL4 and MQTL12, were major MQTLs with potential for use in marker-assisting breeding. As many as 228 candidate genes (CGs) were also identified using 6 of the 13 MQTLs. In-silico expression analysis of these 228 CGs allowed identification of 14 important CGs, with + 3 to - 8 fold change in expression under drought (relative to normal conditions) in a tolerant cv. named TAM107. These CGs encoded proteins belonging to the following families: NAD-dependent epimerase/dehydratase, protein kinase, NAD(P)-binding domain protein, heat shock protein 70 (Hsp70), glycosyltransferase 2-like, etc. Important MQTLs and CGs identified in the present study should prove useful for future molecular breeding and for the study of molecular basis of drought tolerance in cereals in general and wheat in particular.
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Affiliation(s)
- Anuj Kumar
- Department of Genetics and Plant Breeding, Ch. Charan Singh University, Meerut, 250004 India
| | - Gautam Saripalli
- Department of Genetics and Plant Breeding, Ch. Charan Singh University, Meerut, 250004 India
| | - Irfat Jan
- Department of Genetics and Plant Breeding, Ch. Charan Singh University, Meerut, 250004 India
| | - Kuldeep Kumar
- Department of Genetics and Plant Breeding, Ch. Charan Singh University, Meerut, 250004 India
| | - P. K. Sharma
- Department of Genetics and Plant Breeding, Ch. Charan Singh University, Meerut, 250004 India
| | - H. S. Balyan
- Department of Genetics and Plant Breeding, Ch. Charan Singh University, Meerut, 250004 India
| | - P. K. Gupta
- Department of Genetics and Plant Breeding, Ch. Charan Singh University, Meerut, 250004 India
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Chavarro C, Chu Y, Holbrook C, Isleib T, Bertioli D, Hovav R, Butts C, Lamb M, Sorensen R, A Jackson S, Ozias-Akins P. Pod and Seed Trait QTL Identification To Assist Breeding for Peanut Market Preferences. G3 (BETHESDA, MD.) 2020; 10:2297-2315. [PMID: 32398236 PMCID: PMC7341151 DOI: 10.1534/g3.120.401147] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Accepted: 05/01/2020] [Indexed: 12/20/2022]
Abstract
Although seed and pod traits are important for peanut breeding, little is known about the inheritance of these traits. A recombinant inbred line (RIL) population of 156 lines from a cross of Tifrunner x NC 3033 was genotyped with the Axiom_Arachis1 SNP array and SSRs to generate a genetic map composed of 1524 markers in 29 linkage groups (LG). The genetic positions of markers were compared with their physical positions on the peanut genome to confirm the validity of the linkage map and explore the distribution of recombination and potential chromosomal rearrangements. This linkage map was then used to identify Quantitative Trait Loci (QTL) for seed and pod traits that were phenotyped over three consecutive years for the purpose of developing trait-associated markers for breeding. Forty-nine QTL were identified in 14 LG for seed size index, kernel percentage, seed weight, pod weight, single-kernel, double-kernel, pod area and pod density. Twenty QTL demonstrated phenotypic variance explained (PVE) greater than 10% and eight more than 20%. Of note, seven of the eight major QTL for pod area, pod weight and seed weight (PVE >20% variance) were attributed to NC 3033 and located in a single linkage group, LG B06_1. In contrast, the most consistent QTL for kernel percentage were located on A07/B07 and derived from Tifrunner.
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Affiliation(s)
- Carolina Chavarro
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA 30602
| | - Ye Chu
- Department of Horticulture and Institute of Plant Breeding, Genetics & Genomics, University of Georgia, Tifton, GA 31793
| | - Corley Holbrook
- USDA- Agricultural Research Service, Crop Genetics and Breeding Research Unit, Tifton, GA 31793
| | - Thomas Isleib
- Department of Crop Science, North Carolina State University, P.O. Box 7629, Raleigh, NC 27695
| | - David Bertioli
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA 30602
| | - Ran Hovav
- Department of Field and Vegetable Crops, Plant Sciences Institute, ARO (Volcani Center), Bet Dagan, Israel, and
| | - Christopher Butts
- USDA- Agricultural Research Service, National Peanut Research Laboratory, Dawson, GA 39842
| | - Marshall Lamb
- USDA- Agricultural Research Service, National Peanut Research Laboratory, Dawson, GA 39842
| | - Ronald Sorensen
- USDA- Agricultural Research Service, National Peanut Research Laboratory, Dawson, GA 39842
| | - Scott A Jackson
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA 30602
| | - Peggy Ozias-Akins
- Department of Horticulture and Institute of Plant Breeding, Genetics & Genomics, University of Georgia, Tifton, GA 31793,
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Ballén-Taborda C, Chu Y, Ozias-Akins P, Timper P, Holbrook CC, Jackson SA, Bertioli DJ, Leal-Bertioli SCM. A new source of root-knot nematode resistance from Arachis stenosperma incorporated into allotetraploid peanut (Arachis hypogaea). Sci Rep 2019; 9:17702. [PMID: 31776412 PMCID: PMC6881346 DOI: 10.1038/s41598-019-54183-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Accepted: 11/06/2019] [Indexed: 12/18/2022] Open
Abstract
Root-knot nematode is a very destructive pathogen, to which most peanut cultivars are highly susceptible. Strong resistance is present in the wild diploid peanut relatives. Previously, QTLs controlling nematode resistance were identified on chromosomes A02, A04 and A09 of Arachis stenosperma. Here, to study the inheritance of these resistance alleles within the genetic background of tetraploid peanut, an F2 population was developed from a cross between peanut and an induced allotetraploid that incorporated A. stenosperma, [Arachis batizocoi x A. stenosperma]4×. This population was genotyped using a SNP array and phenotyped for nematode resistance. QTL analysis allowed us to verify the major-effect QTL on chromosome A02 and a secondary QTL on A09, each contributing to a percentage reduction in nematode multiplication up to 98.2%. These were validated in selected F2:3 lines. The genome location of the large-effect QTL on A02 is rich in genes encoding TIR-NBS-LRR protein domains that are involved in plant defenses. We conclude that the strong resistance to RKN, derived from the diploid A. stenosperma, is transferrable and expressed in tetraploid peanut. Currently it is being used in breeding programs for introgressing a new source of nematode resistance and to widen the genetic basis of agronomically adapted peanut lines.
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Affiliation(s)
- Carolina Ballén-Taborda
- Center for Applied Genetic Technologies and Institute of Plant Breeding, Genetics and Genomics, University of Georgia, Athens, GA, United States
| | - Ye Chu
- Department of Horticulture and Institute of Plant Breeding, Genetics and Genomics, University of Georgia, Tifton, GA, United States
| | - Peggy Ozias-Akins
- Department of Horticulture and Institute of Plant Breeding, Genetics and Genomics, University of Georgia, Tifton, GA, United States
| | | | | | - Scott A Jackson
- Center for Applied Genetic Technologies and Institute of Plant Breeding, Genetics and Genomics, University of Georgia, Athens, GA, United States.,Department of Crop and Soil Science and Institute of Plant Breeding, Genetics and Genomics, University of Georgia, Athens, GA, United States
| | - David J Bertioli
- Center for Applied Genetic Technologies and Institute of Plant Breeding, Genetics and Genomics, University of Georgia, Athens, GA, United States.,Department of Crop and Soil Science and Institute of Plant Breeding, Genetics and Genomics, University of Georgia, Athens, GA, United States
| | - Soraya C M Leal-Bertioli
- Center for Applied Genetic Technologies and Institute of Plant Breeding, Genetics and Genomics, University of Georgia, Athens, GA, United States. .,Department of Plant Pathology, University of Georgia, Athens, GA, United States.
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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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Mousavi‐Derazmahalleh M, Bayer PE, Hane JK, Valliyodan B, Nguyen HT, Nelson MN, Erskine W, Varshney RK, Papa R, Edwards D. Adapting legume crops to climate change using genomic approaches. PLANT, CELL & ENVIRONMENT 2019; 42:6-19. [PMID: 29603775 PMCID: PMC6334278 DOI: 10.1111/pce.13203] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Accepted: 03/10/2018] [Indexed: 05/05/2023]
Abstract
Our agricultural system and hence food security is threatened by combination of events, such as increasing population, the impacts of climate change, and the need to a more sustainable development. Evolutionary adaptation may help some species to overcome environmental changes through new selection pressures driven by climate change. However, success of evolutionary adaptation is dependent on various factors, one of which is the extent of genetic variation available within species. Genomic approaches provide an exceptional opportunity to identify genetic variation that can be employed in crop improvement programs. In this review, we illustrate some of the routinely used genomics-based methods as well as recent breakthroughs, which facilitate assessment of genetic variation and discovery of adaptive genes in legumes. Although additional information is needed, the current utility of selection tools indicate a robust ability to utilize existing variation among legumes to address the challenges of climate uncertainty.
