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Satasiya P, Patel S, Patel R, Raigar OP, Modha K, Parekh V, Joshi H, Patel V, Chaudhary A, Sharma D, Prajapati M. Meta-analysis of identified genomic regions and candidate genes underlying salinity tolerance in rice (Oryza sativa L.). Sci Rep 2024; 14:5730. [PMID: 38459066 PMCID: PMC10923909 DOI: 10.1038/s41598-024-54764-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Accepted: 02/16/2024] [Indexed: 03/10/2024] Open
Abstract
Rice output has grown globally, yet abiotic factors are still a key cause for worry. Salinity stress seems to have the more impact on crop production out of all abiotic stresses. Currently one of the most significant challenges in paddy breeding for salinity tolerance with the help of QTLs, is to determine the QTLs having the best chance of improving salinity tolerance with the least amount of background noise from the tolerant parent. Minimizing the size of the QTL confidence interval (CI) is essential in order to primarily include the genes responsible for salinity stress tolerance. By considering that, a genome-wide meta-QTL analysis on 768 QTLs from 35 rice populations published from 2001 to 2022 was conducted to identify consensus regions and the candidate genes underlying those regions responsible for the salinity tolerance, as it reduces the confidence interval (CI) to many folds from the initial QTL studies. In the present investigation, a total of 65 MQTLs were extracted with an average CI reduced from 17.35 to 1.66 cM including the smallest of 0.01 cM. Identification of the MQTLs for individual traits and then classifying the target traits into correlated morphological, physiological and biochemical aspects, resulted in more efficient interpretation of the salinity tolerance, identifying the candidate genes and to understand the salinity tolerance mechanism as a whole. The results of this study have a huge potential to improve the rice genotypes for salinity tolerance with the help of MAS and MABC.
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Affiliation(s)
- Pratik Satasiya
- Department of Genetics and Plant Breeding, N. M. College of Agriculture, Navsari Agricultural University, Navsari, Gujarat, India
| | - Sanyam Patel
- Department of Genetics and Plant Breeding, N. M. College of Agriculture, Navsari Agricultural University, Navsari, Gujarat, India
| | - Ritesh Patel
- Department of Genetics and Plant Breeding, N. M. College of Agriculture, Navsari Agricultural University, Navsari, Gujarat, India
| | - Om Prakash Raigar
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, Punjab, India
| | - Kaushal Modha
- Department of Genetics and Plant Breeding, N. M. College of Agriculture, Navsari Agricultural University, Navsari, Gujarat, India
| | - Vipul Parekh
- Department of Biotechnology, College of Forestry, Navsari Agricultural University, Navsari, Gujarat, India
| | - Haimil Joshi
- Coastal Soil Salinity Research Station Danti-Umbharat, Navsari Agricultural University, Navsari, Gujarat, India
| | - Vipul Patel
- Regional Rice Research Station, Vyara, Navsari Agricultural University, Navsari, Gujarat, India
| | - Ankit Chaudhary
- Kishorbhai Institute of Agriculture Sciences and Research Centre, Uka Tarsadia University, Bardoli, Gujarat, India.
| | - Deepak Sharma
- Department of Genetics and Plant Breeding, N. M. College of Agriculture, Navsari Agricultural University, Navsari, Gujarat, India
| | - Maulik Prajapati
- Department of Genetics and Plant Breeding, N. M. College of Agriculture, Navsari Agricultural University, Navsari, Gujarat, India
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Xu S, Fei Y, Wang Y, Zhao W, Hou L, Cao Y, Wu M, Wu H. Identification of a Seed Vigor-Related QTL Cluster Associated with Weed Competitive Ability in Direct-Seeded Rice (Oryza Sativa L.). RICE (NEW YORK, N.Y.) 2023; 16:45. [PMID: 37831291 PMCID: PMC10575835 DOI: 10.1186/s12284-023-00664-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Accepted: 09/30/2023] [Indexed: 10/14/2023]
Abstract
Direct seeding of rice (Oryza sativa L.) is a low-labor and sustainable cultivation method that is used worldwide. Seed vigor and early vigor are important traits associated with seedling stand density (SSD) and weed competitive ability (WCA), which are key factors in direct-seeded rice (DSR) cultivation systems. Here, we developed a set of chromosome segment substitution lines with Xiushui134 as receptor parent and Yangdao6 as donor parent and used these lines as a mapping population to identify quantitative trait loci (QTLs) for seed vigor, which we evaluated based on germinability-related indicators (germination percentage (GP), germination energy (GE), and germination index (GI)) and seedling vigor-related indicators (root number (RN), root length (RL), and shoot length (SL) at 14 days after imbibition) under controlled conditions in an incubator. Ten QTLs were detected across four chromosomes, of which a cluster of QTLs (qGP11, qGE11, qGI11, and qRL11) co-localized on Chr. 11 with high LOD values (12.03, 8.13, 7.14, and 8.75, respectively). Fine mapping narrowed down the QTL cluster to a 0.7-Mb interval between RM26797 and RM6680. Further analysis showed that the QTL cluster has a significant effect (p < 0.01) on early vigor under hydroponic culture (root length, total dry weight) and direct seeding conditions (tiller number, aboveground dry weight). Thus, our combined analysis revealed that the QTL cluster influenced both seed vigor and early vigor. Identifying favorable alleles at this QTL cluster could facilitate the improvement of SSD and WCA, thereby addressing both major factors in DSR cultivation systems.
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Affiliation(s)
- Shan Xu
- College of Advanced Agricultural Sciences, Zhejiang A & F University, Hangzhou, 311300, Zhejiang, China
| | - Yuexin Fei
- College of Advanced Agricultural Sciences, Zhejiang A & F University, Hangzhou, 311300, Zhejiang, China
| | - Yue Wang
- College of Advanced Agricultural Sciences, Zhejiang A & F University, Hangzhou, 311300, Zhejiang, China
| | - Wenjia Zhao
- College of Advanced Agricultural Sciences, Zhejiang A & F University, Hangzhou, 311300, Zhejiang, China
| | - Luyan Hou
- College of Advanced Agricultural Sciences, Zhejiang A & F University, Hangzhou, 311300, Zhejiang, China
| | - Yujie Cao
- College of Advanced Agricultural Sciences, Zhejiang A & F University, Hangzhou, 311300, Zhejiang, China
| | - Min Wu
- College of Advanced Agricultural Sciences, Zhejiang A & F University, Hangzhou, 311300, Zhejiang, China
| | - Hongkai Wu
- College of Advanced Agricultural Sciences, Zhejiang A & F University, Hangzhou, 311300, Zhejiang, China.
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Kaur P, Neelam K, Sarao PS, Babbar A, Kumar K, Vikal Y, Khanna R, Kaur R, Mangat GS, Singh K. Molecular mapping and transfer of a novel brown planthopper resistance gene bph42 from Oryza rufipogon (Griff.) To cultivated rice (Oryza sativa L.). Mol Biol Rep 2022; 49:8597-8606. [PMID: 35764746 DOI: 10.1007/s11033-022-07692-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 06/02/2022] [Accepted: 06/08/2022] [Indexed: 10/17/2022]
Abstract
BACKGROUND Brown planthopper (BPH), Nilaparvata lugens (Stål), is one of the most destructive pests of rice accounting for 52% of annual yield loss. The breakdown of resistance against known BPH biotypes necessitates the identification and deployment of new genes from diverse sources. The current study aimed at mapping and transfer of a novel BPH resistance gene from the wild species of rice O. rufipogon accession CR100441 to the elite rice cultivar against BPH biotype 4. METHODS AND RESULTS The phenotypic screening against BPH biotype 4 was conducted using the standard seedbox screening technique (SSST). Inheritance study using damage score caused by BPH infestation at the seedling stage indicated the presence of a single major recessive gene with the segregation ratio of susceptible to resistant plants in 3:1 (210:66, χ2c = 0.17 ≤ χ20.05,1 = 3.84). The genotyping of the mapping population was done using polymorphic microsatellite markers between PR122 and O.rufipogon acc.CR100441 spanning all the 12 chromosomes of rice. A total of 537 SSR markers were used to map a BPH resistance gene (designated as bph42) on the short arm of chromosome 4 between RM16282 and RM6659. QTL analysis identified a peak marker RM16335 contributing 29% of the phenotypic variance at 40.76 LOD. CONCLUSIONS The identified marker co-segregates with the bph42 and hence could be efficiently used for marker-assisted selection (MAS) for the transfer of resistance into elite rice cultivars. The introgression lines with higher yield and BPH resistance were identified and are under advanced yield trails for further varietal release.
