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Virk PS, Andersson MS, Arcos J, Govindaraj M, Pfeiffer WH. Transition From Targeted Breeding to Mainstreaming of Biofortification Traits in Crop Improvement Programs. Front Plant Sci 2021; 12:703990. [PMID: 34594348 PMCID: PMC8477801 DOI: 10.3389/fpls.2021.703990] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/01/2021] [Accepted: 08/17/2021] [Indexed: 06/13/2023]
Abstract
Biofortification breeding for three important micronutrients for human health, namely, iron (Fe), zinc (Zn), and provitamin A (PVA), has gained momentum in recent years. HarvestPlus, along with its global consortium partners, enhances Fe, Zn, and PVA in staple crops. The strategic and applied research by HarvestPlus is driven by product-based impact pathway that integrates crop breeding, nutrition research, impact assessment, advocacy, and communication to implement country-specific crop delivery plans. Targeted breeding has resulted in 393 biofortified crop varieties by the end of 2020, which have been released or are in testing in 63 countries, potentially benefitting more than 48 million people. Nevertheless, to reach more than a billion people by 2030, future breeding lines that are being distributed by Consultative Group on International Agricultural Research (CGIAR) centers and submitted by National Agricultural Research System (NARS) to varietal release committees should be biofortified. It is envisaged that the mainstreaming of biofortification traits will be driven by high-throughput micronutrient phenotyping, genomic selection coupled with speed breeding for accelerating genetic gains. It is noteworthy that targeted breeding gradually leads to mainstreaming, as the latter capitalizes on the progress made in the former. Efficacy studies have revealed the nutritional significance of Fe, Zn, and PVA biofortified varieties over non-biofortified ones. Mainstreaming will ensure the integration of biofortified traits into competitive varieties and hybrids developed by private and public sectors. The mainstreaming strategy has just been initiated in select CGIAR centers, namely, International Maize and Wheat Improvement Center (CIMMYT), International Rice Research Institute (IRRI), International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), International Institute of Tropical Agriculture (IITA), and International Center for Tropical Agriculture (CIAT). This review will present the key successes of targeted breeding and its relevance to the mainstreaming approaches to achieve scaling of biofortification to billions sustainably.
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Affiliation(s)
- Parminder S. Virk
- HarvestPlus, International Food Policy Research Institute (IFPRI), Washington, DC, United States
- Alliance of Bioversity International and the International Center for Tropical Agriculture (CIAT), Cali, Colombia
| | - Meike S. Andersson
- HarvestPlus, International Food Policy Research Institute (IFPRI), Washington, DC, United States
- Alliance of Bioversity International and the International Center for Tropical Agriculture (CIAT), Cali, Colombia
| | - Jairo Arcos
- HarvestPlus, International Food Policy Research Institute (IFPRI), Washington, DC, United States
- Alliance of Bioversity International and the International Center for Tropical Agriculture (CIAT), Cali, Colombia
| | - Mahalingam Govindaraj
- HarvestPlus, International Food Policy Research Institute (IFPRI), Washington, DC, United States
- Alliance of Bioversity International and the International Center for Tropical Agriculture (CIAT), Cali, Colombia
- Crop Improvement, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India
| | - Wolfgang H. Pfeiffer
- HarvestPlus, International Food Policy Research Institute (IFPRI), Washington, DC, United States
- Alliance of Bioversity International and the International Center for Tropical Agriculture (CIAT), Cali, Colombia
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Nguyen CD, Verdeprado H, Zita D, Sanada-Morimura S, Matsumura M, Virk PS, Brar DS, Horgan FG, Yasui H, Fujita D. The Development and Characterization of Near-Isogenic and Pyramided Lines Carrying Resistance Genes to Brown Planthopper with the Genetic Background of Japonica Rice ( Oryza sativa L.). Plants (Basel) 2019; 8:plants8110498. [PMID: 31726710 PMCID: PMC6918374 DOI: 10.3390/plants8110498] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Revised: 11/04/2019] [Accepted: 11/07/2019] [Indexed: 11/16/2022]
Abstract
The brown planthopper (BPH: Nilaparvata lugens Stål.) is a major pest of rice, Oryza sativa, in Asia. Host plant resistance has tremendous potential to reduce the damage caused to rice by the planthopper. However, the effectiveness of resistance genes varies spatially and temporally according to BPH virulence. Understanding patterns in BPH virulence against resistance genes is necessary to efficiently and sustainably deploy resistant rice varieties. To survey BPH virulence patterns, seven near-isogenic lines (NILs), each with a single BPH resistance gene (BPH2-NIL, BPH3-NIL, BPH17-NIL, BPH20-NIL, BPH21-NIL, BPH32-NIL and BPH17-ptb-NIL) and fifteen pyramided lines (PYLs) carrying multiple resistance genes were developed with the genetic background of the japonica rice variety, Taichung 65 (T65), and assessed for resistance levels against two BPH populations (Hadano-66 and Koshi-2013 collected in Japan in 1966 and 2013, respectively). Many of the NILs and PYLs were resistant against the Hadano-66 population but were less effective against the Koshi-2013 population. Among PYLs, BPH20+BPH32-PYL and BPH2+BPH3+BPH17-PYL granted relatively high BPH resistance against Koshi-2013. The NILs and PYLs developed in this research will be useful to monitor BPH virulence prior to deploying resistant rice varieties and improve rice’s resistance to BPH in the context of regionally increasing levels of virulence.