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Affiliation(s)
- Mahsa Mousavi‐Derazmahalleh
- UWA School of Agriculture and EnvironmentThe University of Western Australia35 Stirling HighwayCrawleyWestern Australia6009Australia
- School of Biological SciencesThe University of Western Australia35 Stirling HighwayCrawleyWestern Australia6009Australia
| | - Philipp E. Bayer
- School of Biological SciencesThe University of Western Australia35 Stirling HighwayCrawleyWestern Australia6009Australia
| | - James K. Hane
- CCDM BioinformaticsCentre for Crop Disease Management, Curtin UniversityBentleyWestern Australia6102Australia
| | - Babu Valliyodan
- Division of Plant Sciences and National Center for Soybean BiotechnologyUniversity of MissouriColumbiaMO65211USA
| | - Henry T. Nguyen
- Division of Plant Sciences and National Center for Soybean BiotechnologyUniversity of MissouriColumbiaMO65211USA
| | - Matthew N. Nelson
- UWA School of Agriculture and EnvironmentThe University of Western Australia35 Stirling HighwayCrawleyWestern Australia6009Australia
- Natural Capital and Plant HealthRoyal Botanic Gardens Kew, Wakehurst PlaceArdinglyWest SussexRH17 6TNUK
- The UWA Institute of AgricultureThe University of Western Australia35 Stirling HighwayPerthWestern Australia6009Australia
| | - William Erskine
- UWA School of Agriculture and EnvironmentThe University of Western Australia35 Stirling HighwayCrawleyWestern Australia6009Australia
- Centre for Plant Genetics and BreedingThe University of Western Australia35 Stirling HighwayCrawleyWestern Australia6009Australia
- The UWA Institute of AgricultureThe University of Western Australia35 Stirling HighwayPerthWestern Australia6009Australia
| | - Rajeev K. Varshney
- UWA School of Agriculture and EnvironmentThe University of Western Australia35 Stirling HighwayCrawleyWestern Australia6009Australia
- The UWA Institute of AgricultureThe University of Western Australia35 Stirling HighwayPerthWestern Australia6009Australia
- International Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)Patancheru502 324India
| | - Roberto Papa
- Department of Agricultural, Food, and Environmental SciencesUniversità Politecnica delle Marche60131AnconaItaly
| | - David Edwards
- School of Biological SciencesThe University of Western Australia35 Stirling HighwayCrawleyWestern Australia6009Australia
- The UWA Institute of AgricultureThe University of Western Australia35 Stirling HighwayPerthWestern Australia6009Australia
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Li L, Yang X, Cui S, Meng X, Mu G, Hou M, He M, Zhang H, Liu L, Chen CY. Construction of High-Density Genetic Map and Mapping Quantitative Trait Loci for Growth Habit-Related Traits of Peanut ( Arachis hypogaea L.). FRONTIERS IN PLANT SCIENCE 2019; 10:745. [PMID: 31263472 PMCID: PMC6584813 DOI: 10.3389/fpls.2019.00745] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Accepted: 05/20/2019] [Indexed: 05/03/2023]
Abstract
Plant growth habit is an important and complex agronomic trait and is associated with yield, disease resistance, and mechanized harvesting in peanuts. There are at least two distinct growth habits (erect and prostrate) and several intermediate forms existing in the peanut germplasm. A recombinant inbred line population containing 188 individuals was developed from a cross of "Jihua 5" and "M130" for genetically dissecting the architecture of the growth habit. A new high-density genetic linkage map was constructed by using specific locus amplified fragment sequencing technology. The map contains 2,808 single-nucleotide polymorphism markers distributed on 20 linkage groups with a total length of 1,308.20 cM and an average inter-marker distance of 0.47 cM. The quantitative trait locus (QTL) analysis of the growth habit-related traits was conducted based on phenotyping data from seven environments. A total of 39 QTLs for growth habit-related traits was detected on 10 chromosomes explaining 4.55-27.74% of the phenotypic variance, in which 6 QTLs were for lateral branch angle, 8 QTLs were for extent radius, 7 QTLs were for the index of plant type, 11 QTLs were for main stem height, and 7 QTLs were for lateral branch length. Among these QTLs, 12 were co-localized on chromosome B05 spanning an approximately 0.17 Mb physical interval in comparison with the allotetraploid reference genome of "Tifrunner." Analysis of the co-localized genome region has shown that the putative genes are involved in light and hormones and will facilitate peanut growth habit molecular breeding and study of peanut domestication.
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Affiliation(s)
- Li Li
- North China Key Laboratory for Crop Germplasm Resources of Education Ministry, College of Agronomy, Hebei Agricultural University, Baoding, China
- Department of Crop, Soil and Environmental Sciences, Auburn University, Auburn, AL, United States
| | - Xinlei Yang
- North China Key Laboratory for Crop Germplasm Resources of Education Ministry, College of Agronomy, Hebei Agricultural University, Baoding, China
- Department of Crop, Soil and Environmental Sciences, Auburn University, Auburn, AL, United States
| | - Shunli Cui
- North China Key Laboratory for Crop Germplasm Resources of Education Ministry, College of Agronomy, Hebei Agricultural University, Baoding, China
| | - Xinhao Meng
- North China Key Laboratory for Crop Germplasm Resources of Education Ministry, College of Agronomy, Hebei Agricultural University, Baoding, China
| | - Guojun Mu
- North China Key Laboratory for Crop Germplasm Resources of Education Ministry, College of Agronomy, Hebei Agricultural University, Baoding, China
| | - Mingyu Hou
- North China Key Laboratory for Crop Germplasm Resources of Education Ministry, College of Agronomy, Hebei Agricultural University, Baoding, China
| | - Meijing He
- North China Key Laboratory for Crop Germplasm Resources of Education Ministry, College of Agronomy, Hebei Agricultural University, Baoding, China
| | - Hui Zhang
- Department of Crop, Soil and Environmental Sciences, Auburn University, Auburn, AL, United States
| | - Lifeng Liu
- North China Key Laboratory for Crop Germplasm Resources of Education Ministry, College of Agronomy, Hebei Agricultural University, Baoding, China
- *Correspondence: Lifeng Liu,
| | - Charles Y. Chen
- Department of Crop, Soil and Environmental Sciences, Auburn University, Auburn, AL, United States
- Charles Y. Chen,
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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: 17] [Impact Index Per Article: 2.8] [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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Lu Q, Liu H, Hong Y, Li H, Liu H, Li X, Wen S, Zhou G, Li S, Chen X, Liang X. Consensus map integration and QTL meta-analysis narrowed a locus for yield traits to 0.7 cM and refined a region for late leaf spot resistance traits to 0.38 cM on linkage group A05 in peanut (Arachis hypogaea L.). BMC Genomics 2018; 19:887. [PMID: 30526476 PMCID: PMC6286586 DOI: 10.1186/s12864-018-5288-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Accepted: 11/20/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Many large-effect quantitative trait loci (QTLs) for yield and disease resistance related traits have been identified in different mapping populations of peanut (Arachis hypogaea L.) under multiple environments. However, only a limited number of QTLs have been used in marker-assisted selection (MAS) because of unfavorable epistatic interactions between QTLs in different genetic backgrounds. Thus, it is essential to identify consensus QTLs across different environments and genetic backgrounds for use in MAS. Here, we used QTL meta-analysis to identify a set of consensus QTLs for yield and disease resistance related traits in peanut. RESULTS A new integrated consensus genetic map with 5874 loci was constructed. The map comprised 20 linkage groups (LGs) and was up to a total length of 2918.62 cM with average marker density of 2.01 loci per centimorgan (cM). A total of 292 initial QTLs were projected on the new consensus map, and 40 meta-QTLs (MQTLs) for yield and disease resistance related traits were detected on four LGs. The genetic intervals of these consensus MQTLs varied from 0.20 cM to 7.4 cM, which is narrower than the genetic intervals of the initial QTLs, meaning they may be suitable for use in MAS. Importantly, a region of the map that previously co-localized multiple major QTLs for pod traits was narrowed from 3.7 cM to 0.7 cM using an overlap region of four MQTLs for yield related traits on LG A05, which corresponds to a physical region of about 630.3 kb on the A05 pseudomolecule of peanut, including 38 annotated candidate genes (54 transcripts) related to catalytic activity and metabolic process. Additionally, one major MQTL for late leaf spot (LLS) was identified in a region of about 0.38 cM. BLAST searches identified 26 candidate genes (30 different transcripts) in this region, some of which were annotated as related to regulation of disease resistance in different plant species. CONCLUSIONS Combined with the high-density marker consensus map, all the detected MQTLs could be useful in MAS. The biological functions of the 64 candidate genes should be validated to unravel the molecular mechanisms of yield and disease resistance in peanut.
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Affiliation(s)
- Qing Lu
- Crops Research Institute, Guangdong Academy of Agricultural Sciences, South China Peanut Sub-Center of National Center of Oilseed Crops Improvement, Guangdong Provincial Key Laboratory of Crop Genetic Improvement, Guangzhou, 510640, China
| | - Hao Liu
- Crops Research Institute, Guangdong Academy of Agricultural Sciences, South China Peanut Sub-Center of National Center of Oilseed Crops Improvement, Guangdong Provincial Key Laboratory of Crop Genetic Improvement, Guangzhou, 510640, China
| | - Yanbin Hong
- Crops Research Institute, Guangdong Academy of Agricultural Sciences, South China Peanut Sub-Center of National Center of Oilseed Crops Improvement, Guangdong Provincial Key Laboratory of Crop Genetic Improvement, Guangzhou, 510640, China
| | - Haifen Li
- Crops Research Institute, Guangdong Academy of Agricultural Sciences, South China Peanut Sub-Center of National Center of Oilseed Crops Improvement, Guangdong Provincial Key Laboratory of Crop Genetic Improvement, Guangzhou, 510640, China
| | - Haiyan Liu
- Crops Research Institute, Guangdong Academy of Agricultural Sciences, South China Peanut Sub-Center of National Center of Oilseed Crops Improvement, Guangdong Provincial Key Laboratory of Crop Genetic Improvement, Guangzhou, 510640, China
| | - Xingyu Li
- Crops Research Institute, Guangdong Academy of Agricultural Sciences, South China Peanut Sub-Center of National Center of Oilseed Crops Improvement, Guangdong Provincial Key Laboratory of Crop Genetic Improvement, Guangzhou, 510640, China
| | - Shijie Wen
- Crops Research Institute, Guangdong Academy of Agricultural Sciences, South China Peanut Sub-Center of National Center of Oilseed Crops Improvement, Guangdong Provincial Key Laboratory of Crop Genetic Improvement, Guangzhou, 510640, China
| | - Guiyuan Zhou
- Crops Research Institute, Guangdong Academy of Agricultural Sciences, South China Peanut Sub-Center of National Center of Oilseed Crops Improvement, Guangdong Provincial Key Laboratory of Crop Genetic Improvement, Guangzhou, 510640, China
| | - Shaoxiong Li
- Crops Research Institute, Guangdong Academy of Agricultural Sciences, South China Peanut Sub-Center of National Center of Oilseed Crops Improvement, Guangdong Provincial Key Laboratory of Crop Genetic Improvement, Guangzhou, 510640, China
| | - Xiaoping Chen
- Crops Research Institute, Guangdong Academy of Agricultural Sciences, South China Peanut Sub-Center of National Center of Oilseed Crops Improvement, Guangdong Provincial Key Laboratory of Crop Genetic Improvement, Guangzhou, 510640, China.
| | - Xuanqiang Liang
- Crops Research Institute, Guangdong Academy of Agricultural Sciences, South China Peanut Sub-Center of National Center of Oilseed Crops Improvement, Guangdong Provincial Key Laboratory of Crop Genetic Improvement, Guangzhou, 510640, China.