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Affiliation(s)
- Pavneet Kaur
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, Punjab, India
| | - Kumari Neelam
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, Punjab, India.
| | - Preetinder Singh Sarao
- Department of Genetics and Plant Breeding, Punjab Agricultural University, Ludhiana, Punjab, India
| | - Ankita Babbar
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, Punjab, India
| | - Kishor Kumar
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, Punjab, India
- Integrated Rural Development and Management Faculty Centre, Ramakrishna Mission Vivekananda Educational and Research Institute, 700103, Narendrapur, Kolkata, India
| | - Yogesh Vikal
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, Punjab, India
| | - Renu Khanna
- Department of Genetics and Plant Breeding, Punjab Agricultural University, Ludhiana, Punjab, India
| | - Rupinder Kaur
- Department of Genetics and Plant Breeding, Punjab Agricultural University, Ludhiana, Punjab, India
| | - Gurjeet Singh Mangat
- Department of Genetics and Plant Breeding, Punjab Agricultural University, Ludhiana, Punjab, India
| | - Kuldeep Singh
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, Punjab, India
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Kaur G, Yadav IS, Bhatia D, Vikal Y, Neelam K, Dhillon NK, Praba UP, Mangat GS, Singh K. BSA-seq Identifies a Major Locus on Chromosome 6 for Root-Knot Nematode (Meloidogyne graminicola) Resistance From Oryza glaberrima. Front Genet 2022; 13:871833. [PMID: 35774507 PMCID: PMC9237506 DOI: 10.3389/fgene.2022.871833] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Accepted: 05/02/2022] [Indexed: 11/13/2022] Open
Abstract
Root-knot nematode (Meloidogyne graminicola) is one of the emerging threats to rice production worldwide that causes substantial yield reductions. There is a progressive shift of the cropping system from traditional transplanting to direct-seeded water-saving rice production that favored the development of M. graminicola. Scouting and deploying new resistance genes is an economical approach to managing the root-knot nematodes. Here, we report that the inheritance of root-knot nematode resistance in Oryza glaberrima acc. IRGC102206 is governed by a single dominant gene. Traditional mapping coupled with BSA-seq is used to map nematode resistance gene(s) using the BC1F1 population derived from a cross of O. sativa cv. PR121 (S) and O. glaberrima acc. IRGC102206 (R). One major novel genomic region spanning a 3.0-Mb interval on chromosome 6 and two minor QTLs on chromosomes 2 and 4 are the potential genomic regions associated with rice root-knot nematode resistance. Within the QTL regions, 19 putative candidate genes contain 81 non-synonymous variants. The detected major candidate region could be fine mapped to accelerate marker-assisted breeding for root-knot nematode resistance in rice.
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Affiliation(s)
- Gurwinder Kaur
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, India
| | - Inderjit Singh Yadav
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, India
| | - Dharminder Bhatia
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, India
| | - Yogesh Vikal
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, India
- *Correspondence: Yogesh Vikal,
| | - Kumari Neelam
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, India
| | | | - Umesh Preethi Praba
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, India
| | - Gurjit Singh Mangat
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, India
| | - Kuldeep Singh
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, India
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
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Zhang Y, Zhou J, Xu P, Li J, Deng X, Deng W, Yang Y, Yu Y, Pu Q, Tao D. A Genetic Resource for Rice Improvement: Introgression Library of Agronomic Traits for All AA Genome Oryza Species. FRONTIERS IN PLANT SCIENCE 2022; 13:856514. [PMID: 35401612 PMCID: PMC8992386 DOI: 10.3389/fpls.2022.856514] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Accepted: 02/07/2022] [Indexed: 05/20/2023]
Abstract
Rice improvement depends on the availability of genetic variation, and AA genome Oryza species are the natural reservoir of favorable alleles that are useful for rice breeding. To systematically evaluate and utilize potentially valuable traits of new QTLs or genes for the Asian cultivated rice improvement from all AA genome Oryza species, 6,372 agronomic trait introgression lines (ILs) from BC2 to BC6 were screened and raised based on the variations in agronomic traits by crossing 170 accessions of 7 AA genome species and 160 upland rice accessions of O. sativa as the donor parents, with three elite cultivars of O. sativa, Dianjingyou 1 (a japonica variety), Yundao 1 (a japonica variety), and RD23 (an indica variety) as the recurrent parents, respectively. The agronomic traits, such as spreading panicle, erect panicle, dense panicle, lax panicle, awn, prostrate growth, plant height, pericarp color, kernel color, glabrous hull, grain size, 1,000-grain weight, drought resistance and aerobic adaption, and blast resistance, were derived from more than one species. Further, 1,401 agronomic trait ILs in the Dianjingyou 1 background were genotyped using 168 SSR markers distributed on the whole genome. A total of twenty-two novel allelic variations were identified to be highly related to the traits of grain length (GL) and grain width (GW), respectively. In addition, allelic variations for the same locus were detected from the different donor species, which suggest that these QTLs or genes were conserved and the different haplotypes of a QTL (gene) were valuable resources for broadening the genetic basis in Asian cultivated rice. Thus, this agronomic trait introgression library from multiple species and accessions provided a powerful resource for future rice improvement and genetic dissection of agronomic traits.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Dayun Tao
- Yunnan Key Laboratory for Rice Genetic Improvement, Food Crops Research Institute, Yunnan Academy of Agricultural Sciences, Kunming, China
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Guo N, Wang Y, Chen W, Tang S, An R, Wei X, Hu S, Tang S, Shao G, Jiao G, Xie L, Wang L, Sheng Z, Hu P. Fine mapping and target gene identification of qSE4, a QTL for stigma exsertion rate in rice ( Oryza sativa L.). FRONTIERS IN PLANT SCIENCE 2022; 13:959859. [PMID: 35923872 PMCID: PMC9341389 DOI: 10.3389/fpls.2022.959859] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Accepted: 06/27/2022] [Indexed: 05/11/2023]
Abstract
The stigma exsertion rate (SER) is a complex agronomy phenotype controlled by multiple genes and climate and a key trait affecting the efficiency of hybrid rice seed production. Using a japonica two-line male sterile line (DaS) with a high SER as the donor and a tropical japonica rice (D50) with a low SER as the acceptor to construct a near-isogenic line [NIL (qSE4 DaS)]. Populations were segregated into 2,143 individuals of BC3F2 and BC4F2, and the stigma exsertion quantitative trait locus (QTL) qSE4 was determined to be located within 410.4 Kb between markers RM17157 and RM17227 on chromosome 4. Bioinformatic analysis revealed 13 candidate genes in this region. Sequencing and haplotype analysis indicated that the promoter region of LOC_Os04g43910 (ARF10) had a one-base substitution between the two parents. Further Reverse Transcription-Polymerase Chain Reaction (RT-PCR) analysis showed that the expression level of ARF10 in DaS was significantly higher than in D50. After knocking out ARF10 in the DaS background, it was found that the SER of arf10 (the total SER of the arf10-1 and the arf10-2 were 62.54 and 66.68%, respectively) was significantly lower than that of the wild type (the total SER was 80.97%). Transcriptome and hormone assay analysis showed that arf10 had significantly higher auxin synthesis genes and contents than the wild type and the expression of auxin signaling-related genes was significantly different, Similar results were observed for abscisic acid and jasmonic acid. These results indicate that LOC_Os04g43910 is mostly likely the target gene of qSE4, and the study of its gene function is of great significance for understanding the molecular mechanisms of SER and improving the efficiency of hybrid seed production.