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Affiliation(s)
- Cuong D. Nguyen
- United Graduate School of Agricultural Sciences, Kagoshima University, Kagoshima 890-0065, Japan;
- College of Food Industry, 101B Le Huu Trac Street, Son Tra District, Da Nang City 550000, Vietnam
| | - Holden Verdeprado
- International Rice Research Institute, DAPO Box 7777, Metro Manila 1301, Philippines; (H.V.); (P.S.V.); (D.S.B.)
| | - Demeter Zita
- Faculty of Agriculture, Saga University, Saga 840-8502, Japan;
| | - Sachiyo Sanada-Morimura
- NARO Kyushu Okinawa Agricultural Research Center, 2421 Suya, Koshi, Kumamoto 861–1192, Japan; (S.S.-M.); (M.M.)
| | - Masaya Matsumura
- NARO Kyushu Okinawa Agricultural Research Center, 2421 Suya, Koshi, Kumamoto 861–1192, Japan; (S.S.-M.); (M.M.)
| | - Parminder S. Virk
- International Rice Research Institute, DAPO Box 7777, Metro Manila 1301, Philippines; (H.V.); (P.S.V.); (D.S.B.)
- International Center for Tropical Agriculture, A.A, 6713 Cali, Colombia
| | - Darshan S. Brar
- International Rice Research Institute, DAPO Box 7777, Metro Manila 1301, Philippines; (H.V.); (P.S.V.); (D.S.B.)
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana 141027, India
| | - Finbarr G. Horgan
- EcoLaVerna Integral Restoration Ecology, Bridestown, Kildinan, Co. Cork, T56 CD39, Ireland;
| | - Hideshi Yasui
- Plant Breeding Laboratory, Graduate School, Kyushu University, Fukuoka 812-8581, Japan;
| | - Daisuke Fujita
- United Graduate School of Agricultural Sciences, Kagoshima University, Kagoshima 890-0065, Japan;
- International Rice Research Institute, DAPO Box 7777, Metro Manila 1301, Philippines; (H.V.); (P.S.V.); (D.S.B.)
- Faculty of Agriculture, Saga University, Saga 840-8502, Japan;
- Plant Breeding Laboratory, Graduate School, Kyushu University, Fukuoka 812-8581, Japan;
- Correspondence: ; Tel.: +81-952-28-8724
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Dixit S, Singh UM, Abbai R, Ram T, Singh VK, Paul A, Virk PS, Kumar A. Identification of genomic region(s) responsible for high iron and zinc content in rice. Sci Rep 2019; 9:8136. [PMID: 31148549 PMCID: PMC6544658 DOI: 10.1038/s41598-019-43888-y] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Accepted: 04/23/2019] [Indexed: 11/15/2022] Open
Abstract
Micronutrient especially iron and zinc-enriched rice hold immense promise for sustainable and cost-effective solutions to overcome malnutrition. In this context, BC2F5 population derived from cross between RP-Bio226 and Sampada was used to localize genomic region(s)/QTL(s) for grain Fe (iron) and Zn (zinc) content together with yield and yield-related traits. Genotyping of mapping population with 108 SSR markers resulted in a genetic map of 2317.5 cM with an average marker distance of 21.5 cM. Mean grain mineral content in the mapping population across the two seasons ranged from 10.5–17.5 ppm for Fe and 11.3–22.1 ppm for Zn. Based on the multi-season phenotypic data together with genotypic data, a total of two major QTLs for Fe (PVE upto 17.1%) and three for Zn (PVE upto 34.2%) were identified. Comparative analysis across the two seasons has revealed four consistent QTLs for Fe (qFe1.1, qFe1.2, qFe6.1 and qFe6.2) and two QTL for Zn content (qZn1.1 and qZn6.2). Additionally, based on the previous and current studies three meta-QTLs for grain Fe and two for grain Zn have been identified. In-silico analysis of the identified QTL regions revealed the presence of potential candidate gene(s) such as, OsPOT, OsZIP4, OsFDR3, OsIAA5 etc., that were previously reported to influence grain Fe and Zn content. The identified QTLs could be utilized in developing high yielding, Fe and Zn denser varieties by marker assisted selection (MAS).