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15
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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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Wang Z, Huai D, Zhang Z, Cheng K, Kang Y, Wan L, Yan L, Jiang H, Lei Y, Liao B. Development of a High-Density Genetic Map Based on Specific Length Amplified Fragment Sequencing and Its Application in Quantitative Trait Loci Analysis for Yield-Related Traits in Cultivated Peanut. FRONTIERS IN PLANT SCIENCE 2018; 9:827. [PMID: 29997635 PMCID: PMC6028809 DOI: 10.3389/fpls.2018.00827] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Accepted: 05/28/2018] [Indexed: 05/20/2023]
Abstract
High-density genetic maps (HDGMs) are very useful for genomic studies and quantitative trait loci (QTL) mapping. However, the low frequency of DNA polymorphisms in peanut has limited the quantity of available markers and hindered the construction of a HDGM. This study generated a peanut genetic map with the highest number of high-quality SNPs based on specific locus amplified fragment sequencing (SLAF-seq) technology and a newly constructed RIL population ("ZH16" × "sd-H1"). The constructed HDGM included 3,630 SNP markers belonging to 2,636 bins on 20 linkage groups (LGs), and it covers 2,098.14 cM in length, with an average marker distance of 0.58 cM. This HDGM was applied for the following collinear comparison, scaffold anchoring and analysis of genomic characterization including recombination rates and segregation distortion in peanut. For QTL mapping of investigated 14 yield-related traits, a total of 62 QTLs were detected on 12 chromosomes across 3 environments, and the co-localization of QTLs was observed for these traits which were significantly correlated on phenotype. Two stable co-located QTLs for seed- and pod-related traits were significantly identified in the chromosomal end of B06 and B07, respectively. The construction of HDGM and QTL analysis for yield-related traits in this study provide useful information for fine mapping and functional analysis of genes as well as molecular marker-assisted breeding.
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17
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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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Chombe D, Bekele E, Bryngelsson T, Teshome A, Geleta M. Genetic structure and relationships within and between cultivated and wild korarima [Aframomum corrorima (Braun) P.C.M. Jansen] in Ethiopia as revealed by simple sequence repeat (SSR) markers. BMC Genet 2017; 18:72. [PMID: 28764649 PMCID: PMC5540420 DOI: 10.1186/s12863-017-0540-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2017] [Accepted: 07/25/2017] [Indexed: 11/28/2022] Open
Abstract
BACKGROUND Korarima [Aframomum corrorima (Braun) P.C.M. Jansen] is a spice crop native to Ethiopia. Understanding the extent and partitioning of diversity within and among crop landraces and their wild relatives is among the first steps in conserving and measuring their genetic potential. The present study is aimed at characterizing the population genetic structure and relationships between cultivated and wild korarima in the southwestern part of Ethiopia. RESULTS We analyzed a total of 195 individuals representing seven wild and fourteen cultivated populations. Eleven polymorphic simple sequence repeat (SSR) markers were used. We observed a total of 53 alleles across the eleven loci and individuals. In total, 32 alleles were detected in the cultivated populations, whereas 49 alleles were detected in the wild populations. We found higher genetic diversity in wild populations than in the cultivated counterpart. This result implies the potential of wild korarima as a possible source for novel alleles contributing to the improvement of cultivated korarima. Analysis of molecular variance (AMOVA) showed significant but low differentiation between cultivated and wild korarima populations. Similarly, neighbour-joining and STRUCTURE analyses did not group cultivated and wild populations into two distinct clusters. The lack of clear differentiation between cultivated and wild populations could be explained by historical and contemporary gene flow between the two gene pools. CONCLUSION The 11 SSR loci developed in this study could be employed to examine genetic diversity and population structure of korarima in other countries as well as other Aframomum species. From the five administrative zones considered in this study, the Bench-Magi and Sheka zone showed populations with high genetic diversity, and these populations could be used as a potential starting point for in-situ and ex-situ germplasm conservation and korarima improvement through breeding programs after proper agronomic evaluation.
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Affiliation(s)
- Dagmawit Chombe
- Department of Microbial, Cellular and Molecular Biology, Addis Ababa University, P. O. Box, 1176, Addis Ababa, Ethiopia.
| | - Endashaw Bekele
- Department of Microbial, Cellular and Molecular Biology, Addis Ababa University, P. O. Box, 1176, Addis Ababa, Ethiopia
| | - Tomas Bryngelsson
- Department of Plant Breeding, Swedish University of Agricultural Sciences, P.O. Box 101, -23053, Alnarp, SE, Sweden
| | - Abel Teshome
- Department of Plant Breeding, Swedish University of Agricultural Sciences, P.O. Box 101, -23053, Alnarp, SE, Sweden
| | - Mulatu Geleta
- Department of Plant Breeding, Swedish University of Agricultural Sciences, P.O. Box 101, -23053, Alnarp, SE, Sweden
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Balsalobre TWA, da Silva Pereira G, Margarido GRA, Gazaffi R, Barreto FZ, Anoni CO, Cardoso-Silva CB, Costa EA, Mancini MC, Hoffmann HP, de Souza AP, Garcia AAF, Carneiro MS. GBS-based single dosage markers for linkage and QTL mapping allow gene mining for yield-related traits in sugarcane. BMC Genomics 2017; 18:72. [PMID: 28077090 PMCID: PMC5225503 DOI: 10.1186/s12864-016-3383-x] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Accepted: 12/07/2016] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND Sugarcane (Saccharum spp.) is predominantly an autopolyploid plant with a variable ploidy level, frequent aneuploidy and a large genome that hampers investigation of its organization. Genetic architecture studies are important for identifying genomic regions associated with traits of interest. However, due to the genetic complexity of sugarcane, the practical applications of genomic tools have been notably delayed in this crop, in contrast to other crops that have already advanced to marker-assisted selection (MAS) and genomic selection. High-throughput next-generation sequencing (NGS) technologies have opened new opportunities for discovering molecular markers, especially single nucleotide polymorphisms (SNPs) and insertion-deletion (indels), at the genome-wide level. The objectives of this study were to (i) establish a pipeline for identifying variants from genotyping-by-sequencing (GBS) data in sugarcane, (ii) construct an integrated genetic map with GBS-based markers plus target region amplification polymorphisms and microsatellites, (iii) detect QTLs related to yield component traits, and (iv) perform annotation of the sequences that originated the associated markers with mapped QTLs to search putative candidate genes. RESULTS We used four pseudo-references to align the GBS reads. Depending on the reference, from 3,433 to 15,906 high-quality markers were discovered, and half of them segregated as single-dose markers (SDMs) on average. In addition to 7,049 non-redundant SDMs from GBS, 629 gel-based markers were used in a subsequent linkage analysis. Of 7,678 SDMs, 993 were mapped. These markers were distributed throughout 223 linkage groups, which were clustered in 18 homo(eo)logous groups (HGs), with a cumulative map length of 3,682.04 cM and an average marker density of 3.70 cM. We performed QTL mapping of four traits and found seven QTLs. Our results suggest the presence of a stable QTL across locations. Furthermore, QTLs to soluble solid content (BRIX) and fiber content (FIB) traits had markers linked to putative candidate genes. CONCLUSIONS This study is the first to report the use of GBS for large-scale variant discovery and genotyping of a mapping population in sugarcane, providing several insights regarding the use of NGS data in a polyploid, non-model species. The use of GBS generated a large number of markers and still enabled ploidy and allelic dosage estimation. Moreover, we were able to identify seven QTLs, two of which had great potential for validation and future use for molecular breeding in sugarcane.
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Affiliation(s)
- Thiago Willian Almeida Balsalobre
- Departamento de Biotecnologia e Produção Vegetal e Animal, Centro de Ciências Agrárias, Universidade Federal de São Carlos, Rodovia Anhanguera, Km 174, Araras, CEP 13600-970 São Paulo Brazil
- Departamento de Biologia Vegetal, Instituto de Biologia, Universidade Estadual de Campinas, Avenida Monteiro Lobato 255, Campinas, CEP 13083-862 São Paulo Brazil
- Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas, Avenida Candido Rondon 400, Campinas, CEP 13083-875 São Paulo Brazil
| | - Guilherme da Silva Pereira
- Departamento de Genética, Escola Superior de Agricultura Luiz de Queiroz, Universidade de São Paulo, Avenida Pádua Dias 11, Piracicaba, CEP 13418-900 São Paulo Brazil
| | - Gabriel Rodrigues Alves Margarido
- Departamento de Genética, Escola Superior de Agricultura Luiz de Queiroz, Universidade de São Paulo, Avenida Pádua Dias 11, Piracicaba, CEP 13418-900 São Paulo Brazil
| | - Rodrigo Gazaffi
- Departamento de Biotecnologia e Produção Vegetal e Animal, Centro de Ciências Agrárias, Universidade Federal de São Carlos, Rodovia Anhanguera, Km 174, Araras, CEP 13600-970 São Paulo Brazil
| | - Fernanda Zatti Barreto
- Departamento de Biotecnologia e Produção Vegetal e Animal, Centro de Ciências Agrárias, Universidade Federal de São Carlos, Rodovia Anhanguera, Km 174, Araras, CEP 13600-970 São Paulo Brazil
| | - Carina Oliveira Anoni
- Departamento de Genética, Escola Superior de Agricultura Luiz de Queiroz, Universidade de São Paulo, Avenida Pádua Dias 11, Piracicaba, CEP 13418-900 São Paulo Brazil
| | - Cláudio Benício Cardoso-Silva
- Departamento de Biologia Vegetal, Instituto de Biologia, Universidade Estadual de Campinas, Avenida Monteiro Lobato 255, Campinas, CEP 13083-862 São Paulo Brazil
- Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas, Avenida Candido Rondon 400, Campinas, CEP 13083-875 São Paulo Brazil
| | - Estela Araújo Costa
- Departamento de Biologia Vegetal, Instituto de Biologia, Universidade Estadual de Campinas, Avenida Monteiro Lobato 255, Campinas, CEP 13083-862 São Paulo Brazil
- Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas, Avenida Candido Rondon 400, Campinas, CEP 13083-875 São Paulo Brazil
| | - Melina Cristina Mancini
- Departamento de Biologia Vegetal, Instituto de Biologia, Universidade Estadual de Campinas, Avenida Monteiro Lobato 255, Campinas, CEP 13083-862 São Paulo Brazil
- Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas, Avenida Candido Rondon 400, Campinas, CEP 13083-875 São Paulo Brazil
| | - Hermann Paulo Hoffmann
- Departamento de Biotecnologia e Produção Vegetal e Animal, Centro de Ciências Agrárias, Universidade Federal de São Carlos, Rodovia Anhanguera, Km 174, Araras, CEP 13600-970 São Paulo Brazil
| | - Anete Pereira de Souza
- Departamento de Biologia Vegetal, Instituto de Biologia, Universidade Estadual de Campinas, Avenida Monteiro Lobato 255, Campinas, CEP 13083-862 São Paulo Brazil
- Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas, Avenida Candido Rondon 400, Campinas, CEP 13083-875 São Paulo Brazil
| | - Antonio Augusto Franco Garcia
- Departamento de Genética, Escola Superior de Agricultura Luiz de Queiroz, Universidade de São Paulo, Avenida Pádua Dias 11, Piracicaba, CEP 13418-900 São Paulo Brazil
| | - Monalisa Sampaio Carneiro
- Departamento de Biotecnologia e Produção Vegetal e Animal, Centro de Ciências Agrárias, Universidade Federal de São Carlos, Rodovia Anhanguera, Km 174, Araras, CEP 13600-970 São Paulo Brazil
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Chen Y, Ren X, Zheng Y, Zhou X, Huang L, Yan L, Jiao Y, Chen W, Huang S, Wan L, Lei Y, Liao B, Huai D, Wei W, Jiang H. Genetic mapping of yield traits using RIL population derived from Fuchuan Dahuasheng and ICG6375 of peanut ( Arachis hypogaea L.). MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2017; 37:17. [PMID: 28216998 PMCID: PMC5285419 DOI: 10.1007/s11032-016-0587-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2016] [Accepted: 11/01/2016] [Indexed: 05/04/2023]
Abstract
The genetic architecture determinants of yield traits in peanut (Arachis hypogaea L.) are poorly understood. In the present study, an effort was made to map quantitative trait loci (QTLs) for yield traits using recombinant inbred lines (RIL). A genetic linkage map was constructed containing 609 loci, covering a total of 1557.48 cM with an average distance of 2.56 cM between adjacent markers. The present map exhibited good collinearity with the physical map of diploid species of Arachis. Ninety-two repeatable QTLs were identified for 11 traits including height of main stem, total branching number, and nine pod- and seed-related traits. Of the 92 QTLs, 15 QTLs were expressed across three environments and 65 QTLs were newly identified. Twelve QTLs for the height of main stem and the pod- and seed-related traits explaining more than 10 % of phenotypic variation showed a great potential for marker-assisted selection in improving these traits. The trait-by-trait meta-analysis revealed 33 consensus QTLs. The consensus QTLs and other QTLs were further integrated into 29 pleiotropic unique QTLs with the confidence interval of 1.86 cM on average. The significant co-localization of QTLs was consistent with the significant phenotypic correlations among these traits. The complexity of the genetic architecture of yield traits was demonstrated. The present QTLs for pod- and seed-related traits could be the most fundamental genetic factors contributing to the yield traits in peanut. The results provide a good foundation for fine mapping, cloning and designing molecular breeding of favorable genes in peanut.