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Affiliation(s)
- Naihui Guo
- State Key Laboratory of Rice Biology, Key Laboratory of Rice Biology and Breeding, Ministry of Agriculture, China National Rice Improvement Centre, China National Rice Research Institute, Hangzhou, China
- Rice Research Institute, Shengyang Agricultural University, Shenyang, China
| | - Yakun Wang
- State Key Laboratory of Rice Biology, Key Laboratory of Rice Biology and Breeding, Ministry of Agriculture, China National Rice Improvement Centre, China National Rice Research Institute, Hangzhou, China
| | - Wei Chen
- State Key Laboratory of Rice Biology, Key Laboratory of Rice Biology and Breeding, Ministry of Agriculture, China National Rice Improvement Centre, China National Rice Research Institute, Hangzhou, China
| | - Shengjia Tang
- State Key Laboratory of Rice Biology, Key Laboratory of Rice Biology and Breeding, Ministry of Agriculture, China National Rice Improvement Centre, China National Rice Research Institute, Hangzhou, China
| | - Ruihu An
- State Key Laboratory of Rice Biology, Key Laboratory of Rice Biology and Breeding, Ministry of Agriculture, China National Rice Improvement Centre, China National Rice Research Institute, Hangzhou, China
| | - Xiangjin Wei
- State Key Laboratory of Rice Biology, Key Laboratory of Rice Biology and Breeding, Ministry of Agriculture, China National Rice Improvement Centre, China National Rice Research Institute, Hangzhou, China
| | - Shikai Hu
- State Key Laboratory of Rice Biology, Key Laboratory of Rice Biology and Breeding, Ministry of Agriculture, China National Rice Improvement Centre, China National Rice Research Institute, Hangzhou, China
| | - Shaoqing Tang
- State Key Laboratory of Rice Biology, Key Laboratory of Rice Biology and Breeding, Ministry of Agriculture, China National Rice Improvement Centre, China National Rice Research Institute, Hangzhou, China
| | - Gaoneng Shao
- State Key Laboratory of Rice Biology, Key Laboratory of Rice Biology and Breeding, Ministry of Agriculture, China National Rice Improvement Centre, China National Rice Research Institute, Hangzhou, China
| | - Guiai Jiao
- State Key Laboratory of Rice Biology, Key Laboratory of Rice Biology and Breeding, Ministry of Agriculture, China National Rice Improvement Centre, China National Rice Research Institute, Hangzhou, China
| | - Lihong Xie
- State Key Laboratory of Rice Biology, Key Laboratory of Rice Biology and Breeding, Ministry of Agriculture, China National Rice Improvement Centre, China National Rice Research Institute, Hangzhou, China
| | - Ling Wang
- State Key Laboratory of Rice Biology, Key Laboratory of Rice Biology and Breeding, Ministry of Agriculture, China National Rice Improvement Centre, China National Rice Research Institute, Hangzhou, China
| | - Zhonghua Sheng
- State Key Laboratory of Rice Biology, Key Laboratory of Rice Biology and Breeding, Ministry of Agriculture, China National Rice Improvement Centre, China National Rice Research Institute, Hangzhou, China
- Zhonghua Sheng,
| | - Peisong Hu
- State Key Laboratory of Rice Biology, Key Laboratory of Rice Biology and Breeding, Ministry of Agriculture, China National Rice Improvement Centre, China National Rice Research Institute, Hangzhou, China
- Rice Research Institute, Shengyang Agricultural University, Shenyang, China
- *Correspondence: Peisong Hu,
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Sandhu N, Pruthi G, Prakash Raigar O, Singh MP, Phagna K, Kumar A, Sethi M, Singh J, Ade PA, Saini DK. Meta-QTL Analysis in Rice and Cross-Genome Talk of the Genomic Regions Controlling Nitrogen Use Efficiency in Cereal Crops Revealing Phylogenetic Relationship. Front Genet 2021; 12:807210. [PMID: 34992638 PMCID: PMC8724540 DOI: 10.3389/fgene.2021.807210] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Accepted: 11/30/2021] [Indexed: 11/13/2022] Open
Abstract
The phenomenal increase in the use of nitrogenous fertilizers coupled with poor nitrogen use efficiency is among the most important threats to the environment, economic, and social health. During the last 2 decades, a number of genomic regions associated with nitrogen use efficiency (NUE) and related traits have been reported by different research groups, but none of the stable and major effect QTL have been utilized in the marker-assisted introgression/pyramiding program. Compiling the data available in the literature could be very useful in identifying stable and major effect genomic regions associated with the root and NUE-related trait improving the rice grain yield. In the present study, we performed meta-QTL analysis on 1,330 QTL from 29 studies published in the past 2 decades. A total of 76 MQTL with a stable effect over different genetic backgrounds and environments were identified. The significant reduction in the confidence interval of the MQTL compared to the initial QTL resulted in the identification of annotated and putative candidate genes related to the traits considered in the present study. A hot spot region associated with correlated traits on chr 1, 4, and 8 and candidate genes associated with nitrate transporters, nitrogen content, and ammonium uptake on chromosomes 2, 4, 6, and 8 have been identified. The identified MQTL, putative candidate genes, and their orthologues were validated on our previous studies conducted on rice and wheat. The research-based interventions such as improving nitrogen use efficiency via identification of major genomic regions and candidate genes can be a plausible, simple, and low-cost solution to address the challenges of the crop improvement program.
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Affiliation(s)
| | | | | | | | - Kanika Phagna
- Indian Institute of Science Education and Research, Berhampur, India
| | - Aman Kumar
- Punjab Agricultural University, Ludhiana, India
| | - Mehak Sethi
- Punjab Agricultural University, Ludhiana, India
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8
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Utilization of genetic diversity and population structure to reveal prospective drought-tolerant donors in rice. GENE REPORTS 2021. [DOI: 10.1016/j.genrep.2021.101151] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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9
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Hechanova SL, Bhattarai K, Simon EV, Clave G, Karunarathne P, Ahn EK, Li CP, Lee JS, Kohli A, Hamilton NRS, Hernandez JE, Gregorio GB, Jena KK, An G, Kim SR. Development of a genome-wide InDel marker set for allele discrimination between rice (Oryza sativa) and the other seven AA-genome Oryza species. Sci Rep 2021; 11:8962. [PMID: 33903715 PMCID: PMC8076200 DOI: 10.1038/s41598-021-88533-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2020] [Accepted: 04/09/2021] [Indexed: 02/02/2023] Open
Abstract
Wild relatives of rice in the genus Oryza (composed of 24 species with 11 different genome types) have been significantly contributing to the varietal improvement of rice (Oryza sativa). More than 4000 accessions of wild rice species are available and they are regarded as a "genetic reservoir" for further rice improvement. DNA markers are essential tools in genetic analysis and breeding. To date, genome-wide marker sets for wild rice species have not been well established and this is one of the major difficulties for the efficient use of wild germplasm. Here, we developed 541 genome-wide InDel markers for the discrimination of alleles between the cultivated species O. sativa and the other seven AA-genome species by positional multiple sequence alignments among five AA-genome species with four rice varieties. The newly developed markers were tested by PCR-agarose gel analysis of 24 accessions from eight AA genome species (three accessions per species) along with two representative cultivars (O. sativa subsp. indica cv. IR24 and subsp. japonica cv. Nipponbare). Marker polymorphism was validated for 475 markers. The number of polymorphic markers between IR24 and each species (three accessions) ranged from 338 (versus O. rufipogon) to 416 (versus O. longistaminata) and the values in comparison with Nipponbare ranged from 179 (versus O. glaberrima) to 323 (versus O. glumaepatula). These marker sets will be useful for genetic studies and use of the AA-genome wild rice species.