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Affiliation(s)
- Shilpi Dixit
- International Rice Research Institute (IRRI), South-Asia Hub, ICRISAT Campus, Hyderabad, 502324, India.,Visva-Bharati University, Santiniketan, West Bengal, 731235, India
| | - Uma Maheshwar Singh
- International Rice Research Institute (IRRI), South-Asia Hub, ICRISAT Campus, Hyderabad, 502324, India
| | - Ragavendran Abbai
- International Rice Research Institute (IRRI), South-Asia Hub, ICRISAT Campus, Hyderabad, 502324, India
| | - T Ram
- Indian Institute of Rice Research (IIRR), Hyderabad, 500030, India
| | - Vikas Kumar Singh
- International Rice Research Institute (IRRI), South-Asia Hub, ICRISAT Campus, Hyderabad, 502324, India
| | - Amitava Paul
- Visva-Bharati University, Santiniketan, West Bengal, 731235, India
| | - P S Virk
- HarvestPlus, ICRISAT Campus, Hyderabad, 502324, India
| | - Arvind Kumar
- International Rice Research Institute (IRRI), South-Asia Hub, ICRISAT Campus, Hyderabad, 502324, India. .,International Rice Research Institute, DAPO BOX 7777, Metro Manila, Philippines.
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Kim SR, Ramos JM, Hizon RJM, Ashikari M, Virk PS, Torres EA, Nissila E, Jena KK. Introgression of a functional epigenetic OsSPL14 WFP allele into elite indica rice genomes greatly improved panicle traits and grain yield. Sci Rep 2018; 8:3833. [PMID: 29497052 PMCID: PMC5832747 DOI: 10.1038/s41598-018-21355-4] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Accepted: 02/01/2018] [Indexed: 12/20/2022] Open
Abstract
Rice yield potential has been stagnant since the Green Revolution in the late 1960s, especially in tropical rice cultivars. We evaluated the effect of two major genes that regulate grain number, Gn1a/OsCKX2 and IPA1/WFP/OsSPL14, in elite indica cultivar backgrounds. The yield-positive Gn1a-type 3 and OsSPL14WFP alleles were introgressed respectively through marker-assisted selection (MAS). The grain numbers per panicle (GNPP) were compared between the recipient allele and the donor allele groups using segregating plants in BC3F2 and BC3F3 generations. There was no significant difference in GNPP between the two Gn1a alleles, suggesting that the Gn1a-type 3 allele was not effective in indica cultivars. However, the OsSPL14WFP allele dramatically increased GNPP by 10.6–59.3% in all four different backgrounds across cropping seasons and generations, indicating that this allele provides strong genetic gain to elite indica cultivars. Eventually, five high-yielding breeding lines were bred using the OsSPL14WFP allele by MAS with a conventional breeding approach that showed increased grain yield by 28.4–83.5% (7.87–12.89 t/ha) vis-à-vis the recipient cultivars and exhibited higher yield (~64.7%) than the top-yielding check cultivar, IRRI 156 (7.82 t/ha). We demonstrated a strong possibility to increase the genetic yield potential of indica rice varieties through allele mining and its application.