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Affiliation(s)
- Yuning Chen
- Oil Crop Research Institute, Chinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agricultural, Wuhan, 430062 People’s Republic of China
| | - Xiaoping Ren
- Oil Crop Research Institute, Chinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agricultural, Wuhan, 430062 People’s Republic of China
| | - Yanli Zheng
- Oil Crop Research Institute, Chinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agricultural, Wuhan, 430062 People’s Republic of China
| | - Xiaojing Zhou
- Oil Crop Research Institute, Chinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agricultural, Wuhan, 430062 People’s Republic of China
| | - Li Huang
- Oil Crop Research Institute, Chinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agricultural, Wuhan, 430062 People’s Republic of China
| | - Liying Yan
- Oil Crop Research Institute, Chinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agricultural, Wuhan, 430062 People’s Republic of China
| | - Yongqing Jiao
- Oil Crop Research Institute, Chinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agricultural, Wuhan, 430062 People’s Republic of China
| | - Weigang Chen
- Oil Crop Research Institute, Chinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agricultural, Wuhan, 430062 People’s Republic of China
| | - Shunmou Huang
- Oil Crop Research Institute, Chinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agricultural, Wuhan, 430062 People’s Republic of China
| | - Liyun Wan
- Oil Crop Research Institute, Chinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agricultural, Wuhan, 430062 People’s Republic of China
| | - Yong Lei
- Oil Crop Research Institute, Chinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agricultural, Wuhan, 430062 People’s Republic of China
| | - Boshou Liao
- Oil Crop Research Institute, Chinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agricultural, Wuhan, 430062 People’s Republic of China
| | - Dongxin Huai
- Oil Crop Research Institute, Chinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agricultural, Wuhan, 430062 People’s Republic of China
| | - Wenhui Wei
- Oil Crop Research Institute, Chinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agricultural, Wuhan, 430062 People’s Republic of China
| | - Huifang Jiang
- Oil Crop Research Institute, Chinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agricultural, Wuhan, 430062 People’s Republic of China
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21
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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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22
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Ahmad NS, Redjeki ES, Ho WK, Aliyu S, Mayes K, Massawe F, Kilian A, Mayes S. Construction of a genetic linkage map and QTL analysis in bambara groundnut. Genome 2016; 59:459-72. [DOI: 10.1139/gen-2015-0153] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Bambara groundnut (Vigna subterranea (L.) Verdc.) is an indigenous underutilized legume that has the potential to improve food security in semi-arid Africa. So far, there are a lack of reports of controlled breeding populations that could be used for variety development and genetic studies. We report here the construction of the first genetic linkage map of bambara groundnut using a F3 population derived from a “narrow” cross between two domesticated landraces (Tiga Nicuru and DipC) with marked divergence in phenotypic traits. The map consists of 238 DArT array and SSR based markers in 21 linkage groups with a total genetic distance of 608.3 cM. In addition, phenotypic traits were evaluated for a quantitative trait loci (QTL) analysis over two generations. A total of 36 significant QTLs were detected for 19 traits. The phenotypic effect explained by a single QTL ranged from 11.6% to 49.9%. Two stable QTLs were mapped for internode length and growth habit. The identified QTLs could be useful for marker-assisted selection in bambara groundnut breeding programmes.
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Affiliation(s)
- Nariman Salih Ahmad
- Crop Science Department, Faculty of Agricultural Sciences, Sulaimani University, Kurdistan, Iraq
| | | | - Wai Kuan Ho
- University of Nottingham Malaysia Campus, Jalan Broga, 43500 Semenyih, Selangor, Malaysia
- Crops For the Future, Jalan Broga, 43500 Semenyih, Selangor, Malaysia
| | - Siise Aliyu
- University of Nottingham Malaysia Campus, Jalan Broga, 43500 Semenyih, Selangor, Malaysia
- Crops For the Future, Jalan Broga, 43500 Semenyih, Selangor, Malaysia
- CSIR-Savannah Agricultural Research Institute, Nyankpala N/R, Ghana
| | - Katie Mayes
- University of Nottingham, Plant and Crop Sciences Division, Sutton Bonington Campus, Loughborough, Leicestershire LE12 5RD, UK
| | - Festo Massawe
- University of Nottingham Malaysia Campus, Jalan Broga, 43500 Semenyih, Selangor, Malaysia
| | - Andrzej Kilian
- Diversity Array Technology Pty Ltd., Building 3, Level D, University of Canberra, Kirinari St. Bruce, ACT2617, Australia
| | - Sean Mayes
- Crops For the Future, Jalan Broga, 43500 Semenyih, Selangor, Malaysia
- University of Nottingham, Plant and Crop Sciences Division, Sutton Bonington Campus, Loughborough, Leicestershire LE12 5RD, UK
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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: 471] [Impact Index Per Article: 58.9] [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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Chen W, Jiao Y, Cheng L, Huang L, Liao B, Tang M, Ren X, Zhou X, Chen Y, Jiang H. Quantitative trait locus analysis for pod- and kernel-related traits in the cultivated peanut (Arachis hypogaea L.). BMC Genet 2016; 17:25. [PMID: 26810040 PMCID: PMC4727316 DOI: 10.1186/s12863-016-0337-x] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2015] [Accepted: 01/15/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The cultivated peanut (Arachis hypogaea L.) is an important oil and food crop in the world. Pod- and kernel-related traits are direct factors involved in determining the yield of the peanut. However, the genetic basis underlying pod- and kernel-related traits in the peanut remained largely unknown, which hampered the improvement of peanut through marker-assisted selection. To understand the genetic basis underlying pod- and kernel-related traits in the peanut and provide more useful information for marker-assisted breeding, we conducted quantitative trait locus (QTL) analysis for pod length and width and seed length and width by use of two F2:3 populations derived from cultivar Fuchuan Dahuasheng × ICG 6375 (FI population) and cultivar Xuhua 13 × cultivar Zhonghua 6 (XZ population) in this study. RESULTS Two genetic maps containing 347 and 228 polymorphic markers were constructed for FI and XZ populations respectively. In total, 39 QTLs explaining 1.25-26.11% of the phenotypic variations were detected in two populations. For the FI population, 26 QTLs were detected between the two environments, among which twelve were not mapped before. For the XZ population, thirteen QTLs were detected, among which eight were not reported before. One QTL for pod width was repeatedly mapped between the two populations. CONCLUSION The QTL analyses for pod length and width and seed length and width were conducted in this study using two mapping populations. Novel QTLs were identified, which included two for pod length, four for pod width, five for seed length and one for seed width in the FI population, and three for pod length, three for pod width and two for seed width in the XZ population. Our results will be helpful for improving pod- and seed-related traits in peanuts through marker-assisted selection.
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Affiliation(s)
- 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, 430062, China.
| | - Yongqing Jiao
- 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, China.
| | - Liangqiang Cheng
- 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, 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, 430062, 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, 430062, China.
| | - Mei Tang
- 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, 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, 430062, 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, 430062, 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, 430062, 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, 430062, China.
