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Spindel J, Begum H, Akdemir D, Virk P, Collard B, Redoña E, Atlin G, Jannink JL, McCouch SR. Genomic selection and association mapping in rice (Oryza sativa): effect of trait genetic architecture, training population composition, marker number and statistical model on accuracy of rice genomic selection in elite, tropical rice breeding lines. PLoS Genet 2015; 11:e1004982. [PMID: 25689273 PMCID: PMC4334555 DOI: 10.1371/journal.pgen.1004982] [Citation(s) in RCA: 239] [Impact Index Per Article: 26.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2014] [Accepted: 01/05/2015] [Indexed: 12/22/2022] Open
Abstract
Genomic Selection (GS) is a new breeding method in which genome-wide markers are used to predict the breeding value of individuals in a breeding population. GS has been shown to improve breeding efficiency in dairy cattle and several crop plant species, and here we evaluate for the first time its efficacy for breeding inbred lines of rice. We performed a genome-wide association study (GWAS) in conjunction with five-fold GS cross-validation on a population of 363 elite breeding lines from the International Rice Research Institute's (IRRI) irrigated rice breeding program and herein report the GS results. The population was genotyped with 73,147 markers using genotyping-by-sequencing. The training population, statistical method used to build the GS model, number of markers, and trait were varied to determine their effect on prediction accuracy. For all three traits, genomic prediction models outperformed prediction based on pedigree records alone. Prediction accuracies ranged from 0.31 and 0.34 for grain yield and plant height to 0.63 for flowering time. Analyses using subsets of the full marker set suggest that using one marker every 0.2 cM is sufficient for genomic selection in this collection of rice breeding materials. RR-BLUP was the best performing statistical method for grain yield where no large effect QTL were detected by GWAS, while for flowering time, where a single very large effect QTL was detected, the non-GS multiple linear regression method outperformed GS models. For plant height, in which four mid-sized QTL were identified by GWAS, random forest produced the most consistently accurate GS models. Our results suggest that GS, informed by GWAS interpretations of genetic architecture and population structure, could become an effective tool for increasing the efficiency of rice breeding as the costs of genotyping continue to decline.
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Affiliation(s)
- Jennifer Spindel
- Department of Plant Breeding and Genetics, Cornell University, Ithaca, New York, United States of America
| | - Hasina Begum
- International Rice Research Institute, Los Baños, Philippines
| | - Deniz Akdemir
- Department of Plant Breeding and Genetics, Cornell University, Ithaca, New York, United States of America
| | - Parminder Virk
- International Center for Tropical Agriculture, Cali, Colombia
| | | | | | - Gary Atlin
- Bill & Melinda Gates Foundation, Seattle, Washington, United States of America
| | - Jean-Luc Jannink
- Department of Plant Breeding and Genetics, Cornell University, Ithaca, New York, United States of America
- US Department of Agriculture—Agricultural Research Service (USDA-ARS), Ithaca, New York, United States of America
| | - Susan R. McCouch
- Department of Plant Breeding and Genetics, Cornell University, Ithaca, New York, United States of America
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Spindel J, Begum H, Akdemir D, Virk P, Collard B, Redoña E, Atlin G, Jannink JL, McCouch SR. Genomic selection and association mapping in rice (Oryza sativa): effect of trait genetic architecture, training population composition, marker number and statistical model on accuracy of rice genomic selection in elite, tropical rice breeding lines. PLoS Genet 2015. [PMID: 25689273 DOI: 10.5061/dryad.7369p] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/26/2023] Open
Abstract
Genomic Selection (GS) is a new breeding method in which genome-wide markers are used to predict the breeding value of individuals in a breeding population. GS has been shown to improve breeding efficiency in dairy cattle and several crop plant species, and here we evaluate for the first time its efficacy for breeding inbred lines of rice. We performed a genome-wide association study (GWAS) in conjunction with five-fold GS cross-validation on a population of 363 elite breeding lines from the International Rice Research Institute's (IRRI) irrigated rice breeding program and herein report the GS results. The population was genotyped with 73,147 markers using genotyping-by-sequencing. The training population, statistical method used to build the GS model, number of markers, and trait were varied to determine their effect on prediction accuracy. For all three traits, genomic prediction models outperformed prediction based on pedigree records alone. Prediction accuracies ranged from 0.31 and 0.34 for grain yield and plant height to 0.63 for flowering time. Analyses using subsets of the full marker set suggest that using one marker every 0.2 cM is sufficient for genomic selection in this collection of rice breeding materials. RR-BLUP was the best performing statistical method for grain yield where no large effect QTL were detected by GWAS, while for flowering time, where a single very large effect QTL was detected, the non-GS multiple linear regression method outperformed GS models. For plant height, in which four mid-sized QTL were identified by GWAS, random forest produced the most consistently accurate GS models. Our results suggest that GS, informed by GWAS interpretations of genetic architecture and population structure, could become an effective tool for increasing the efficiency of rice breeding as the costs of genotyping continue to decline.