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Affiliation(s)
- Sung-Ryul Kim
- Strategic Innovation Platform, International Rice Research Institute (IRRI), DAPO Box, 7777, Metro Manila, Philippines
| | - Joie M Ramos
- Strategic Innovation Platform, International Rice Research Institute (IRRI), DAPO Box, 7777, Metro Manila, Philippines
| | - Rona Joy M Hizon
- Strategic Innovation Platform, International Rice Research Institute (IRRI), DAPO Box, 7777, Metro Manila, Philippines
| | - Motoyuki Ashikari
- Bioscience and Biotechnology Center, Nagoya University, Nagoya, Japan
| | - Parminder S Virk
- International Center for Tropical Agriculture (CIAT), A.A, 6713, Cali, Colombia
| | | | - Eero Nissila
- Strategic Innovation Platform, International Rice Research Institute (IRRI), DAPO Box, 7777, Metro Manila, Philippines
| | - Kshirod K Jena
- Strategic Innovation Platform, International Rice Research Institute (IRRI), DAPO Box, 7777, Metro Manila, Philippines.
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Kim SR, Ramos J, Ashikari M, Virk PS, Torres EA, Nissila E, Hechanova SL, Mauleon R, Jena KK. Development and validation of allele-specific SNP/indel markers for eight yield-enhancing genes using whole-genome sequencing strategy to increase yield potential of rice, Oryza sativa L. Rice (N Y) 2016; 9:12. [PMID: 26987543 PMCID: PMC4797370 DOI: 10.1186/s12284-016-0084-7] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2015] [Accepted: 03/11/2016] [Indexed: 05/18/2023]
Abstract
BACKGROUND Rice is one of the major staple foods in the world, especially in the developing countries of Asia. Its consumption as a dietary source is also increasing in Africa. To meet the demand for rice to feed the increasing human population, increasing rice yield is essential. Improving the genetic yield potential of rice is one ideal solution. It is imperative to introduce the identified yield-enhancing gene(s) into modern rice cultivars for the rapid improvement of yield potential through marker-assisted breeding. RESULTS We report the development of PCR-gel-based markers for eight yield-related functional genes (Gn1a, OsSPL14, SCM2, Ghd7, DEP1, SPIKE, GS5, and TGW6) to introduce yield-positive alleles from the donor lines. Six rice cultivars, including three each of donor and recipient lines, respectively, were sequenced by next-generation whole-genome sequencing to detect DNA polymorphisms between the genotypes. Additionally, PCR products containing functional nucleotide polymorphism (FNP) or putative FNPs for yield-related genes were sequenced. DNA polymorphisms discriminating yield-positive alleles and non-target alleles for each gene were selected through sequence analysis and the allele-specific PCR-gel-based markers were developed. The markers were validated with our intermediate breeding lines produced from crosses between the donors and 12 elite indica rice cultivars as recipients. Automated capillary electrophoresis was tested and fluorescence-labeled SNP genotyping markers (Fluidigm SNP genotyping platform) for Gn1a, OsSPL14, Ghd7, GS5, and GS3 genes were developed for high-throughput genotyping. CONCLUSIONS The SNP/indel markers linked to yield related genes functioned properly in our marker-assisted breeding program with identified high yield potential lines. These markers can be utilized in local favorite rice cultivars for yield enhancement. The marker designing strategy using both next generation sequencing and Sanger sequencing methods can be used for suitable marker development of other genes associated with useful agronomic traits.