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25
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Jogi A, Kerry JW, Brenneman TB, Leebens-Mack JH, Gold SE. Identification of genes differentially expressed during early interactions between the stem rot fungus (Sclerotium rolfsii) and peanut (Arachis hypogaea) cultivars with increasing disease resistance levels. Microbiol Res 2015; 184:1-12. [PMID: 26856448 DOI: 10.1016/j.micres.2015.11.003] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2015] [Revised: 11/12/2015] [Accepted: 11/14/2015] [Indexed: 10/22/2022]
Abstract
Sclerotium rolfsii, a destructive soil-borne fungal pathogen causes stem rot of the cultivated peanut, Arachis hypogaea. This study aimed to identify differentially expressed genes associated with peanut resistance and fungal virulence. Four peanut cultivars (A100-32, Georgia Green, GA-07W and York) with increasing resistance levels were inoculated with a virulent S. rolfsii strain to study the early plant-pathogen interaction. 454 sequencing was performed on RNAs from infected tissue collected at 4 days post inoculation, generating 225,793 high-quality reads. Normalized read counts and fold changes were calculated and statistical analysis used to identify differentially expressed genes. Several genes identified as differential in the RNA-seq experiment were selected based on functions of interest and real-time PCR employed to corroborate their differential expression. Expanding the analysis to include all four cultivars revealed a small but interesting set of genes showing colinearity between cultivar resistance and expression levels. This study identified a set of genes possibly related to pathogen response that may be useful marker assisted selection or transgenic disease control strategies. Additionally, a set of differentially expressed genes that have not been functionally characterized in peanut or other plants and warrant additional investigation were identified.
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Affiliation(s)
- Ansuya Jogi
- Department of Plant Pathology, University of Georgia, Athens, GA, USA
| | - John W Kerry
- Department of Plant Biology, University of Georgia, Athens, GA, USA
| | | | | | - Scott E Gold
- Department of Plant Pathology, University of Georgia, Athens, GA, USA; USDA, ARS, Russell Research Center, Toxicology & Mycotoxin Research Unit, 950 College Station Road, Athens, GA 30605, USA.
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26
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Verma P, Goyal R, Chahota RK, Sharma TR, Abdin MZ, Bhatia S. Construction of a Genetic Linkage Map and Identification of QTLs for Seed Weight and Seed Size Traits in Lentil (Lens culinaris Medik.). PLoS One 2015; 10:e0139666. [PMID: 26436554 PMCID: PMC4593543 DOI: 10.1371/journal.pone.0139666] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2014] [Accepted: 09/16/2015] [Indexed: 01/05/2023] Open
Abstract
Seed weight and seed size both are quantitative traits and have been considered as important components of grain yield, thus identification of quantitative trait loci (QTL) for seed traits in lentil (Lens culinaris) would be beneficial for the improvement of grain yield. Hence the main objective of this study was to identify QTLs for seed traits using an intraspecific mapping population derived from a cross between L. culinaris cv. Precoz (seed weight-5.1g, seed size-5.7mm) and L. culinaris cv. L830 (seed weight-2.2g, seed size-4mm) comprising 126 F8-RILs. For this, two microsatellite genomic libraries enriched for (GA/CT) and (GAA/CTT) motif were constructed which resulted in the development of 501 new genomic SSR markers. Six hundred forty seven SSR markers (including 146 previously published) were screened for parental polymorphism and 219 (33.8%) were found to be polymorphic among the parents. Of these 216 were mapped on seven linkage groups at LOD4.0 spanning 1183.7cM with an average marker density of 5.48cM. Phenotypic data from the RILs was used to identify QTLs for the seed weight and seed size traits by single marker analysis (SMA) followed by composite interval mapping (CIM) which resulted in one QTL each for the 2 traits (qSW and qSS) that were co-localized on LG4 and explained 48.4% and 27.5% of phenotypic variance respectively. The current study would serve as a strong foundation for further validation and fine mapping for utilization in lentil breeding programs.
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Affiliation(s)
- Priyanka Verma
- National Institute of Plant Genome Research, Post Box No. 10531, Aruna Asaf Ali Marg, New Delhi, 110067, India
- Department of Biotechnology, Faculty of Science, Jamia Hamdard, New Delhi, 110062, India
| | - Richa Goyal
- National Institute of Plant Genome Research, Post Box No. 10531, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - R. K. Chahota
- Department of Agricultural Biotechnology, Chaudhary Sarwan Kumar Himachal Pradesh Agricultural University, Palampur, 176 062, India
| | - Tilak R. Sharma
- Department of Agricultural Biotechnology, Chaudhary Sarwan Kumar Himachal Pradesh Agricultural University, Palampur, 176 062, India
| | - M. Z. Abdin
- Department of Biotechnology, Faculty of Science, Jamia Hamdard, New Delhi, 110062, India
| | - Sabhyata Bhatia
- National Institute of Plant Genome Research, Post Box No. 10531, Aruna Asaf Ali Marg, New Delhi, 110067, India
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27
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Genetic Map Construction and Quantitative Trait Locus (QTL) Detection of Six Economic Traits Using an F2 Population of the Hybrid from Saccharina longissima and Saccharina japonica. PLoS One 2015; 10:e0128588. [PMID: 26010152 PMCID: PMC4444332 DOI: 10.1371/journal.pone.0128588] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2014] [Accepted: 04/28/2015] [Indexed: 12/21/2022] Open
Abstract
Saccharina (Laminaria) is one of the most important economic seaweeds. Previously, four genetic linkage maps of Saccharina have been constructed and five QTLs have been identified. However, they were not enough for its breeding. In this work, Saccharina longissima (♀) and Saccharina japonica (♂), which showed obvious differences in morphology and genetics, were applied in hybridization to yield the F2 mapping population with 102 individuals. Using these 102 F2 hybrids, the genetic linkage map of Saccharina was constructed by MapMaker software based on 37 amplified fragment length polymorphisms (AFLPs), 22 sequence-related amplified polymorphisms (SRAPs) and 139 simple sequence repeats (SSRs) markers. Meanwhile, QTL analysis was performed for six economic traits. The linkage map constructed in this research consisted of 422 marker loci (137 AFLPs, 57 SRAPs and 228 SSRs), which formed 45 linkage groups (LGs) with an average marker space of 7.92 cM; they spanned a total length of 2233.1 cM, covering the whole estimated genome size. A total of 29 QTLs were identified for six economic traits, which explained 1.06 to 64.00% of phenotypic variation, including three QTLs for frond length (FL) and raw weight (RW), five QTLs for frond width (FW), two QTLs for frond fascia width (FFW) and frond thickness (FT), and fourteen QTLs for base shape (BS). The results of this research will improve the breeding efficiency and be beneficial for marker-assisted selection (MAS) schemes in Saccharina breeding.
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Tetrasomic recombination is surprisingly frequent in allotetraploid Arachis. Genetics 2015; 199:1093-105. [PMID: 25701284 PMCID: PMC4391553 DOI: 10.1534/genetics.115.174607] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2015] [Accepted: 02/14/2015] [Indexed: 11/18/2022] Open
Abstract
Arachis hypogaea L. (cultivated peanut) is an allotetraploid (2n = 4x = 40) with an AABB genome type. Based on cytogenetic studies it has been assumed that peanut and wild-derived induced AABB allotetraploids have classic allotetraploid genetic behavior with diploid-like disomic recombination only between homologous chromosomes, at the exclusion of recombination between homeologous chromosomes. Using this assumption, numerous linkage map and quantitative trait loci studies have been carried out. Here, with a systematic analysis of genotyping and gene expression data, we show that this assumption is not entirely valid. In fact, autotetraploid-like tetrasomic recombination is surprisingly frequent in recombinant inbred lines generated from a cross of cultivated peanut and an induced allotetraploid derived from peanut’s most probable ancestral species. We suggest that a better, more predictive genetic model for peanut is that of a “segmental allotetraploid” with partly disomic, partly tetrasomic genetic behavior. This intermediate genetic behavior has probably had a previously overseen, but significant, impact on the genome and genetics of cultivated peanut.
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Next-generation transcriptome sequencing, SNP discovery and validation in four market classes of peanut, Arachis hypogaea L. Mol Genet Genomics 2015; 290:1169-80. [PMID: 25663138 DOI: 10.1007/s00438-014-0976-4] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2014] [Accepted: 12/06/2014] [Indexed: 10/24/2022]
Abstract
Single-nucleotide polymorphisms, which can be identified in the thousands or millions from comparisons of transcriptome or genome sequences, are ideally suited for making high-resolution genetic maps, investigating population evolutionary history, and discovering marker-trait linkages. Despite significant results from their use in human genetics, progress in identification and use in plants, and particularly polyploid plants, has lagged. As part of a long-term project to identify and use SNPs suitable for these purposes in cultivated peanut, which is tetraploid, we generated transcriptome sequences of four peanut cultivars, namely OLin, New Mexico Valencia C, Tamrun OL07 and Jupiter, which represent the four major market classes of peanut grown in the world, and which are important economically to the US southwest peanut growing region. CopyDNA libraries of each genotype were used to generate 2 × 54 paired-end reads using an Illumina GAIIx sequencer. Raw reads were mapped to a custom reference consisting of Tifrunner 454 sequences plus peanut ESTs in GenBank, compromising 43,108 contigs; 263,840 SNP and indel variants were identified among four genotypes compared to the reference. A subset of 6 variants was assayed across 24 genotypes representing four market types using KASP chemistry to assess the criteria for SNP selection. Results demonstrated that transcriptome sequencing can identify SNPs usable as selectable DNA-based markers in complex polyploid species such as peanut. Criteria for effective use of SNPs as markers are discussed in this context.
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30
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Hong Y, Pandey MK, Liu Y, Chen X, Liu H, Varshney RK, Liang X, Huang S. Identification and Evaluation of Single-Nucleotide Polymorphisms in Allotetraploid Peanut (Arachis hypogaea L.) Based on Amplicon Sequencing Combined with High Resolution Melting (HRM) Analysis. FRONTIERS IN PLANT SCIENCE 2015; 6:1068. [PMID: 26697032 PMCID: PMC4667090 DOI: 10.3389/fpls.2015.01068] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2015] [Accepted: 11/16/2015] [Indexed: 05/06/2023]
Abstract
The cultivated peanut (Arachis hypogaea L.) is an allotetraploid (AABB) species derived from the A-genome (Arachis duranensis) and B-genome (Arachis ipaensis) progenitors. Presence of two versions of a DNA sequence based on the two progenitor genomes poses a serious technical and analytical problem during single nucleotide polymorphism (SNP) marker identification and analysis. In this context, we have analyzed 200 amplicons derived from expressed sequence tags (ESTs) and genome survey sequences (GSS) to identify SNPs in a panel of genotypes consisting of 12 cultivated peanut varieties and two diploid progenitors representing the ancestral genomes. A total of 18 EST-SNPs and 44 genomic-SNPs were identified in 12 peanut varieties by aligning the sequence of A. hypogaea with diploid progenitors. The average frequency of sequence polymorphism was higher for genomic-SNPs than the EST-SNPs with one genomic-SNP every 1011 bp as compared to one EST-SNP every 2557 bp. In order to estimate the potential and further applicability of these identified SNPs, 96 peanut varieties were genotyped using high resolution melting (HRM) method. Polymorphism information content (PIC) values for EST-SNPs ranged between 0.021 and 0.413 with a mean of 0.172 in the set of peanut varieties, while genomic-SNPs ranged between 0.080 and 0.478 with a mean of 0.249. Total 33 SNPs were used for polymorphism detection among the parents and 10 selected lines from mapping population Y13Zh (Zhenzhuhei × Yueyou13). Of the total 33 SNPs, nine SNPs showed polymorphism in the mapping population Y13Zh, and seven SNPs were successfully mapped into five linkage groups. Our results showed that SNPs can be identified in allotetraploid peanut with high accuracy through amplicon sequencing and HRM assay. The identified SNPs were very informative and can be used for different genetic and breeding applications in peanut.