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Affiliation(s)
- Sherry Lou Hechanova
- Gene Identification and Validation Group, Genetic Design and Validation Unit, International Rice Research Institute (IRRI), 4031, Los Baños, Laguna, Philippines
| | - Kamal Bhattarai
- Gene Identification and Validation Group, Genetic Design and Validation Unit, International Rice Research Institute (IRRI), 4031, Los Baños, Laguna, Philippines
- Institute of Crop Science (ICropS), College of Agriculture and Food Science, University of the Philippines Los Baños (UPLB), 4031, Los Baños, Laguna, Philippines
| | - Eliza Vie Simon
- Gene Identification and Validation Group, Genetic Design and Validation Unit, International Rice Research Institute (IRRI), 4031, Los Baños, Laguna, Philippines
- Institute of Crop Science (ICropS), College of Agriculture and Food Science, University of the Philippines Los Baños (UPLB), 4031, Los Baños, Laguna, Philippines
| | - Graciana Clave
- Gene Identification and Validation Group, Genetic Design and Validation Unit, International Rice Research Institute (IRRI), 4031, Los Baños, Laguna, Philippines
| | - Pathmasiri Karunarathne
- Gene Identification and Validation Group, Genetic Design and Validation Unit, International Rice Research Institute (IRRI), 4031, Los Baños, Laguna, Philippines
- Institute of Crop Science (ICropS), College of Agriculture and Food Science, University of the Philippines Los Baños (UPLB), 4031, Los Baños, Laguna, Philippines
| | - Eok-Keun Ahn
- National Institute of Crop Science, Rural Development Administration (RDA), Suwon, 16429, Republic of Korea
| | - Charng-Pei Li
- Taiwan Agricultural Research Institute (TARI), Council of Agriculture, Taichung City, Taiwan
| | - Jeom-Sig Lee
- National Institute of Crop Science, Rural Development Administration (RDA), Suwon, 16429, Republic of Korea
| | - Ajay Kohli
- Gene Identification and Validation Group, Genetic Design and Validation Unit, International Rice Research Institute (IRRI), 4031, Los Baños, Laguna, Philippines
| | - N Ruaraidh Sackville Hamilton
- Gene Identification and Validation Group, Genetic Design and Validation Unit, International Rice Research Institute (IRRI), 4031, Los Baños, Laguna, Philippines
| | - Jose E Hernandez
- Institute of Crop Science (ICropS), College of Agriculture and Food Science, University of the Philippines Los Baños (UPLB), 4031, Los Baños, Laguna, Philippines
| | - Glenn B Gregorio
- Institute of Crop Science (ICropS), College of Agriculture and Food Science, University of the Philippines Los Baños (UPLB), 4031, Los Baños, Laguna, Philippines
| | - Kshirod K Jena
- Gene Identification and Validation Group, Genetic Design and Validation Unit, International Rice Research Institute (IRRI), 4031, Los Baños, Laguna, Philippines
- School of Biotechnology, KIIT Deemed University, Bhubaneswar, Odisha, India
| | - Gynheung An
- Crop Biotech Institute and Graduate School of Biotechnology, Kyung Hee University, Yongin, Republic of Korea
| | - Sung-Ryul Kim
- Gene Identification and Validation Group, Genetic Design and Validation Unit, International Rice Research Institute (IRRI), 4031, Los Baños, Laguna, Philippines.
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Singh N, Wang DR, Ali L, Kim H, Akther KM, Harrington SE, Kang JW, Shakiba E, Shi Y, DeClerck G, Meadows B, Govindaraj V, Ahn SN, Eizenga GC, McCouch SR. A Coordinated Suite of Wild-Introgression Lines in Indica and Japonica Elite Backgrounds. FRONTIERS IN PLANT SCIENCE 2020; 11:564824. [PMID: 33281840 PMCID: PMC7688981 DOI: 10.3389/fpls.2020.564824] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Accepted: 10/12/2020] [Indexed: 05/27/2023]
Abstract
Rice, Oryza sativa L., is a cultivated, inbreeding species that serves as the staple food for the largest number of people on earth. It has two strongly diverged varietal groups, Indica and Japonica, which result from a combination of natural and human selection. The genetic divergence of these groups reflects the underlying population structure of their wild ancestors, and suggests that a pre-breeding strategy designed to take advantage of existing genetic, geographic and ecological substructure may provide a rational approach to the utilization of crop wild ancestors in plant improvement. Here we describe the coordinated development of six introgression libraries (n = 63 to 81 lines per library) in both Indica (cv. IR64) and Japonica (cv. Cybonnet) backgrounds using three bio-geographically diverse wild donors representing the Oryza rufipogon Species Complex from China, Laos and Indonesia. The final libraries were genotyped using an Infinium 7K rice SNP array (C7AIR) and analyzed under greenhouse conditions for several simply inherited (Mendelian) traits. These six interspecific populations can be used as individual Chromosome Segment Substitution Line libraries and, when considered together, serve as a powerful genetic resource for systematic genetic dissection of agronomic, physiological and developmental traits in rice.
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Affiliation(s)
- Namrata Singh
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, United States
| | - Diane R. Wang
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, United States
| | - Liakat Ali
- Rice Research and Extension Center, University of Arkansas, Stuttgart, AR, United States
| | - HyunJung Kim
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, United States
| | - Kazi M. Akther
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, United States
| | - Sandra E. Harrington
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, United States
| | - Ju-Won Kang
- Department of Agronomy, Chungnam National University, Daejeon, South Korea
| | - Ehsan Shakiba
- Rice Research and Extension Center, University of Arkansas, Stuttgart, AR, United States
| | - Yuxin Shi
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, United States
| | - Genevieve DeClerck
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, United States
| | - Byron Meadows
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, United States
| | - Vishnu Govindaraj
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, United States
| | - Sang-Nag Ahn
- Department of Agronomy, Chungnam National University, Daejeon, South Korea
| | - Georgia C. Eizenga
- USDA-ARS Dale Bumpers National Rice Research Center, Stuttgart, AR, United States
| | - Susan R. McCouch
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, United States
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Arbelaez JD, Dwiyanti MS, Tandayu E, Llantada K, Jarana A, Ignacio JC, Platten JD, Cobb J, Rutkoski JE, Thomson MJ, Kretzschmar T. 1k-RiCA (1K-Rice Custom Amplicon) a novel genotyping amplicon-based SNP assay for genetics and breeding applications in rice. RICE (NEW YORK, N.Y.) 2019; 12:55. [PMID: 31350673 PMCID: PMC6660535 DOI: 10.1186/s12284-019-0311-0] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Accepted: 07/02/2019] [Indexed: 05/04/2023]
Abstract
BACKGROUND While a multitude of genotyping platforms have been developed for rice, the majority of them have not been optimized for breeding where cost, turnaround time, throughput and ease of use, relative to density and informativeness are critical parameters of their utility. With that in mind we report the development of the 1K-Rice Custom Amplicon, or 1k-RiCA, a robust custom sequencing-based amplicon panel of ~ 1000-SNPs that are uniformly distributed across the rice genome, designed to be highly informative within indica rice breeding pools, and tailored for genomic prediction in elite indica rice breeding programs. RESULTS Empirical validation tests performed on the 1k-RiCA showed average marker call rates of 95% with marker repeatability and concordance rates of 99%. These technical properties were not affected when two common DNA extraction protocols were used. The average distance between SNPs in the 1k-RiCA was 1.5 cM, similar to the theoretical distance which would be expected between 1,000 uniformly distributed markers across the rice genome. The average minor allele frequencies on a panel of indica lines was 0.36 and polymorphic SNPs estimated on pairwise comparisons between indica by indica accessions and indica by japonica accessions were on average 430 and 450 respectively. The specific design parameters of the 1k-RiCA allow for a detailed view of genetic relationships and unambiguous molecular IDs within indica accessions and good cost vs. marker-density balance for genomic prediction applications in elite indica germplasm. Predictive abilities of Genomic Selection models for flowering time, grain yield, and plant height were on average 0.71, 0.36, and 0.65 respectively based on cross-validation analysis. Furthermore the inclusion of important trait markers associated with 11 different genes and QTL adds value to parental selection in crossing schemes and marker-assisted selection in forward breeding applications. CONCLUSIONS This study validated the marker quality and robustness of the 1k-RiCA genotypic platform for genotyping populations derived from indica rice subpopulation for genetic and breeding purposes including MAS and genomic selection. The 1k-RiCA has proven to be an alternative cost-effective genotyping system for breeding applications.