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Affiliation(s)
- Jennifer Spindel
- Department of Plant Breeding and Genetics, Cornell University, Ithaca, New York, United States of America
| | - Hasina Begum
- International Rice Research Institute, Los Baños, Philippines
| | - Deniz Akdemir
- Department of Plant Breeding and Genetics, Cornell University, Ithaca, New York, United States of America
| | - Parminder Virk
- International Center for Tropical Agriculture, Cali, Colombia
| | | | | | - Gary Atlin
- Bill & Melinda Gates Foundation, Seattle, Washington, United States of America
| | - Jean-Luc Jannink
- Department of Plant Breeding and Genetics, Cornell University, Ithaca, New York, United States of America; US Department of Agriculture-Agricultural Research Service (USDA-ARS), Ithaca, New York, United States of America
| | - Susan R McCouch
- Department of Plant Breeding and Genetics, Cornell University, Ithaca, New York, United States of America
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Arbelaez JD, Moreno LT, Singh N, Tung CW, Maron LG, Ospina Y, Martinez CP, Grenier C, Lorieux M, McCouch S. Development and GBS-genotyping of introgression lines (ILs) using two wild species of rice, O. meridionalis and O. rufipogon, in a common recurrent parent, O. sativa cv. Curinga. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2015; 35:81. [PMID: 25705117 PMCID: PMC4328105 DOI: 10.1007/s11032-015-0276-7] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2014] [Accepted: 01/29/2015] [Indexed: 05/04/2023]
Abstract
Two populations of interspecific introgression lines (ILs) in a common recurrent parent were developed for use in pre-breeding and QTL mapping. The ILs were derived from crosses between cv Curinga, a tropical japonica upland cultivar, and two different wild donors, Oryza meridionalis Ng. accession (W2112) and Oryza rufipogon Griff. accession (IRGC 105491). The lines were genotyped using genotyping-by-sequencing (GBS) and SSRs. The 32 Curinga/O. meridionalis ILs contain 76.73 % of the donor genome in individual introgressed segments, and each line has an average of 94.9 % recurrent parent genome. The 48 Curinga/O. rufipogon ILs collectively contain 97.6 % of the donor genome with an average of 89.9 % recurrent parent genome per line. To confirm that these populations were segregating for traits of interest, they were phenotyped for pericarp color in the greenhouse and for four agronomic traits-days to flowering, plant height, number of tillers, and number of panicles-in an upland field environment. Seeds from these IL libraries and the accompanying GBS datasets are publicly available and represent valuable genetic resources for exploring the genetics and breeding potential of rice wild relatives.
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Affiliation(s)
- Juan D. Arbelaez
- Department of Plant Breeding and Genetics, Cornell University, 162 Emerson Hall, Ithaca, NY 14853-1901 USA
| | - Laura T. Moreno
- School of Botany, The University of Melbourne, Parkville, VIC 3010 Australia
| | - Namrata Singh
- Department of Plant Breeding and Genetics, Cornell University, 162 Emerson Hall, Ithaca, NY 14853-1901 USA
| | - Chih-Wei Tung
- Department of Agronomy, National Taiwan University, No. 1, Section 4, Roosevelt Road, Taipei, 106 Taiwan
| | - Lyza G. Maron
- Department of Plant Breeding and Genetics, Cornell University, 162 Emerson Hall, Ithaca, NY 14853-1901 USA
| | - Yolima Ospina
- Rice Program, International Center for Tropical Agriculture (CIAT), AA6713 Cali, Colombia
| | - César P. Martinez
- Rice Program, International Center for Tropical Agriculture (CIAT), AA6713 Cali, Colombia
| | | | - Mathias Lorieux
- DIADE Research Unit, Institut de Recherche Pour le Développement, 34394 Montpellier Cedex 5, France
- Rice Genetics and Genomics Laboratory, International Center for Tropical Agriculture (CIAT), AA6713 Cali, Colombia
| | - Susan McCouch
- Department of Plant Breeding and Genetics, Cornell University, 162 Emerson Hall, Ithaca, NY 14853-1901 USA
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Baldwin S, Revanna R, Pither-Joyce M, Shaw M, Wright K, Thomson S, Moya L, Lee R, Macknight R, McCallum J. Genetic analyses of bolting in bulb onion (Allium cepa L.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2014; 127:535-547. [PMID: 24247236 DOI: 10.1007/s00122-013-2232-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2013] [Accepted: 10/31/2013] [Indexed: 06/02/2023]
Abstract