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Affiliation(s)
- Sung-Ryul Kim
- />Plant Breeding, Genetics, and Biotechnology Division, International Rice Research Institute, Metro Manila, Philippines
| | - Joie Ramos
- />Plant Breeding, Genetics, and Biotechnology Division, International Rice Research Institute, Metro Manila, Philippines
| | - Motoyuki Ashikari
- />Bioscience and Biotechnology Center, Nagoya University, Nagoya, Japan
| | | | - Edgar A. Torres
- />International Center for Tropical Agriculture, A.A. 6713 Cali, Colombia
| | - Eero Nissila
- />Plant Breeding, Genetics, and Biotechnology Division, International Rice Research Institute, Metro Manila, Philippines
| | - Sherry Lou Hechanova
- />Plant Breeding, Genetics, and Biotechnology Division, International Rice Research Institute, Metro Manila, Philippines
| | - Ramil Mauleon
- />Plant Breeding, Genetics, and Biotechnology Division, International Rice Research Institute, Metro Manila, Philippines
| | - Kshirod K. Jena
- />Plant Breeding, Genetics, and Biotechnology Division, International Rice Research Institute, Metro Manila, Philippines
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Suh JP, Jeung JU, Lee JI, Choi YH, Yea JD, Virk PS, Mackill DJ, Jena KK. Identification and analysis of QTLs controlling cold tolerance at the reproductive stage and validation of effective QTLs in cold-tolerant genotypes of rice (Oryza sativa L.). Theor Appl Genet 2010; 120:985-95. [PMID: 20012263 DOI: 10.1007/s00122-009-1226-8] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2009] [Accepted: 11/18/2009] [Indexed: 05/03/2023]
Abstract
Low temperature or cold stress is one of the major constraints of rice production and productivity in temperate rice-growing countries and high-altitude areas in the tropics. Even though low temperature affects the rice plant in all stages of growth, the percent seed set is damaged severely by cold and this reduces the yield potential of cultivars significantly. In this study, a new source of cold-tolerant line, IR66160-121-4-4-2, was used as a donor parent with a cold-sensitive cultivar, Geumobyeo, to produce 153 F(8) recombinant inbred lines (RILs) for quantitative trait locus (QTL) analysis. QTL analysis with 175 polymorphic simple sequence repeat (SSR) markers and composite interval mapping identified three main-effect QTLs (qPSST-3, qPSST-7, and qPSST-9) on chromosomes 3, 7, and 9. The SSR markers RM569, RM1377, and RM24545 were linked to the identified QTLs for cold tolerance with respect to percent seed set using cold-water (18-19 degrees C) irrigation in the field and controlled air temperature (17 degrees C) in the greenhouse. The total phenotypic variation for cold tolerance contributed by the three QTLs was 27.4%. RILs with high percent seed set under cold stress were validated with linked DNA markers and by haplotype analysis that revealed the contribution of progenitor genomes from the tropical japonica cultivar Jimbrug (Javanica) and temperate japonica cultivar Shen-Nung89-366. Three QTLs contributed by the cold-tolerant parent were identified which showed additive effect on percent seed set under cold treatment. This study demonstrated the utility of a new phenotyping method as well as the identification of SSR markers associated with QTLs for selection of cold-tolerant genotypes to improve temperate rice production.
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Affiliation(s)
- J P Suh
- IRRI-Korea Office, National Institute of Crop Science, RDA, 209 Seodun-Dong, Suwon, 441-857, Republic of Korea
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Collard BCY, Vera Cruz CM, McNally KL, Virk PS, Mackill DJ. Rice molecular breeding laboratories in the genomics era: Current status and future considerations. Int J Plant Genomics 2008; 2008:524847. [PMID: 18528527 PMCID: PMC2408710 DOI: 10.1155/2008/524847] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2007] [Accepted: 03/15/2008] [Indexed: 05/20/2023]
Abstract
Using DNA markers in plant breeding with marker-assisted selection (MAS) could greatly improve the precision and efficiency of selection, leading to the accelerated development of new crop varieties. The numerous examples of MAS in rice have prompted many breeding institutes to establish molecular breeding labs. The last decade has produced an enormous amount of genomics research in rice, including the identification of thousands of QTLs for agronomically important traits, the generation of large amounts of gene expression data, and cloning and characterization of new genes, including the detection of single nucleotide polymorphisms. The pinnacle of genomics research has been the completion and annotation of genome sequences for indica and japonica rice. This information-coupled with the development of new genotyping methodologies and platforms, and the development of bioinformatics databases and software tools-provides even more exciting opportunities for rice molecular breeding in the 21st century. However, the great challenge for molecular breeders is to apply genomics data in actual breeding programs. Here, we review the current status of MAS in rice, current genomics projects and promising new genotyping methodologies, and evaluate the probable impact of genomics research. We also identify critical research areas to "bridge the application gap" between QTL identification and applied breeding that need to be addressed to realize the full potential of MAS, and propose ideas and guidelines for establishing rice molecular breeding labs in the postgenome sequence era to integrate molecular breeding within the context of overall rice breeding and research programs.