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Affiliation(s)
- Juan David Arbelaez
- International Rice Research Institute, DAPO Box 7777, 1301 Los Baños, Metro Manila Philippines
| | | | - Erwin Tandayu
- International Rice Research Institute, DAPO Box 7777, 1301 Los Baños, Metro Manila Philippines
| | - Krizzel Llantada
- International Rice Research Institute, DAPO Box 7777, 1301 Los Baños, Metro Manila Philippines
| | - Annalhea Jarana
- International Rice Research Institute, DAPO Box 7777, 1301 Los Baños, Metro Manila Philippines
| | - John Carlos Ignacio
- International Rice Research Institute, DAPO Box 7777, 1301 Los Baños, Metro Manila Philippines
| | - John Damien Platten
- International Rice Research Institute, DAPO Box 7777, 1301 Los Baños, Metro Manila Philippines
| | - Joshua Cobb
- International Rice Research Institute, DAPO Box 7777, 1301 Los Baños, Metro Manila Philippines
| | - Jessica Elaine Rutkoski
- International Rice Research Institute, DAPO Box 7777, 1301 Los Baños, Metro Manila Philippines
| | - Michael J. Thomson
- Department of Soil and Crop Sciences, Texas A&M University, College Station, Houston, TX 77843 USA
| | - Tobias Kretzschmar
- Southern Cross Plant Sciences, Southern Cross University, PO Box 157, Lismore, NSW 2480 Australia
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Balakrishnan D, Surapaneni M, Mesapogu S, Neelamraju S. Development and use of chromosome segment substitution lines as a genetic resource for crop improvement. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2019; 132:1-25. [PMID: 30483819 DOI: 10.1007/s00122-018-3219-y] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Accepted: 10/24/2018] [Indexed: 05/27/2023]
Abstract
CSSLs are a complete library of introgression lines with chromosomal segments of usually a distant genotype in an adapted background and are valuable genetic resources for basic and applied research on improvement of complex traits. Chromosome segment substitution lines (CSSLs) are genetic stocks representing the complete genome of any genotype in the background of a cultivar as overlapping segments. Ideally, each CSSL has a single chromosome segment from the donor with a maximum recurrent parent genome recovered in the background. CSSL development program requires population-wide backcross breeding and genome-wide marker-assisted selection followed by selfing. Each line in a CSSL library has a specific marker-defined large donor segment. CSSLs are evaluated for any target phenotype to identify lines significantly different from the parental line. These CSSLs are then used to map quantitative trait loci (QTLs) or causal genes. CSSLs are valuable prebreeding tools for broadening the genetic base of existing cultivars and harnessing the genetic diversity from the wild- and distant-related species. These are resources for genetic map construction, mapping QTLs, genes or gene interactions and their functional analysis for crop improvement. In the last two decades, the utility of CSSLs in identification of novel genomic regions and QTL hot spots influencing a wide range of traits has been well demonstrated in food and commercial crops. This review presents an overview of how CSSLs are developed, their status in major crops and their use in genomic studies and gene discovery.
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Affiliation(s)
- Divya Balakrishnan
- ICAR- National Professor Project, ICAR- Indian Institute of Rice Research, Hyderabad, India
| | - Malathi Surapaneni
- ICAR- National Professor Project, ICAR- Indian Institute of Rice Research, Hyderabad, India
| | - Sukumar Mesapogu
- ICAR- National Professor Project, ICAR- Indian Institute of Rice Research, Hyderabad, India
| | - Sarla Neelamraju
- ICAR- National Professor Project, ICAR- Indian Institute of Rice Research, Hyderabad, India.
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13
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Wu J, Zhao Q, Zhang L, Li S, Ma Y, Pan L, Lin H, Wu G, Yuan H, Yu Y, Wang X, Yang X, Li Z, Jiang T, Sun D. QTL Mapping of Fiber-Related Traits Based on a High-Density Genetic Map in Flax ( Linum usitatissimum L.). FRONTIERS IN PLANT SCIENCE 2018; 9:885. [PMID: 30065730 PMCID: PMC6056681 DOI: 10.3389/fpls.2018.00885] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Accepted: 06/07/2018] [Indexed: 05/18/2023]
Abstract
UNLABELLED A genetic map is an important and valuable tool for quantitative trait locus (QTL) mapping, marker-assisted selection (MAS)-based breeding, and reference-assisted chromosome assembly. In this study, 112 F2 plants from a cross between Linum usitatissimum L. "DIANE" and "NY17" and parent plants were subjected to high-throughput sequencing and specific-locus amplified fragment (SLAF) library construction. After preprocessing, 61.64 Gb of raw data containing 253.71 Mb paired-end reads, each 101 bp in length, were obtained. A total of 192,797 SLAFs were identified, of which 23,115 were polymorphic, with a polymorphism rate of 11.99%. Finally, 2,339 SLAFs were organized into a linkage map consisting of 15 linkage groups (LGs). The total length of the genetic map was 1483.25 centimorgans (cM) and the average distance between adjacent markers was 0.63 cM. Combined with flax chromosome-scale pseudomolecules, 12 QTLs associating with 6 flax fiber-related traits were mapped on the chromosomal scaffolds. This high-density genetic map of flax should serve as a foundation for flax fine QTL mapping, draft genome assembly, and MAS-guided breeding. Ultimately, the genomic regions identified in this research could potentially be valuable for improving flax fiber cultivars, as well as for identification of candidate genes involved in flax fiber formation processes. SIGNIFICANCE STATEMENT A high-density genetic map of flax was constructed, and QTLs were identified on the sequence scaffolds to be interrelated with fiber-related traits. The results of this study will not only provide a platform for gene/QTL fine mapping, map-based gene isolation, and molecular breeding for flax, but also provide a reference to help position sequence scaffolds on the physical map and assist in the process of assembling the flax genome sequence.
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Affiliation(s)
- Jianzhong Wu
- Institute of Forage and Grassland Sciences, Heilongjiang Academy of Agricultural Sciences, Harbin, China
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Qian Zhao
- Heilongjiang Academy of Agricultural Sciences, Harbin, China
| | - Liyan Zhang
- Heilongjiang Academy of Agricultural Sciences, Harbin, China
| | - Suiyan Li
- Institute of Forage and Grassland Sciences, Heilongjiang Academy of Agricultural Sciences, Harbin, China
| | - Yanhua Ma
- Institute of Forage and Grassland Sciences, Heilongjiang Academy of Agricultural Sciences, Harbin, China
| | - Liyan Pan
- Institute of Forage and Grassland Sciences, Heilongjiang Academy of Agricultural Sciences, Harbin, China
| | - Hong Lin
- Institute of Forage and Grassland Sciences, Heilongjiang Academy of Agricultural Sciences, Harbin, China
| | - Guangwen Wu
- Heilongjiang Academy of Agricultural Sciences, Harbin, China
| | - Hongmei Yuan
- Heilongjiang Academy of Agricultural Sciences, Harbin, China
| | - Ying Yu
- Heilongjiang Academy of Agricultural Sciences, Harbin, China
| | - Xun Wang
- Heilongjiang Academy of Agricultural Sciences, Harbin, China
| | - Xue Yang
- Heilongjiang Academy of Agricultural Sciences, Harbin, China
| | - Zhugang Li
- Heilongjiang Academy of Agricultural Sciences, Harbin, China
- *Correspondence: Zhugang Li
| | - Tingbo Jiang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
- Tingbo Jiang
| | - Dequan Sun
- Institute of Forage and Grassland Sciences, Heilongjiang Academy of Agricultural Sciences, Harbin, China
- Dequan Sun
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Chen G, Zhang W, Fang J, Dong L. Identification of massive molecular markers in Echinochloa phyllopogon using a restriction-site associated DNA approach. PLANT DIVERSITY 2017; 39:287-293. [PMID: 30159521 PMCID: PMC6112297 DOI: 10.1016/j.pld.2017.08.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/22/2017] [Revised: 08/23/2017] [Accepted: 08/28/2017] [Indexed: 06/08/2023]
Abstract
Echinochloa phyllopogon proliferation seriously threatens rice production worldwide. We combined a restriction-site associated DNA (RAD) approach with Illumina DNA sequencing for rapid and mass discovery of simple sequence repeat (SSR) and single nucleotide polymorphism (SNP) markers for E. phyllopogon. RAD tags were generated from the genomic DNA of two E. phyllopogon plants, and sequenced to produce 5197.7 Mb and 5242.9 Mb high quality sequences, respectively. The GC content of E. phyllopogon was 45.8%, which is high for monocots. In total, 4710 putative SSRs were identified in 4132 contigs, which permitted the design of PCR primers for E. phyllopogon. Most repeat motifs among the SSRs identified were dinucleotide (>82%), and most of these SSRs were four motif-repeats (>75%). The most frequent motif was AT, accounting for 36.3%-37.2%, followed by AG and AC. In total, 78 putative polymorphic SSR loci were found. A total of 49,179 SNPs were discovered between the two samples of E. phyllopogon, 67.1% of which were transversions and 32.9% were transitions. We used eight SSRs to study the genetic diversity of four E. phyllopogon populations collected from rice fields in China and all eight loci tested were polymorphic.