We present the first evidence for a QTL conditioning an adaptive trait in bulb onion, and the first linkage and population genetics analyses of candidate genes involved in photoperiod and vernalization physiology. Economic production of bulb onion (Allium cepa L.) requires adaptation to photoperiod and temperature such that a bulb is formed in the first year and a flowering umbel in the second. 'Bolting', or premature flowering before bulb maturation, is an undesirable trait strongly selected against by breeders during adaptation of germplasm. To identify genome regions associated with adaptive traits we conducted linkage mapping and population genetic analyses of candidate genes, and QTL analysis of bolting using a low-density linkage map. We performed tagged amplicon sequencing of ten candidate genes, including the FT-like gene family, in eight diverse populations to identify polymorphisms and seek evidence of differentiation. Low nucleotide diversity and negative estimates of Tajima's D were observed for most genes, consistent with purifying selection. Significant population differentiation was observed only in AcFT2 and AcSOC1. Selective genotyping in a large 'Nasik Red × CUDH2150' F2 family revealed genome regions on chromosomes 1, 3 and 6 associated (LOD > 3) with bolting. Validation genotyping of two F2 families grown in two environments confirmed that a QTL on chromosome 1, which we designate AcBlt1, consistently conditions bolting susceptibility in this cross. The chromosome 3 region, which coincides with a functionally characterised acid invertase, was not associated with bolting in other environments, but showed significant association with bulb sucrose content in this and other mapping pedigrees. These putative QTL and candidate genes were placed on the onion map, enabling future comparative studies of adaptive traits.
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Affiliation(s)
- Samantha Baldwin
- New Zealand Institute for Plant and Food Research, Private Bag, 4704, Christchurch, New Zealand
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den Boer E, Zhang NW, Pelgrom K, Visser RGF, Niks RE, Jeuken MJW. Fine mapping quantitative resistances to downy mildew in lettuce revealed multiple sub-QTLs with plant stage dependent effects reducing or even promoting the infection. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2013; 126:2995-3007. [PMID: 24037018 DOI: 10.1007/s00122-013-2188-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2013] [Accepted: 08/29/2013] [Indexed: 06/02/2023]
Abstract
KEY MESSAGE Three regions with quantitative resistance to downy mildew of non-host and wild lettuce species, Lactuca saligna , disintegrate into seventeen sub-QTLs with plant-stage-dependent effects, reducing or even promoting the infection. Previous studies on the genetic dissection of the complete resistance of wild lettuce, Lactuca saligna, to downy mildew revealed 15 introgression regions that conferred plant stage dependent quantitative resistances (QTLs). Three backcross inbred lines (BILs), carrying an individual 30-50 cM long introgression segment from L. saligna in a cultivated lettuce, L. sativa, background, reduced infection by 60-70 % at young plant stage and by 30-50 % at adult plant stage in field situations. We studied these three quantitative resistances in order to narrow down their mapping interval and determine their number of loci, either single or multiple. We performed recombinant screenings and developed near isogenic lines (NILs) with smaller overlapping L. saligna introgressions (substitution mapping). In segregating introgression line populations, recombination was suppressed up to 17-fold compared to the original L. saligna × L. sativa F 2 population. Recombination suppression depended on the chromosome region and was stronger suppressed at the smallest introgression lengths. Disease evaluation of the NILs revealed that the resistance of all three BILs was not explained by a single locus but by multiple sub-QTLs. The 17 L. saligna-derived sub-QTLs had a smaller and plant stage dependent resistance effect, some segments reducing; others even promoting downy mildew infection. Implications for lettuce breeding are outlined.
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Affiliation(s)
- Erik den Boer
- Laboratory of Plant Breeding, Wageningen University, P.O.Box 386, 6700 AJ, Wageningen, The Netherlands
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Jacquemin J, Bhatia D, Singh K, Wing RA. The International Oryza Map Alignment Project: development of a genus-wide comparative genomics platform to help solve the 9 billion-people question. CURRENT OPINION IN PLANT BIOLOGY 2013; 16:147-56. [PMID: 23518283 DOI: 10.1016/j.pbi.2013.02.014] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2013] [Revised: 02/27/2013] [Accepted: 02/28/2013] [Indexed: 05/03/2023]
Abstract
The wild relatives of rice contain a virtually untapped reservoir of traits that can be used help drive the 21st century green revolution aimed at solving world food security issues by 2050. To better understand and exploit the 23 species of the Oryza genus the rice research community is developing foundational resources composed of: 1) reference genomes and transcriptomes for all 23 species; 2) advanced mapping populations for functional and breeding studies; and 3) in situ conservation sites for ecological, evolutionary and population genomics. To this end, 16 genome sequencing projects are currently underway, and all completed assemblies have been annotated; and several advanced mapping populations have been developed, and more will be generated, mapped, and phenotyped, to uncover useful alleles. As wild Oryza populations are threatened by human activity and climate change, we also discuss the urgent need for sustainable in situ conservation of the genus.