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Affiliation(s)
- Yanbin Hong
- Peanut Research Center, Crops Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
- School of Life Sciences, Sun Yat-Sen UniversityGuangzhou, China
| | - Manish K. Pandey
- Center of Excellence in Genomics, International Crops Research Institute for the Semi-Arid TropicsHyderabad, India
| | - Ying Liu
- Peanut Research Center, Crops Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Xiaoping Chen
- Peanut Research Center, Crops Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Hong Liu
- College of Agriculture, South China Agricultural UniversityGuangzhou, China
| | - Rajeev K. Varshney
- Center of Excellence in Genomics, International Crops Research Institute for the Semi-Arid TropicsHyderabad, India
- School of Plant Biology and Institute of Agriculture, The University of Western AustraliaCrawley, WA, Australia
| | - Xuanqiang Liang
- Peanut Research Center, Crops Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Shangzhi Huang
- School of Life Sciences, Sun Yat-Sen UniversityGuangzhou, China
- *Correspondence: Shangzhi Huang
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Liu L, Dang PM, Chen CY. Development and Utilization of InDel Markers to Identify Peanut (Arachis hypogaea) Disease Resistance. FRONTIERS IN PLANT SCIENCE 2015; 6:988. [PMID: 26617627 PMCID: PMC4643128 DOI: 10.3389/fpls.2015.00988] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Accepted: 10/29/2015] [Indexed: 05/04/2023]
Abstract
Peanut diseases, such as leaf spot and spotted wilt caused by Tomato Spotted Wilt Virus, can significantly reduce yield and quality. Application of marker assisted plant breeding requires the development and validation of different types of DNA molecular markers. Nearly 10,000 SSR-based molecular markers have been identified by various research groups around the world, but less than 14.5% showed polymorphism in peanut and only 6.4% have been mapped. Low levels of polymorphism limit the application of marker assisted selection (MAS) in peanut breeding programs. Insertion/deletion (InDel) markers have been reported to be more polymorphic than SSRs in some crops. The goals of this study were to identify novel InDel markers and to evaluate the potential use in peanut breeding. Forty-eight InDel markers were developed from conserved sequences of functional genes and tested in a diverse panel of 118 accessions covering six botanical types of cultivated peanut, of which 104 were from the U.S. mini-core. Results showed that 16 InDel markers were polymorphic with polymorphic information content (PIC) among InDels ranged from 0.017 to 0.660. With respect to botanical types, PICs varied from 0.176 for fastigiata var., 0.181 for hypogaea var., 0.306 for vulgaris var., 0.534 for aequatoriana var., 0.556 for peruviana var., to 0.660 for hirsuta var., implying that aequatoriana var., peruviana var., and hirsuta var. have higher genetic diversity than the other types and provide a basis for gene functional studies. Single marker analysis was conducted to associate specific marker to disease resistant traits. Five InDels from functional genes were identified to be significantly correlated to tomato spotted wilt virus (TSWV) infection and leaf spot, and these novel markers will be utilized to identify disease resistant genotype in breeding populations.
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Affiliation(s)
- Lifeng Liu
- Department of Crop, Soil and Environmental Sciences, Auburn UniversityAuburn, AL, USA
- Department of Agronomy, Agricultural University of HebeiBaoding, China
| | - Phat M. Dang
- National Peanut Research Laboratory, United States Department of Agriculture-Agricultural Research ServiceDawson, GA, USA
| | - Charles Y. Chen
- Department of Crop, Soil and Environmental Sciences, Auburn UniversityAuburn, AL, USA
- *Correspondence: Charles Y. Chen
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Cavagnaro PF, Iorizzo M, Yildiz M, Senalik D, Parsons J, Ellison S, Simon PW. A gene-derived SNP-based high resolution linkage map of carrot including the location of QTL conditioning root and leaf anthocyanin pigmentation. BMC Genomics 2014; 15:1118. [PMID: 25514876 PMCID: PMC4378384 DOI: 10.1186/1471-2164-15-1118] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2014] [Accepted: 12/11/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Purple carrots accumulate large quantities of anthocyanins in their roots and leaves. These flavonoid pigments possess antioxidant activity and are implicated in providing health benefits. Informative, saturated linkage maps associated with well characterized populations segregating for anthocyanin pigmentation have not been developed. To investigate the genetic architecture conditioning anthocyanin pigmentation we scored root color visually, quantified root anthocyanin pigments by high performance liquid chromatography in segregating F2, F3 and F4 generations of a mapping population, mapped quantitative trait loci (QTL) onto a dense gene-derived single nucleotide polymorphism (SNP)-based linkage map, and performed comparative trait mapping with two unrelated populations. RESULTS Root pigmentation, scored visually as presence or absence of purple coloration, segregated in a pattern consistent with a two gene model in an F2, and progeny testing of F3-F4 families confirmed the proposed genetic model. Purple petiole pigmentation was conditioned by a single dominant gene that co-segregates with one of the genes conditioning root pigmentation. Root total pigment estimate (RTPE) was scored as the percentage of the root with purple color.All five anthocyanin glycosides previously reported in carrot, as well as RTPE, varied quantitatively in the F2 population. For the purpose of QTL analysis, a high resolution gene-derived SNP-based linkage map of carrot was constructed with 894 markers covering 635.1 cM with a 1.3 cM map resolution. A total of 15 significant QTL for all anthocyanin pigments and for RTPE mapped to six chromosomes. Eight QTL with the largest phenotypic effects mapped to two regions of chromosome 3 with co-localized QTL for several anthocyanin glycosides and for RTPE. A single dominant gene conditioning anthocyanin acylation was identified and mapped.Comparative mapping with two other carrot populations segregating for purple color indicated that carrot anthocyanin pigmentation is controlled by at least three genes, in contrast to monogenic control reported previously. CONCLUSIONS This study generated the first high resolution gene-derived SNP-based linkage map in the Apiaceae. Two regions of chromosome 3 with co-localized QTL for all anthocyanin pigments and for RTPE, largely condition anthocyanin accumulation in carrot roots and leaves. Loci controlling root and petiole anthocyanin pigmentation differ across diverse carrot genetic backgrounds.
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Affiliation(s)
- Pablo F Cavagnaro
- />Department of Horticulture, University of Wisconsin-Madison, 1575 Linden Drive, Madison, WI 53706 USA
- />CONICET, Facultad de Ciencias Agrarias – Universidad Nacional de Cuyo, and INTA E.E.A. La Consulta, Ex Ruta 40. km 96, La Consulta CC 8, Mendoza, 5567 Argentina
| | - Massimo Iorizzo
- />Department of Horticulture, University of Wisconsin-Madison, 1575 Linden Drive, Madison, WI 53706 USA
| | - Mehtap Yildiz
- />Department of Agricultural Biotechnology, Faculty of Agriculture, Yuzuncu Yil University, 65080 Van, Turkey
| | - Douglas Senalik
- />Department of Horticulture, University of Wisconsin-Madison, 1575 Linden Drive, Madison, WI 53706 USA
- />USDA-Agricultural Research Service, Vegetable Crops Unit, University of Wisconsin-Madison, 1575 Linden Drive, Madison, WI 53706 USA
| | - Joshua Parsons
- />Department of Horticulture, University of Wisconsin-Madison, 1575 Linden Drive, Madison, WI 53706 USA
| | - Shelby Ellison
- />Department of Horticulture, University of Wisconsin-Madison, 1575 Linden Drive, Madison, WI 53706 USA
| | - Philipp W Simon
- />Department of Horticulture, University of Wisconsin-Madison, 1575 Linden Drive, Madison, WI 53706 USA
- />USDA-Agricultural Research Service, Vegetable Crops Unit, University of Wisconsin-Madison, 1575 Linden Drive, Madison, WI 53706 USA
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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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Ren X, Jiang H, Yan Z, Chen Y, Zhou X, Huang L, Lei Y, Huang J, Yan L, Qi Y, Wei W, Liao B. Genetic diversity and population structure of the major peanut (Arachis hypogaea L.) cultivars grown in China by SSR markers. PLoS One 2014; 9:e88091. [PMID: 24520347 PMCID: PMC3919752 DOI: 10.1371/journal.pone.0088091] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2013] [Accepted: 01/05/2014] [Indexed: 11/18/2022] Open
Abstract
One hundred and forty-six highly polymorphic simple sequence repeat (SSR) markers were used to assess the genetic diversity and population structure of 196 peanut (Arachis Hypogaea L.) cultivars which had been extensively planted in different regions in China. These SSR markers amplified 440 polymorphic bands with an average of 2.99, and the average gene diversity index was 0.11. Eighty-six rare alleles with a frequency of less than 1% were identified in these cultivars. The largest Fst or genetic distance was found between the cultivars that adapted to the south regions and those to the north regions in China. A neighbor-joining tree of cultivars adapted to different ecological regions was constructed based on pairwise Nei's genetic distances, which showed a significant difference between cultivars from the south and the north regions. A model-based population structure analysis divided these peanut cultivars into five subpopulations (P1a, P1b, P2, P3a and P3b). P1a and P1b included most the cultivars from the southern provinces including Guangdong, Guangxi and Fujian. P2 population consisted of the cultivars from Hubei province and parts from Shandong and Henan. P3a and P3b had cultivars from the northern provinces including Shandong, Anhui, Henan, Hebei, Jiangsu and the Yangtze River region including Sichuan province. The cluster analysis, PCoA and PCA based on the marker genotypes, revealed five distinct clusters for the entire population that were related to their germplasm regions. The results indicated that there were obvious genetic variations between cultivars from the south and the north, and there were distinct genetic differentiation among individual cultivars from the south and the north. Taken together, these results provided a molecular basis for understanding genetic diversity of Chinese peanut cultivars.