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Affiliation(s)
- Bert C. Y. Collard
- Hermitage Research Station, Queensland Department of Primary Industries & Fisheries, 604 Yangan Road, Warwick, Queensland 4370, Australia
| | - Casiana M. Vera Cruz
- International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines
- *Casiana M. Vera Cruz:
| | - Kenneth L. McNally
- International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines
| | - Parminder S. Virk
- International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines
| | - David J. Mackill
- International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines
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Abstract
One hundred and twenty-two AFLP markers were mapped using an IR64 x Azucena rice doubled-haploid (DH) population. The distribution of these mapped markers was monitored across a set of 48 diverse landraces of rice. Strong statistical associations were observed between 960 of the 7381 possible pairs of markers across the diverse material. These 960 strongly associated pairs of markers mapped to the same chromosomes in only 111 cases. The remaining 849 pairs were the result of association between markers found on different chromosomes. More than 21% of these genetically unlinked but strongly associated markers are not randomly distributed across the genome but instead occupy blocks of DNA on different rice chromosomes. Amongst associated blocks, there has clearly been maintenance of combinations of marker alleles across very diverse germplasm. Analyses have also revealed that markers are found in association with performance for each of four quantitative traits in both the diverse landrace material and a DH mapping population. It is proposed that the present data provide strong evidence for the co-adaptation of geographically distinct landraces and that this has resulted over time in the maintenance of 'adaptive gene complexes' involving agronomically important quantitative traits.
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Affiliation(s)
- B V Ford-Lloyd
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK.
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Saier MH, Beatty JT, Goffeau A, Harley KT, Heijne WH, Huang SC, Jack DL, Jähn PS, Lew K, Liu J, Pao SS, Paulsen IT, Tseng TT, Virk PS. The major facilitator superfamily. J Mol Microbiol Biotechnol 1999; 1:257-79. [PMID: 10943556] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/17/2023] Open
Abstract
In 1998 we updated earlier descriptions of the largest family of secondary transport carriers found in living organisms, the major facilitator superfamily (MFS). Seventeen families of transport proteins were shown to comprise this superfamily. We here report expansion of the MFS to include 29 established families as well as five probable families. Structural, functional, and mechanistic features of the constituent permeases are described, and each newly identified family is shown to exhibit specificity for a single class of substrates. Phylogenetic analyses define the evolutionary relationships of the members of each family to each other, and multiple alignments allow definition of family-specific signature sequences as well as all well-conserved sequence motifs. The work described serves to update previous publications and allows extrapolation of structural, functional and mechanistic information obtained with any one member of the superfamily to other members with limitations determined by the degrees of sequence divergence.
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Affiliation(s)
- M H Saier
- Department of Biology, University of California at San Diego, La Jolla 92093-0116, USA.
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Virk PS, Ford-lloyd BV, Newbury HJ. Mapping AFLP markers associated with subspecific differentiation of Oryza sativa (rice) and an investigation of segregation distortion. Heredity (Edinb) 1998. [DOI: 10.1046/j.1365-2540.1998.00441.x] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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Virk PS, Ford-Lloyd BV, Jackson MT, Pooni HS, Clemeno TP, Newbury HJ. Predicting quantitative variation within rice germplasm using molecular markers. Heredity (Edinb) 1996. [DOI: 10.1038/hdy.1996.43] [Citation(s) in RCA: 91] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
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Virk PS, Newbury HJ, Jackson MT, Ford-Lloyd BV. The identification of duplicate accessions within a rice germplasm collection using RAPD analysis. Theor Appl Genet 1995; 90:1049-55. [PMID: 24173061 DOI: 10.1007/bf00222920] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/1994] [Accepted: 12/08/1994] [Indexed: 05/08/2023]
Abstract
A set of accessions of Oryza sativa from the International Rice Research Institute (Philippines) that included known and suspected duplicates as well as closely related germplasm has been subjected to RAPD analysis. The number of primers, the number of polymorphic bands and the total number of bands were determined that will allow the accurate discrimination of these categories of accessions, including the identification of true and suspected duplicates. Two procedures have been described that could be employed on a more general basis for identifying duplicates in genetic resources collections, and further discussion on the values of such activities is presented.
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Affiliation(s)
- P S Virk
- School of Biological Sciences, University of Birmingham, B15 2TT, Edgbaston, Birmingham, UK
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Abstract
As part of the development of a molecular toolkit for the study of diversity within large plant germplasm collections, RAPD technology has been applied to accessions of rice (Oryza sativa) obtained from the major world collection held at IRRI (the International Rice Research Institute) which supplies germplasm to breeders. Methods for the speedy extraction of DNA representative of a rice accession, its amplification by PCR to reveal reproducible products, and the analysis of the banding data using numerical techniques have been established. The biological meaningfulness of RAPD data has also been demonstrated by reference to previous work on classification and crossability.