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Affiliation(s)
- Guoqi Chen
- College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
- Key Laboratory of Integrated Pest Management on Crops in East China (Nanjing Agricultural University), Ministry of Agriculture, Nanjing 210095, China
| | - Wei Zhang
- College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
- Key Laboratory of Integrated Pest Management on Crops in East China (Nanjing Agricultural University), Ministry of Agriculture, Nanjing 210095, China
| | - Jiapeng Fang
- College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
- Key Laboratory of Integrated Pest Management on Crops in East China (Nanjing Agricultural University), Ministry of Agriculture, Nanjing 210095, China
| | - Liyao Dong
- College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
- Key Laboratory of Integrated Pest Management on Crops in East China (Nanjing Agricultural University), Ministry of Agriculture, Nanjing 210095, China
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15
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Genetic characterization and population structure of Indian rice cultivars and wild genotypes using core set markers. 3 Biotech 2016; 6:95. [PMID: 28330165 PMCID: PMC4808523 DOI: 10.1007/s13205-016-0409-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2015] [Accepted: 03/01/2016] [Indexed: 11/12/2022] Open
Abstract
Genetic diversity among 23 rice genotypes including wild species and cultivars of indica, japonica, aus and aromatic type was investigated using 165 genomewide core set microsatellite (SSR) markers. This genotypic characterization was undertaken to know the genetic similarity among the parental lines to be used in developing a set of chromosome segment substitution lines. In all, 253 alleles were identified using 77 polymorphic SSRs, and polymorphism information content ranged from 0.31 to 0.97 with a mean of 0.79. Cluster analysis grouped the genotypes into three clusters at a genetic similarity of 0.26–0.75. Wild accessions grouped together in cluster-I, indica cultivars formed cluster-II, and aromatic, japonica and aus types came under cluster-III. Principal component analysis also showed similar results. The genotypic data was analyzed using STRUCTURE, and genotypes were grouped into four populations. RM1018 on chromosome 4, RM8009 on chromosome 7, and RM273 on chromosome 12 amplified alleles specific to wild accessions. The information obtained from core set markers would help in selecting diverse parents including wild accessions and for tracking alleles in mapping or breeding populations.
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16
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Balakrishnan D, Subrahmanyam D, Badri J, Raju AK, Rao YV, Beerelli K, Mesapogu S, Surapaneni M, Ponnuswamy R, Padmavathi G, Babu VR, Neelamraju S. Genotype × Environment Interactions of Yield Traits in Backcross Introgression Lines Derived from Oryza sativa cv. Swarna/ Oryza nivara. FRONTIERS IN PLANT SCIENCE 2016; 7:1530. [PMID: 27807437 PMCID: PMC5070172 DOI: 10.3389/fpls.2016.01530] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2016] [Accepted: 09/29/2016] [Indexed: 05/17/2023]
Abstract
Advanced backcross introgression lines (BILs) developed from crosses of Oryza sativa var. Swarna/O. nivara accessions were grown and evaluated for yield and related traits. Trials were conducted for consecutive three seasons in field conditions in a randomized complete block design with three replications. Data on yield traits under irrigated conditions were analyzed using the Additive Main Effect and Multiplicative Interaction (AMMI), Genotype and Genotype × Environment Interaction (GGE) and modified rank-sum statistic (YSi) for yield stability. BILs viz., G3 (14S) and G6 (166S) showed yield stability across the seasons along with high mean yield performance. G3 is early in flowering with high yield and has good grain quality and medium height, hence could be recommended for most of the irrigated locations. G6 is a late duration genotype, with strong culm strength, high grain number and panicle weight. G6 has higher yield and stability than Swarna but has Swarna grain type. Among the varieties tested DRRDhan 40 and recurrent parent Swarna showed stability for yield traits across the seasons. The component traits thousand grain weight, panicle weight, panicle length, grain number and plant height explained highest genotypic percentage over environment and interaction factors and can be prioritized to dissect stable QTLs/ genes. These lines were genotyped using microsatellite markers covering the entire rice genome and also using a set of markers linked to previously reported yield QTLs. It was observed that wild derived lines with more than 70% of recurrent parent genome were stable and showed enhanced yield levels compared to genotypes with higher donor genome introgressions.
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17
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Genetic mapping of a QTL controlling source-sink size and heading date in rice. Gene 2015; 571:263-70. [PMID: 26123916 DOI: 10.1016/j.gene.2015.06.065] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2015] [Revised: 06/23/2015] [Accepted: 06/25/2015] [Indexed: 11/20/2022]
Abstract
Source size, sink size and heading date (HD) are three important classes of traits that determine the productivity of rice. In this study, a set of recombinant inbred lines (RILs) derived from the cross between an elite indica line Big Grain1 (BG1) and a japonica line Xiaolijing (XLJ) were used to map quantitative trait loci (QTLs) for source-sink size and heading date. Totally, thirty-one QTLs for source size, twenty-two for sink size, four for heading date and seven QTL clusters which included QTLs for multiple traits were identified in three environmental trials. Thirty QTLs could be consistently detected in at least two trials and generally located in the clusters. Using a set of BC4F2 lines, the QTL cluster in C5-1-C5-2 on chromosome 5 was validated to be a major QTL pleiotropically affecting heading date, source size (flag leaf area) and panicle type (neck length of panicle, primary branching number and the ratio of secondary branching number to primary branching number), and was narrowed down to a 309.52Kb region. QTL clusters described above have a large effect on source-sink size and/or heading date, therefore they should be good resources to improve the adaptability and high yield potential of cultivars genetically.
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18
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Wang Y, Yang C, Jin Q, Zhou D, Wang S, Yu Y, Yang L. Genome-wide distribution comparative and composition analysis of the SSRs in Poaceae. BMC Genet 2015; 16:18. [PMID: 25886726 PMCID: PMC4333251 DOI: 10.1186/s12863-015-0178-z] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2014] [Accepted: 02/05/2015] [Indexed: 11/21/2022] Open
Abstract
Background The Poaceae family is of great importance to human beings since it comprises the cereal grasses which are the main sources for human food and animal feed. With the rapid growth of genomic data from Poaceae members, comparative genomics becomes a convinent method to study genetics of diffierent species. The SSRs (Simple Sequence Repeats) are widely used markers in the studies of Poaceae for their high abundance and stability. Results In this study, using the genomic sequences of 9 Poaceae species, we detected 11,993,943 SSR loci and developed 6,799,910 SSR primer pairs. The results show that SSRs are distributed on all the genomic elements in grass. Hexamer is the most frequent motif and AT/TA is the most frequent motif in dimer. The abundance of the SSRs has a positive linear relationship with the recombination rate. SSR sequences in the coding regions involve a higher GC content in the Poaceae than that in the other species. SSRs of 70-80 bp in length showed the highest AT/GC base ratio among all of these loci. The result shows the highest polymorphism rate belongs to the SSRs ranged from 30 bp to 40 bp. Using all the SSR primers of Japonica, nineteen universal primers were selected and located on the genome of the grass family. The information of SSR loci, the SSR primers and the tools of mining and analyzing SSR are provided in the PSSRD (Poaceae SSR Database, http://biodb.sdau.edu.cn/pssrd/). Conclusions Our study and the PSSRD database provide a foundation for the comparative study in the Poaceae and it will accelerate the study on markers application, gene mapping and molecular breeding.