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Affiliation(s)
- Julie Jacquemin
- Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, AZ 85721, USA
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Ebana K, Shibaya T, Wu J, Matsubara K, Kanamori H, Yamane H, Yamanouchi U, Mizubayashi T, Kono I, Shomura A, Ito S, Ando T, Hori K, Matsumoto T, Yano M. Uncovering of major genetic factors generating naturally occurring variation in heading date among Asian rice cultivars. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2011; 122:1199-210. [PMID: 21229229 PMCID: PMC3057013 DOI: 10.1007/s00122-010-1524-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2010] [Accepted: 12/11/2010] [Indexed: 05/04/2023]
Abstract
To dissect the genetic factors controlling naturally occurring variation of heading date in Asian rice cultivars, we performed QTL analyses using F(2) populations derived from crosses between a japonica cultivar, Koshihikari, and each of 12 cultivars originating from various regions in Asia. These 12 diverse cultivars varied in heading date under natural field conditions in Tsukuba, Japan. Transgressive segregation was observed in 10 F(2) combinations. QTL analyses using multiple crosses revealed a comprehensive series of loci involved in natural variation in flowering time. One to four QTLs were detected in each cross combination, and some QTLs were shared among combinations. The chromosomal locations of these QTLs corresponded well with those detected in other studies. The allelic effects of the QTLs varied among the cross combinations. Sequence analysis of several previously cloned genes controlling heading date, including Hd1, Hd3a, Hd6, RFT1, and Ghd7, identified several functional polymorphisms, indicating that allelic variation at these loci probably contributes to variation in heading date. Taken together, the QTL and sequencing results indicate that a large portion of the phenotypic variation in heading date in Asian rice cultivars could be generated by combinations of different alleles (possibly both loss- and gain-of-function) of the QTLs detected in this study.
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Affiliation(s)
- Kaworu Ebana
- QTL Genomics Research Center, National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602 Japan
| | - Taeko Shibaya
- QTL Genomics Research Center, National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602 Japan
| | - Jianzhong Wu
- Plant Genome Research Unit, National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602 Japan
| | - Kazuki Matsubara
- QTL Genomics Research Center, National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602 Japan
- Present Address: National Institute of Crop Science, 2-1-18 Kannondai, Tsukuba, Ibaraki 305-8518 Japan
| | - Hiroyuki Kanamori
- Institute of Society for Techno-innovation of Agriculture, Forestry and Fisheries, Tsukuba, Ibaraki 305-0854 Japan
| | - Hiroko Yamane
- Institute of Society for Techno-innovation of Agriculture, Forestry and Fisheries, Tsukuba, Ibaraki 305-0854 Japan
| | - Utako Yamanouchi
- QTL Genomics Research Center, National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602 Japan
| | - Tatsumi Mizubayashi
- Institute of Society for Techno-innovation of Agriculture, Forestry and Fisheries, Tsukuba, Ibaraki 305-0854 Japan
| | - Izumi Kono
- Institute of Society for Techno-innovation of Agriculture, Forestry and Fisheries, Tsukuba, Ibaraki 305-0854 Japan
| | - Ayahiko Shomura
- Institute of Society for Techno-innovation of Agriculture, Forestry and Fisheries, Tsukuba, Ibaraki 305-0854 Japan
| | - Sachie Ito
- Institute of Society for Techno-innovation of Agriculture, Forestry and Fisheries, Tsukuba, Ibaraki 305-0854 Japan
| | - Tsuyu Ando
- Institute of Society for Techno-innovation of Agriculture, Forestry and Fisheries, Tsukuba, Ibaraki 305-0854 Japan
| | - Kiyosumi Hori
- QTL Genomics Research Center, National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602 Japan
| | - Takashi Matsumoto
- Plant Genome Research Unit, National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602 Japan
| | - Masahiro Yano
- QTL Genomics Research Center, National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602 Japan
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Yasui H, Yamagata Y, Yoshimura A. Development of chromosome segment substitution lines derived from indica rice donor cultivars DV85 and ARC10313 in the genetic background of japonica cultivar Taichung 65. BREEDING SCIENCE 2010; 60:620-628. [PMID: 0 DOI: 10.1270/jsbbs.60.620] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Affiliation(s)
- Hideshi Yasui
- Plant Breeding Laboratory, Faculty of Agriculture, Graduate School, Kyushu University
| | - Yoshiyuki Yamagata
- Plant Breeding Laboratory, Faculty of Agriculture, Graduate School, Kyushu University
| | - Atsushi Yoshimura
- Plant Breeding Laboratory, Faculty of Agriculture, Graduate School, Kyushu University
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