51
|
Vinoth A, Ravindhran R. Biofortification in Millets: A Sustainable Approach for Nutritional Security. FRONTIERS IN PLANT SCIENCE 2017; 8:29. [PMID: 28167953 PMCID: PMC5253353 DOI: 10.3389/fpls.2017.00029] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2016] [Accepted: 01/05/2017] [Indexed: 05/04/2023]
Abstract
Nutritional insecurity is a major threat to the world's population that is highly dependent on cereals-based diet, deficient in micronutrients. Next to cereals, millets are the primary sources of energy in the semi-arid tropics and drought-prone regions of Asia and Africa. Millets are nutritionally superior as their grains contain high amount of proteins, essential amino acids, minerals, and vitamins. Biofortification of staple crops is proved to be an economically feasible approach to combat micronutrient malnutrition. HarvestPlus group realized the importance of millet biofortification and released conventionally bred high iron pearl millet in India to tackle iron deficiency. Molecular basis of waxy starch has been identified in foxtail millet, proso millet, and barnyard millet to facilitate their use in infant foods. With close genetic-relatedness to cereals, comparative genomics has helped in deciphering quantitative trait loci and genes linked to protein quality in finger millet. Recently, transgenic expression of zinc transporters resulted in the development of high grain zinc while transcriptomics revealed various calcium sensor genes involved in uptake, translocation, and accumulation of calcium in finger millet. Biofortification in millets is still limited by the presence of antinutrients like phytic acid, polyphenols, and tannins. RNA interference and genome editing tools [zinc finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs), and clustered regularly interspaced short palindromic repeats (CRISPR)] needs to be employed to reduce these antinutrients. In this review paper, we discuss the strategies to accelerate biofortification in millets by summarizing the opportunities and challenges to increase the bioavailability of macro and micronutrients.
Collapse
Affiliation(s)
- A Vinoth
- T. A. Lourdusamy Unit for Plant Tissue Culture and Molecular Biology, Department of Plant Biology and Biotechnology, Loyola College Chennai, India
| | - R Ravindhran
- T. A. Lourdusamy Unit for Plant Tissue Culture and Molecular Biology, Department of Plant Biology and Biotechnology, Loyola College Chennai, India
| |
Collapse
|
52
|
Butardo VM, Anacleto R, Parween S, Samson I, de Guzman K, Alhambra CM, Misra G, Sreenivasulu N. Systems Genetics Identifies a Novel Regulatory Domain of Amylose Synthesis. PLANT PHYSIOLOGY 2017; 173:887-906. [PMID: 27881726 PMCID: PMC5210722 DOI: 10.1104/pp.16.01248] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2016] [Accepted: 11/21/2016] [Indexed: 05/20/2023]
Abstract
A deeper understanding of the regulation of starch biosynthesis in rice (Oryza sativa) endosperm is crucial in tailoring digestibility without sacrificing grain quality. In this study, significant association peaks on chromosomes 6 and 7 were identified through a genomewide association study (GWAS) of debranched starch structure from grains of a 320 indica rice diversity panel using genotyping data from the high-density rice array. A systems genetics approach that interrelates starch structure data from GWAS to functional pathways from a gene regulatory network identified known genes with high correlation to the proportion of amylose and amylopectin. An SNP in the promoter region of Granule Bound Starch Synthase I was identified along with seven other SNPs to form haplotypes that discriminate samples into different phenotypic ranges of amylose. A GWAS peak on chromosome 7 between LOC_Os07g11020 and LOC_Os07g11520 indexed by a nonsynonymous SNP mutation on exon 5 of a bHLH transcription factor was found to elevate the proportion of amylose at the expense of reduced short-chain amylopectin. Linking starch structure with starch digestibility by determining the kinetics of cooked grain amylolysis of selected haplotypes revealed strong association of starch structure with estimated digestibility kinetics. Combining all results from grain quality genomics, systems genetics, and digestibility phenotyping, we propose target haplotypes for fine-tuning starch structure in rice through marker-assisted breeding that can be used to alter the digestibility of rice grain, thus offering rice consumers a new diet-based intervention to mitigate the impact of nutrition-related noncommunicable diseases.