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Affiliation(s)
- Xiaoping Ren
- Key Laboratory of the Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture/Oil Crop Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, Hubei, China
| | - Huifang Jiang
- Key Laboratory of the Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture/Oil Crop Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, Hubei, China
- * E-mail: (HJ); (BL)
| | - Zhongyuan Yan
- Key Laboratory of the Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture/Oil Crop Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, Hubei, China
| | - Yuning Chen
- Key Laboratory of the Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture/Oil Crop Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, Hubei, China
| | - Xiaojing Zhou
- Key Laboratory of the Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture/Oil Crop Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, Hubei, China
| | - Li Huang
- Key Laboratory of the Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture/Oil Crop Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, Hubei, China
| | - Yong Lei
- Key Laboratory of the Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture/Oil Crop Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, Hubei, China
| | - Jiaquan Huang
- Key Laboratory of the Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture/Oil Crop Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, Hubei, China
| | - Liying Yan
- Key Laboratory of the Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture/Oil Crop Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, Hubei, China
| | - Yue Qi
- National Facility for Training Personnel in Life Sciences and Biotechnology, College of Life Sciences, Wuhan University, Wuhan, Hubei, China
| | - Wenhui Wei
- Key Laboratory of the Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture/Oil Crop Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, Hubei, China
| | - Boshou Liao
- Key Laboratory of the Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture/Oil Crop Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, Hubei, China
- * E-mail: (HJ); (BL)
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Yagi M, Yamamoto T, Isobe S, Hirakawa H, Tabata S, Tanase K, Yamaguchi H, Onozaki T. Construction of a reference genetic linkage map for carnation (Dianthus caryophyllus L.). BMC Genomics 2013; 14:734. [PMID: 24160306 PMCID: PMC3870981 DOI: 10.1186/1471-2164-14-734] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2013] [Accepted: 09/25/2013] [Indexed: 02/07/2023] Open
Abstract
Background Genetic linkage maps are important tools for many genetic applications including mapping of quantitative trait loci (QTLs), identifying DNA markers for fingerprinting, and map-based gene cloning. Carnation (Dianthus caryophyllus L.) is an important ornamental flower worldwide. We previously reported a random amplified polymorphic DNA (RAPD)-based genetic linkage map derived from Dianthus capitatus ssp. andrezejowskianus and a simple sequence repeat (SSR)-based genetic linkage map constructed using data from intraspecific F2 populations; however, the number of markers was insufficient, and so the number of linkage groups (LGs) did not coincide with the number of chromosomes (x = 15). Therefore, we aimed to produce a high-density genetic map to improve its usefulness for breeding purposes and genetic research. Results We improved the SSR-based genetic linkage map using SSR markers derived from a genomic library, expression sequence tags, and RNA-seq data. Linkage analysis revealed that 412 SSR loci (including 234 newly developed SSR loci) could be mapped to 17 linkage groups (LGs) covering 969.6 cM. Comparison of five minor LGs covering less than 50 cM with LGs in our previous RAPD-based genetic map suggested that four LGs could be integrated into two LGs by anchoring common SSR loci. Consequently, the number of LGs corresponded to the number of chromosomes (x = 15). We added 192 new SSRs, eight RAPD, and two sequence-tagged site loci to refine the RAPD-based genetic linkage map, which comprised 15 LGs consisting of 348 loci covering 978.3 cM. The two maps had 125 SSR loci in common, and most of the positions of markers were conserved between them. We identified 635 loci in carnation using the two linkage maps. We also mapped QTLs for two traits (bacterial wilt resistance and anthocyanin pigmentation in the flower) and a phenotypic locus for flower-type by analyzing previously reported genotype and phenotype data. Conclusions The improved genetic linkage maps and SSR markers developed in this study will serve as reference genetic linkage maps for members of the genus Dianthus, including carnation, and will be useful for mapping QTLs associated with various traits, and for improving carnation breeding programs.
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Affiliation(s)
- Masafumi Yagi
- NARO Institute of Floricultural Science (NIFS), 2-1 Fujimoto, Tsukuba, Ibaraki 305-8519, Japan.
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Park I, Kim J, Lee J, Kim S, Cho O, Yang K, Ahn J, Nahm S, Kim H. Development of SSR markers by next-generation sequencing of Korean landraces of chamoe (Cucumis melo var. makuwa). Mol Biol Rep 2013; 40:6855-62. [PMID: 24096890 DOI: 10.1007/s11033-013-2803-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2013] [Accepted: 09/26/2013] [Indexed: 01/25/2023]
Abstract
The oriental melon (Cucumis melo var. makuwa), called 'chamoe' in Korean, is a popular fruit crop cultivated mainly in Asia and a high-market value crop in Korea. To provide molecular breeding resources for chamoe, we developed and characterized genomic SSR markers from the preliminary Illumina read assemblies of Gotgam chamoe (one of the major landraces; KM) and SW3 (the breeding parent). Mononucleotide motifs were the most abundant type of markers, followed by di-, tri-, tetra-, and pentanucleotide motifs. The most abundant dinucleotide was AT, followed by AG and AC, and AAT was the most abundant trinucleotide motif in both assemblies. Following our SSR-marker development strategy, we designed a total of 370 primer sets. Of these, 236 primer sets were tested, exhibiting 93 % polymorphism between KM and SW3. Those polymorphic SSRs were successfully amplified in the netted and Kirkagac melons, which respectively exhibited 81 and 76 % polymorphism relative to KM, and 32 and 38 % polymorphism relative to SW3. Seven selected SSR markers with a total of 17 alleles (2-3 alleles per locus) were used to distinguish between KM, SW3, and four chamoe cultivars. Our results represent the first attempt to provide genomic resources for Korean landraces for the purposes of chamoe breeding, as well as to discover a set of SSR markers capable of discriminating chamoe varieties from Korea and the rest of Asia, which possess little genetic diversity. This study establishes a highly efficient strategy for developing SSR markers from preliminary Illumina assemblies of AT-rich genomes.
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Affiliation(s)
- Inkyu Park
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahangno, Daejeon, 305-806, Republic of Korea
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Barkley NA, Isleib TG, Wang ML, Pittman RN. Genotypic effect of ahFAD2 on fatty acid profiles in six segregating peanut (Arachis hypogaea L) populations. BMC Genet 2013; 14:62. [PMID: 23866023 PMCID: PMC3722029 DOI: 10.1186/1471-2156-14-62] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2012] [Accepted: 06/28/2013] [Indexed: 12/03/2022] Open
Abstract
Background Fatty acid composition of oil extracted from peanut (Arachis hypogaea L.) seed is an important quality trait because it may affect the flavor and shelf life of resulting food products. In particular, a high ratio of oleic (C18:1) relative to linoleic (C18:2) fatty acid (O/L ≥ 10) results in a longer shelf life. Previous reports suggest that the high oleic (~80%) trait was controlled by recessive alleles of ahFAD2A and ahFAD2B, the former of which is thought to have a high frequency in US runner- and virginia-type cultivars. Functional mutations, G448A in ahFAD2A and 442insA in ahFAD2B eliminate or knock down desaturase activity and have been demonstrated to produce peanut oil with high O/L ratios. In order to employ marker assisted selection (MAS) to select a high oleic disease resistant peanut and to evaluate genotypic and phenotypic variation, crosses were made between high oleic (~80%) and normal oleic (~50%) peanuts to produce segregating populations. Results A total of 539 F2 progenies were randomly selected to empirically determine each ahFAD2 genotype and the resulting fatty acid composition. Five of the six crosses segregated for the high oleic trait in a digenic fashion. The remaining cross was consistent with monogenic segregation because both parental genotypes were fixed for the ahFAD2A mutation. Segregation distortion was significant in ahFAD2A in one cross; however, the remaining crosses showed no distortion. Quantitative analyses revealed that dominance was incomplete for the wild type allele of ahFAD2, and both loci showed significant additive effects. Oleic and linoleic acid displayed five unique phenotypes, based on the number of ahFAD2 mutant alleles. Further, the ahFAD2 loci did exhibit pleiotropic interactions with palmitic (C16:0), oleic (C18:1), linoleic (C18:2) acids and the O/L ratio. Fatty acid levels in these progeny were affected by the parental genotype suggesting that other genes also influence fatty acid composition in peanut. As far as the authors are aware, this is the first study in which all of the nine possible ahFAD2 genotypes were quantitatively measured. Conclusions The inheritance of the high oleic trait initially was suggested to be controlled by dominant gene action from two homoeologous genes (ahFAD2A and ahFAD2B) exhibiting complete recessivity. Analyzing the ahFAD2 genotypes and fatty acid compositions of these segregating peanut populations clearly demonstrated that the fatty acid contents are quantitative in nature although much of the variability in the predominant fatty acids (oleic, linoleic, and palmitic) is controlled by only two loci.
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Affiliation(s)
- Noelle A Barkley
- USDA ARS Plant Germplasm Resources Conservation Unit, 1109 Experiment Street, Griffin, GA 30223, USA.
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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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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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Liu Z, Feng S, Pandey MK, Chen X, Culbreath AK, Varshney RK, Guo B. Identification of expressed resistance gene analogs from peanut (Arachis hypogaea L.) expressed sequence tags. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2013; 55:453-461. [PMID: 23384141 DOI: 10.1111/jipb.12037] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2012] [Accepted: 01/24/2013] [Indexed: 06/01/2023]
Abstract
Low genetic diversity makes peanut (Arachis hypogaea L.) very vulnerable to plant pathogens, causing severe yield loss and reduced seed quality. Several hundred partial genomic DNA sequences as nucleotide-binding-site leucine-rich repeat (NBS-LRR) resistance genes (R) have been identified, but a small portion with expressed transcripts has been found. We aimed to identify resistance gene analogs (RGAs) from peanut expressed sequence tags (ESTs) and to develop polymorphic markers. The protein sequences of 54 known R genes were used to identify homologs from peanut ESTs from public databases. A total of 1,053 ESTs corresponding to six different classes of known R genes were recovered, and assembled 156 contigs and 229 singletons as peanut-expressed RGAs. There were 69 that encoded for NBS-LRR proteins, 191 that encoded for protein kinases, 82 that encoded for LRR-PK/transmembrane proteins, 28 that encoded for Toxin reductases, 11 that encoded for LRR-domain containing proteins and four that encoded for TM-domain containing proteins. Twenty-eight simple sequence repeats (SSRs) were identified from 25 peanut expressed RGAs. One SSR polymorphic marker (RGA121) was identified. Two polymerase chain reaction-based markers (Ahsw-1 and Ahsw-2) developed from RGA013 were homologous to the Tomato Spotted Wilt Virus (TSWV) resistance gene. All three markers were mapped on the same linkage group AhIV. These expressed RGAs are the source for RGA-tagged marker development and identification of peanut resistance genes.