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Affiliation(s)
- Yi Wang
- Key Laboratory of Crop Biology of China, Shandong Agricultural University, Taian, 271018, China.
| | - Chao Yang
- Key Laboratory of Crop Biology of China, Shandong Agricultural University, Taian, 271018, China.
| | - Qiaojun Jin
- College of Plant Protection, Northwest Agriculture and Forestry University, Yangling, 712100, China.
| | - Dongjie Zhou
- Agricultural Big-Data Research Center, Shandong Agricultural University, Taian, 271018, China.
| | - Shuangshuang Wang
- Agricultural Big-Data Research Center, Shandong Agricultural University, Taian, 271018, China.
| | - Yuanjie Yu
- Key Laboratory of Crop Biology of China, Shandong Agricultural University, Taian, 271018, China.
| | - Long Yang
- Key Laboratory of Crop Biology of China, Shandong Agricultural University, Taian, 271018, China. .,Agricultural Big-Data Research Center, Shandong Agricultural University, Taian, 271018, China.
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Saxena MS, Bajaj D, Kujur A, Das S, Badoni S, Kumar V, Singh M, Bansal KC, Tyagi AK, Parida SK. Natural allelic diversity, genetic structure and linkage disequilibrium pattern in wild chickpea. PLoS One 2014; 9:e107484. [PMID: 25222488 PMCID: PMC4164632 DOI: 10.1371/journal.pone.0107484] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2014] [Accepted: 08/11/2014] [Indexed: 01/23/2023] Open
Abstract
Characterization of natural allelic diversity and understanding the genetic structure and linkage disequilibrium (LD) pattern in wild germplasm accessions by large-scale genotyping of informative microsatellite and single nucleotide polymorphism (SNP) markers is requisite to facilitate chickpea genetic improvement. Large-scale validation and high-throughput genotyping of genome-wide physically mapped 478 genic and genomic microsatellite markers and 380 transcription factor gene-derived SNP markers using gel-based assay, fluorescent dye-labelled automated fragment analyser and matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) mass array have been performed. Outcome revealed their high genotyping success rate (97.5%) and existence of a high level of natural allelic diversity among 94 wild and cultivated Cicer accessions. High intra- and inter-specific polymorphic potential and wider molecular diversity (11-94%) along with a broader genetic base (13-78%) specifically in the functional genic regions of wild accessions was assayed by mapped markers. It suggested their utility in monitoring introgression and transferring target trait-specific genomic (gene) regions from wild to cultivated gene pool for the genetic enhancement. Distinct species/gene pool-wise differentiation, admixed domestication pattern, and differential genome-wide recombination and LD estimates/decay observed in a six structured population of wild and cultivated accessions using mapped markers further signifies their usefulness in chickpea genetics, genomics and breeding.
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Affiliation(s)
- Maneesha S. Saxena
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, India
| | - Deepak Bajaj
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, India
| | - Alice Kujur
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, India
| | - Shouvik Das
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, India
| | - Saurabh Badoni
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, India
| | - Vinod Kumar
- National Research Centre on Plant Biotechnology (NRCPB), New Delhi, India
| | - Mohar Singh
- National Bureau of Plant Genetic Resources (NBPGR), New Delhi, India
| | - Kailash C. Bansal
- National Bureau of Plant Genetic Resources (NBPGR), New Delhi, India
| | - Akhilesh K. Tyagi
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, India
| | - Swarup K. Parida
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, India
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20
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Li Z, Zhang Y, Liu L, Liu Q, Bi Z, Yu N, Cheng S, Cao L. Fine mapping of the lesion mimic and early senescence 1 (lmes1) in rice (Oryza sativa). PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2014; 80:300-7. [PMID: 24832615 DOI: 10.1016/j.plaphy.2014.03.031] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2014] [Accepted: 03/30/2014] [Indexed: 05/05/2023]
Abstract
A novel rice mutant, lesion mimic and early senescence 1 (lmes1), was induced from the rice 93-11 cultivar in a γ-ray field. This mutant exhibited spontaneous disease-like lesions in the absence of pathogen attack at the beginning of the tillering stage. Moreover, at the booting stage, lmes1 mutants exhibited a significantly increased MDA but decreased chlorophyll content, soluble protein content and photosynthetic rate in the leaves, which are indicative of an early senescence phenotype. The lmes1 mutant was significantly more resistant than 93-11 against rice bacterial blight infection, which was consistent with a marked increase in the expression of three resistance-related genes. Here, we employed a map-based cloning approach to finely map the lmes1 gene. In an initial mapping with 94 F2 individuals derived from a cross between the lmes1 mutant and Nipponbare, the lmes1 gene was located in a 10.6-cM region on the telomere of the long arm of chromosome 7 using simple sequence repeat (SSR) markers. To finely map lmes1, we derived two F2 populations with 940 individuals from two crosses between the lmes1 mutant and two japonica rice varieties, Nipponbare and 02428. Finally, the lmes1 gene was mapped to an 88-kb region between two newly developed inDel markers, Zl-3 and Zl-22, which harbored 15 ORFs.
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Affiliation(s)
- Zhi Li
- State Key Laboratory for Rice Biology, China National Rice Research Institute, Hangzhou 310006, China; Hangzhou Normal University, Xuelin Road, Hangzhou 310036, China; Key Laboratory for Zhejiang Super Rice Research, China National Rice Research Institute Hangzhou 310006, China
| | - Yingxin Zhang
- State Key Laboratory for Rice Biology, China National Rice Research Institute, Hangzhou 310006, China; Key Laboratory for Zhejiang Super Rice Research, China National Rice Research Institute Hangzhou 310006, China
| | - Lin Liu
- State Key Laboratory for Rice Biology, China National Rice Research Institute, Hangzhou 310006, China
| | - Qunen Liu
- State Key Laboratory for Rice Biology, China National Rice Research Institute, Hangzhou 310006, China
| | - Zhenzhen Bi
- State Key Laboratory for Rice Biology, China National Rice Research Institute, Hangzhou 310006, China
| | - Ning Yu
- State Key Laboratory for Rice Biology, China National Rice Research Institute, Hangzhou 310006, China
| | - Shihua Cheng
- State Key Laboratory for Rice Biology, China National Rice Research Institute, Hangzhou 310006, China; Key Laboratory for Zhejiang Super Rice Research, China National Rice Research Institute Hangzhou 310006, China
| | - Liyong Cao
- State Key Laboratory for Rice Biology, China National Rice Research Institute, Hangzhou 310006, China; Key Laboratory for Zhejiang Super Rice Research, China National Rice Research Institute Hangzhou 310006, China.
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Rizal G, Karki S, Thakur V, Chatterjee J, A. Coe R, Wanchana S, Quick WP. Towards a C4 Rice. ACTA ACUST UNITED AC 2012. [DOI: 10.3923/ajcb.2012.13.31] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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Patterns of sequence divergence and evolution of the S orthologous regions between Asian and African cultivated rice species. PLoS One 2011; 6:e17726. [PMID: 21423767 PMCID: PMC3053390 DOI: 10.1371/journal.pone.0017726] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2010] [Accepted: 02/08/2011] [Indexed: 12/17/2022] Open
Abstract
A strong postzygotic reproductive barrier separates the recently diverged Asian and African cultivated rice species, Oryza sativa and O. glaberrima. Recently a model of genetic incompatibilities between three adjacent loci: S1A, S1 and S1B (called together the S1 regions) interacting epistatically, was postulated to cause the allelic elimination of female gametes in interspecific hybrids. Two candidate factors for the S1 locus (including a putative F-box gene) were proposed, but candidates for S1A and S1B remained undetermined. Here, to better understand the basis of the evolution of regions involved in reproductive isolation, we studied the genic and structural changes accumulated in the S1 regions between orthologous sequences. First, we established an 813 kb genomic sequence in O. glaberrima, covering completely the S1A, S1 and the majority of the S1B regions, and compared it with the orthologous regions of O. sativa. An overall strong structural conservation was observed, with the exception of three isolated regions of disturbed collinearity: (1) a local invasion of transposable elements around a putative F-box gene within S1, (2) the multiple duplication and subsequent divergence of the same F-box gene within S1A, (3) an interspecific chromosomal inversion in S1B, which restricts recombination in our O. sativa×O. glaberrima crosses. Beside these few structural variations, a uniform conservative pattern of coding sequence divergence was found all along the S1 regions. Hence, the S1 regions have undergone no drastic variation in their recent divergence and evolution between O. sativa and O. glaberrima, suggesting that a small accumulation of genic changes, following a Bateson-Dobzhansky-Muller (BDM) model, might be involved in the establishment of the sterility barrier. In this context, genetic incompatibilities involving the duplicated F-box genes as putative candidates, and a possible strengthening step involving the chromosomal inversion might participate to the reproductive barrier between Asian and African rice species.