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Affiliation(s)
- P S Virk
- School of Biological Sciences, University of Birmingham, U.K
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Pooni HS, Virk PS, Coombs DT, Chowdhury MK. The genetical basis of hybrid vigour in a highly heterotic cross of Nicotiana tabacum. Theor Appl Genet 1994; 89:1027-1031. [PMID: 24178120 DOI: 10.1007/bf00224534] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/1994] [Accepted: 07/28/1994] [Indexed: 06/02/2023]
Abstract
The genetical control of F1 heterosis, observed in a cross of desirable Nicotiana tabacum varieties, was investigated by analysing the data of the basic generations, triple test cross-families and random samples of doubled haploids (DH) and single-seed descent (SSD) lines. Analyses of the first-degree statistics revealed a complex control underlying the genetic variation, including the presence of epistasis, linkage, maternal effects and their interactions, in addition to the additive and dominance effects of the genes segregating in the cross. These analyses identified gene dispersion, directional dominance, and duplicate epistasis, as the main causes of heterosis. The triple test-cross analysis also confirmed the presence of non-allelic interactions and indicated that the dominance ratio, although inflated by epistasis, is consistently partial for all the traits. The extent of transgression in the recombinant inbred lines finally established unequivocally that, as in numerous other crosses, gene dispersion and unidirectional, but partial, dominance are the true causes of heterosis in this cross too.
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Affiliation(s)
- H S Pooni
- School of Biological Sciences, The University of Birmingham, B15 2TT, Birmingham, England, UK
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Virk DS, Virk PS, Mangat BK, Harinarayana G. Weighted regression analysis for comparing varietal adaptation. Theor Appl Genet 1991; 81:559-561. [PMID: 24221324 DOI: 10.1007/bf00219449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/1990] [Accepted: 10/30/1990] [Indexed: 06/02/2023]
Abstract
The normally used joint linear regression analysis (OLS) is not appropriate for comparing estimates of stability parameters of varieties when the error variances of site means are heterogeneous. Weighted regression analysis (WLS), in these situations, yields more precise estimates of stability parameters. A comparison of the two analytical methods using the grain yield (kg ha(-1)) data of 12 varieties and one hybrid of pearl millet [Pennisetum typhoides (Burm.) S. & H.], tested at 26 sites in India, revealed that the weighted regression analysis yields more efficient estimates of regression coefficients (b i ) than the ordinary regression analysis, and that the standard errors of b i values were reduced by up to 43%. The estimated b i differed with the two procedures. The number of varieties with b i ssignificantly deviating from unity was not only more (five varieties) with weighted regression analysis than the ordinary regression analysis (one variety), but the classification of varieties as possessing general or specific adaptation differed with the two procedures.
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Affiliation(s)
- D S Virk
- Department of Plant Breeding, Punjab Agricultural University, Ludhiana, India
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Pooni HS, Coombs DT, Virk PS, Jinks JL. Detection of epistasis and linkage of interacting genes in the presence of reciprocal differences. Heredity (Edinb) 1987. [DOI: 10.1038/hdy.1987.40] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
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Virk DS, Khehra AS, Virk PS, Dhillon BS. Comparative genetic analyses of metric traits using diallel and factorial mating designs in bread wheat. Theor Appl Genet 1985; 69:325-328. [PMID: 24253828 DOI: 10.1007/bf00662454] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/1983] [Accepted: 06/25/1984] [Indexed: 06/02/2023]
Abstract
For studying the inheritance of metric traits, diallel cross and factorial mating designs are commonly used. Since factorial mating design is less restrictive in crossing plans, the genetic information drawn from it was compared with that from a diallel cross. The comparison was made using graphical, genetic components and combining ability analyses for grain yield, grain weight and spike length in a field experiment of bread wheat (Triticum aestivum L.). Analyses were made on a nine parent diallel cross and a 4 ♀ × 5 ♂ factorial mating design which was sampled from the diallel cross. In general, there was a high degree of agreement between the results obtained from factorial mating design and diallel cross analyses showing thereby that the former provides almost equivalent genetic information to the latter.
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Affiliation(s)
- D S Virk
- Department of Plant Breeding, Punjab Agricultural University, Ludhiana-141 004, India
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