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Affiliation(s)
- Zhanji Liu
- University of Georgia, Department of Plant Pathology, Tifton, GA 31793, USA
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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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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: 136] [Impact Index Per Article: 12.4] [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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Cloutier S, Ragupathy R, Miranda E, Radovanovic N, Reimer E, Walichnowski A, Ward K, Rowland G, Duguid S, Banik M. Integrated consensus genetic and physical maps of flax (Linum usitatissimum L.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2012; 125:1783-95. [PMID: 22890805 PMCID: PMC3493668 DOI: 10.1007/s00122-012-1953-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2012] [Accepted: 07/21/2012] [Indexed: 05/06/2023]
Abstract
Three linkage maps of flax (Linum usitatissimum L.) were constructed from populations CDC Bethune/Macbeth, E1747/Viking and SP2047/UGG5-5 containing between 385 and 469 mapped markers each. The first consensus map of flax was constructed incorporating 770 markers based on 371 shared markers including 114 that were shared by all three populations and 257 shared between any two populations. The 15 linkage group map corresponds to the haploid number of chromosomes of this species. The marker order of the consensus map was largely collinear in all three individual maps but a few local inversions and marker rearrangements spanning short intervals were observed. Segregation distortion was present in all linkage groups which contained 1-52 markers displaying non-Mendelian segregation. The total length of the consensus genetic map is 1,551 cM with a mean marker density of 2.0 cM. A total of 670 markers were anchored to 204 of the 416 fingerprinted contigs of the physical map corresponding to ~274 Mb or 74 % of the estimated flax genome size of 370 Mb. This high resolution consensus map will be a resource for comparative genomics, genome organization, evolution studies and anchoring of the whole genome shotgun sequence.
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Affiliation(s)
- Sylvie Cloutier
- Cereal Research Centre, Agriculture and Agri-Food Canada, 195 Dafoe Road, Winnipeg, MB, R3T 2M9, Canada.
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Bohra A, Saxena RK, Gnanesh BN, Saxena K, Byregowda M, Rathore A, KaviKishor PB, Cook DR, Varshney RK. An intra-specific consensus genetic map of pigeonpea [Cajanus cajan (L.) Millspaugh] derived from six mapping populations. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2012; 125:1325-38. [PMID: 22772726 PMCID: PMC3442162 DOI: 10.1007/s00122-012-1916-5] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2012] [Accepted: 06/05/2012] [Indexed: 05/21/2023]
Abstract
Pigeonpea (Cajanus cajan L.) is an important food legume crop of rainfed agriculture. Owing to exposure of the crop to a number of biotic and abiotic stresses, the crop productivity has remained stagnant for almost last five decades at ca. 750 kg/ha. The availability of a cytoplasmic male sterility (CMS) system has facilitated the development and release of hybrids which are expected to enhance the productivity of pigeonpea. Recent advances in genomics and molecular breeding such as marker-assisted selection (MAS) offer the possibility to accelerate hybrid breeding. Molecular markers and genetic maps are pre-requisites for deploying MAS in breeding. However, in the case of pigeonpea, only one inter- and two intra-specific genetic maps are available so far. Here, four new intra-specific genetic maps comprising 59-140 simple sequence repeat (SSR) loci with map lengths ranging from 586.9 to 881.6 cM have been constructed. Using these four genetic maps together with two recently published intra-specific genetic maps, a consensus map was constructed, comprising of 339 SSR loci spanning a distance of 1,059 cM. Furthermore, quantitative trait loci (QTL) analysis for fertility restoration (Rf) conducted in three mapping populations identified four major QTLs explaining phenotypic variances up to 24 %. To the best of our knowledge, this is the first report on construction of a consensus genetic map in pigeonpea and on the identification of QTLs for fertility restoration. The developed consensus genetic map should serve as a reference for developing new genetic maps as well as correlating with the physical map in pigeonpea to be developed in near future. The availability of more informative markers in the bins harbouring QTLs for sterility mosaic disease (SMD) and Rf will facilitate the selection of the most suitable markers for genetic analysis and molecular breeding applications in pigeonpea.
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Affiliation(s)
- Abhishek Bohra
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, 502324 India
- Osmania University, Hyderabad, 500007 India
| | - Rachit K. Saxena
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, 502324 India
- Osmania University, Hyderabad, 500007 India
| | - B. N. Gnanesh
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, 502324 India
- University of Agricultural Sciences, Bengaluru (UAS-B), 560065 India
| | - Kulbhushan Saxena
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, 502324 India
| | - M. Byregowda
- University of Agricultural Sciences, Bengaluru (UAS-B), 560065 India
| | - Abhishek Rathore
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, 502324 India
| | | | | | - Rajeev K. Varshney
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, 502324 India
- CGIAR Generation Challenge Programme (GCP), c/o CIMMYT, 06600 Mexico DF, Mexico
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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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Gautami B, Pandey MK, Vadez V, Nigam SN, Ratnakumar P, Krishnamurthy L, Radhakrishnan T, Gowda MVC, Narasu ML, Hoisington DA, Knapp SJ, Varshney RK. Quantitative trait locus analysis and construction of consensus genetic map for drought tolerance traits based on three recombinant inbred line populations in cultivated groundnut (Arachis hypogaea L.). MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2012; 30:757-772. [PMID: 22924017 PMCID: PMC3410028 DOI: 10.1007/s11032-011-9660-0] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2011] [Accepted: 10/14/2011] [Indexed: 05/19/2023]
Abstract
Groundnut (Arachis hypogaea L.) is an important food and cash crop grown mainly in semi-arid tropics (SAT) regions of the world where drought is the major constraint on productivity. With the aim of understanding the genetic basis and identification of quantitative trait loci (QTL) for drought tolerance, two new recombinant inbred line (RIL) mapping populations, namely ICGS 76 × CSMG 84-1 (RIL-2) and ICGS 44 × ICGS 76 (RIL-3), were used. After screening of 3,215 simple sequence repeat (SSR) markers on the parental genotypes of these populations, two new genetic maps were developed with 119 (RIL-2) and 82 (RIL-3) SSR loci. Together with these maps and the reference map with 191 SSR loci based on TAG 24 × ICGV 86031 (RIL-1), a consensus map was constructed with 293 SSR loci distributed over 20 linkage groups, spanning 2,840.8 cM. As all these three populations segregate for drought-tolerance-related traits, a comprehensive QTL analysis identified 153 main effect QTL (M-QTL) and 25 epistatic QTL (E-QTL) for drought-tolerance-related traits. Localization of these QTL on the consensus map provided 16 genomic regions that contained 125 QTL. A few key genomic regions were selected on the basis of the QTL identified in each region, and their expected role in drought adaptation is also discussed. Given that no major QTL for drought adaptation were identified, novel breeding approaches such as marker-assisted recurrent selection (MARS) and genomic selection (GS) approaches are likely to be the preferred approaches for introgression of a larger number of QTL in order to breed drought-tolerant groundnut genotypes. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1007/s11032-011-9660-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- B. Gautami
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, 502 324 India
- Institute of Science and Technology, Jawaharlal Nehru Technological University Hyderabad (JNTUH), Greater Hyderabad, 500 085 India
| | - M. K. Pandey
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, 502 324 India
| | - V. Vadez
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, 502 324 India
| | - S. N. Nigam
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, 502 324 India
| | - P. Ratnakumar
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, 502 324 India
| | - L. Krishnamurthy
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, 502 324 India
| | - T. Radhakrishnan
- Directorate of Groundnut Research (DGR), Junagadh, 362 001 India
| | - M. V. C. Gowda
- University of Agricultural Sciences, Dharwad, 580 005 India
| | - M. L. Narasu
- Institute of Science and Technology, Jawaharlal Nehru Technological University Hyderabad (JNTUH), Greater Hyderabad, 500 085 India
| | - D. A. Hoisington
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, 502 324 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, 06600 Mexico, DF 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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Babaei N, Abdullah NAP, Saleh G, Abdullah TL. Isolation and characterization of microsatellite markers and analysis of genetic variability in Curculigo latifolia Dryand. Mol Biol Rep 2012; 39:9869-77. [PMID: 22752726 PMCID: PMC3459080 DOI: 10.1007/s11033-012-1853-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2012] [Accepted: 06/11/2012] [Indexed: 11/26/2022]
Abstract
Curculin, a sweet protein found in Curculigo latifolia fruit has great potential for the pharmaceutical industry. This protein interestingly has been found to have both sweet taste and taste-modifying capacities comparable with other natural sweeteners. According to our knowledge this is the first reported case on the isolation of microsatellite loci in this genus. Hence, the current development of microsatellite markers for C. latifolia will facilitate future population genetic studies and breeding programs for this valuable plant. In this study 11 microsatellite markers were developed using 3' and 5' ISSR markers. The primers were tested on 27 accessions from all states of Peninsular Malaysia. The number of alleles per locus ranged from three to seven, with allele size ranging from 141 to 306 bp. The observed and expected heterozygosity ranged between 0.00-0.65 and 0.38-0.79, respectively. The polymorphic information content ranged from 0.35 to 0.74 and the Shannon's information index ranged from 0.82 to 1.57. These developed polymorphic microsatellites were used for constructing a dendrogram by unweighted pair group method with arithmetic mean cluster analysis using the Dice's similarity coefficient. Accessions association according to their geographical origin was observed. Based on characteristics of isolated microsatellites for C. latifolia accessions all genotype can be distinguished using these 11 microsatellite markers. These polymorphic markers could also be applied to studies on uniformity determination and somaclonal variation of tissue culture plantlets, varieties identification, genetic diversity, analysis of phylogenetic relationship, genetic linkage maps and quantitative trait loci in C. latifolia.
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Affiliation(s)
- Nahid Babaei
- Department of Crop Science, Faculty of Agriculture, Universiti Putra Malaysia, 43400 Serdang, Selangor Malaysia
| | | | - Ghizan Saleh
- Department of Crop Science, Faculty of Agriculture, Universiti Putra Malaysia, 43400 Serdang, Selangor Malaysia
| | - Thohirah Lee Abdullah
- Department of Crop Science, Faculty of Agriculture, Universiti Putra Malaysia, 43400 Serdang, Selangor Malaysia
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