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Wu ZH, Wang SZ, Hu JH, Li F, Ke WD, Ding Y. Development and characterization of microsatellite markers for Sagittaria trifolia var. sinensis (Alismataceae). AMERICAN JOURNAL OF BOTANY 2011; 98:e36-e38. [PMID: 21613103 DOI: 10.3732/ajb.1000434] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
PREMISE OF THE STUDY Microsatellite markers were developed for the aquatic plant Sagittaria trifolia var. sinensis to assess its genetic diversity and population structure. Cross-species transferability was assayed in eight congeneric species. METHODS AND RESULTS Seventeen microsatellite markers were isolated and characterized in Sagittaria trifolia var. sinensis using Fast Isolation by AFLP of Sequence COntaining Repeats (FIASCO) protocol. Across the evaluated populations, 14 of the markers showed polymorphisms with 3 to 11 alleles per locus; the observed and expected heterozygosity (H(o) and H(E)) ranged from 0.0000 to 0.6364 and from 0.0000 to 0.8386, respectively. Nine of the loci were successfully amplified in the congeneric species. CONCLUSIONS These markers will be useful for further investigation of population genetics in Sagittaria trifolia var. sinensis and related research in Sagittaria species.
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Affiliation(s)
- Zhi-Hua Wu
- Key Laboratory of MOE for Plant Development Biology, Department of Genetics, College of Life Sciences, Wuhan University, Wuhan 430072, P. R. China
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Garavito A, Guyot R, Lozano J, Gavory F, Samain S, Panaud O, Tohme J, Ghesquière A, Lorieux M. A genetic model for the female sterility barrier between Asian and African cultivated rice species. Genetics 2010; 185:1425-40. [PMID: 20457876 PMCID: PMC2927767 DOI: 10.1534/genetics.110.116772] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2010] [Accepted: 04/28/2010] [Indexed: 02/07/2023] Open
Abstract
S(1) is the most important locus acting as a reproductive barrier between Oryza sativa and O. glaberrima. It is a complex locus, with factors that may affect male and female fertility separately. Recently, the component causing the allelic elimination of pollen was fine mapped. However, the position and nature of the component causing female sterility remains unknown. To fine map the factor of the S(1) locus affecting female fertility, we developed a mapping approach based on the evaluation of the degree of female transmission ratio distortion (fTRD) of markers. Through implementing this methodology in four O. sativa x O. glaberrima crosses, the female component of the S(1) locus was mapped into a 27.8-kb (O. sativa) and 50.3-kb (O. glaberrima) region included within the interval bearing the male component of the locus. Moreover, evidence of additional factors interacting with S(1) was also found. In light of the available data, a model where incompatibilities in epistatic interactions between S(1) and the additional factors are the cause of the female sterility barrier between O. sativa and O. glaberrima was developed to explain the female sterility and the TRD mediated by S(1). According to our model, the recombination ratio and allelic combinations between these factors would determine the final allelic frequencies observed for a given cross.
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Affiliation(s)
- Andrea Garavito
- Plant Genome and Development Laboratory, Institut de Recherche pour le Développement (IRD), 34394 Montpellier Cedex 5, France, Agrobiodiversity and Biotechnology Project, International Center for Tropical Agriculture (CIAT), A.A. 6713, Cali, Colombia, Génoscope, Institut de Génomique, Commissariat à l'Énergie Atomique (CEA), 91057 Evry, France and Plant Genome and Development Laboratory, Université de Perpignan, 66860 Perpignan, France
| | - Romain Guyot
- Plant Genome and Development Laboratory, Institut de Recherche pour le Développement (IRD), 34394 Montpellier Cedex 5, France, Agrobiodiversity and Biotechnology Project, International Center for Tropical Agriculture (CIAT), A.A. 6713, Cali, Colombia, Génoscope, Institut de Génomique, Commissariat à l'Énergie Atomique (CEA), 91057 Evry, France and Plant Genome and Development Laboratory, Université de Perpignan, 66860 Perpignan, France
| | - Jaime Lozano
- Plant Genome and Development Laboratory, Institut de Recherche pour le Développement (IRD), 34394 Montpellier Cedex 5, France, Agrobiodiversity and Biotechnology Project, International Center for Tropical Agriculture (CIAT), A.A. 6713, Cali, Colombia, Génoscope, Institut de Génomique, Commissariat à l'Énergie Atomique (CEA), 91057 Evry, France and Plant Genome and Development Laboratory, Université de Perpignan, 66860 Perpignan, France
| | - Frédérick Gavory
- Plant Genome and Development Laboratory, Institut de Recherche pour le Développement (IRD), 34394 Montpellier Cedex 5, France, Agrobiodiversity and Biotechnology Project, International Center for Tropical Agriculture (CIAT), A.A. 6713, Cali, Colombia, Génoscope, Institut de Génomique, Commissariat à l'Énergie Atomique (CEA), 91057 Evry, France and Plant Genome and Development Laboratory, Université de Perpignan, 66860 Perpignan, France
| | - Sylvie Samain
- Plant Genome and Development Laboratory, Institut de Recherche pour le Développement (IRD), 34394 Montpellier Cedex 5, France, Agrobiodiversity and Biotechnology Project, International Center for Tropical Agriculture (CIAT), A.A. 6713, Cali, Colombia, Génoscope, Institut de Génomique, Commissariat à l'Énergie Atomique (CEA), 91057 Evry, France and Plant Genome and Development Laboratory, Université de Perpignan, 66860 Perpignan, France
| | - Olivier Panaud
- Plant Genome and Development Laboratory, Institut de Recherche pour le Développement (IRD), 34394 Montpellier Cedex 5, France, Agrobiodiversity and Biotechnology Project, International Center for Tropical Agriculture (CIAT), A.A. 6713, Cali, Colombia, Génoscope, Institut de Génomique, Commissariat à l'Énergie Atomique (CEA), 91057 Evry, France and Plant Genome and Development Laboratory, Université de Perpignan, 66860 Perpignan, France
| | - Joe Tohme
- Plant Genome and Development Laboratory, Institut de Recherche pour le Développement (IRD), 34394 Montpellier Cedex 5, France, Agrobiodiversity and Biotechnology Project, International Center for Tropical Agriculture (CIAT), A.A. 6713, Cali, Colombia, Génoscope, Institut de Génomique, Commissariat à l'Énergie Atomique (CEA), 91057 Evry, France and Plant Genome and Development Laboratory, Université de Perpignan, 66860 Perpignan, France
| | - Alain Ghesquière
- Plant Genome and Development Laboratory, Institut de Recherche pour le Développement (IRD), 34394 Montpellier Cedex 5, France, Agrobiodiversity and Biotechnology Project, International Center for Tropical Agriculture (CIAT), A.A. 6713, Cali, Colombia, Génoscope, Institut de Génomique, Commissariat à l'Énergie Atomique (CEA), 91057 Evry, France and Plant Genome and Development Laboratory, Université de Perpignan, 66860 Perpignan, France
| | - Mathias Lorieux
- Plant Genome and Development Laboratory, Institut de Recherche pour le Développement (IRD), 34394 Montpellier Cedex 5, France, Agrobiodiversity and Biotechnology Project, International Center for Tropical Agriculture (CIAT), A.A. 6713, Cali, Colombia, Génoscope, Institut de Génomique, Commissariat à l'Énergie Atomique (CEA), 91057 Evry, France and Plant Genome and Development Laboratory, Université de Perpignan, 66860 Perpignan, France
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