Collapse
Affiliation(s)
- Vito M Butardo
- Grain Quality and Nutrition Center, Plant Breeding Division, International Rice Research Institute, Los Baños, Laguna, Philippines
| | - Roslen Anacleto
- Grain Quality and Nutrition Center, Plant Breeding Division, International Rice Research Institute, Los Baños, Laguna, Philippines
| | - Sabiha Parween
- Grain Quality and Nutrition Center, Plant Breeding Division, International Rice Research Institute, Los Baños, Laguna, Philippines
| | - Irene Samson
- Grain Quality and Nutrition Center, Plant Breeding Division, International Rice Research Institute, Los Baños, Laguna, Philippines
| | - Krishna de Guzman
- Grain Quality and Nutrition Center, Plant Breeding Division, International Rice Research Institute, Los Baños, Laguna, Philippines
| | - Crisline Mae Alhambra
- Grain Quality and Nutrition Center, Plant Breeding Division, International Rice Research Institute, Los Baños, Laguna, Philippines
| | - Gopal Misra
- Grain Quality and Nutrition Center, Plant Breeding Division, International Rice Research Institute, Los Baños, Laguna, Philippines
| | - Nese Sreenivasulu
- Grain Quality and Nutrition Center, Plant Breeding Division, International Rice Research Institute, Los Baños, Laguna, Philippines
| |
Collapse
|
53
|
Lu Q, Niu X, Zhang M, Wang C, Xu Q, Feng Y, Yang Y, Wang S, Yuan X, Yu H, Wang Y, Chen X, Liang X, Wei X. Genome-Wide Association Study of Seed Dormancy and the Genomic Consequences of Improvement Footprints in Rice ( Oryza sativa L.). FRONTIERS IN PLANT SCIENCE 2017; 8:2213. [PMID: 29354150 PMCID: PMC5760558 DOI: 10.3389/fpls.2017.02213] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Accepted: 12/18/2017] [Indexed: 05/03/2023]
Abstract
Seed dormancy is an important agronomic trait affecting grain yield and quality because of pre-harvest germination and is influenced by both environmental and genetic factors. However, our knowledge of the factors controlling seed dormancy remains limited. To better reveal the molecular mechanism underlying this trait, a genome-wide association study was conducted in an indica-only population consisting of 453 accessions genotyped using 5,291 SNPs. Nine known and new significant SNPs were identified on eight chromosomes. These lead SNPs explained 34.9% of the phenotypic variation, and four of them were designed as dCAPS markers in the hope of accelerating molecular breeding. Moreover, a total of 212 candidate genes was predicted and eight candidate genes showed plant tissue-specific expression in expression profile data from different public bioinformatics databases. In particular, LOC_Os03g10110, which had a maize homolog involved in embryo development, was identified as a candidate regulator for further biological function investigations. Additionally, a polymorphism information content ratio method was used to screen improvement footprints and 27 selective sweeps were identified, most of which harbored domestication-related genes. Further studies suggested that three significant SNPs were adjacent to the candidate selection signals, supporting the accuracy of our genome-wide association study (GWAS) results. These findings show that genome-wide screening for selective sweeps can be used to identify new improvement-related DNA regions, although the phenotypes are unknown. This study enhances our knowledge of the genetic variation in seed dormancy, and the new dormancy-associated SNPs will provide real benefits in molecular breeding.
Collapse
Affiliation(s)
- Qing Lu
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
- Crops Research Institute, Guangdong Academy of Agricultural Sciences, South China Peanut Sub-Center of National Center of Oilseed Crops Improvement and Guangdong Provincial Key Laboratory of Crop Genetic Improvement, Guangzhou, China
| | - Xiaojun Niu
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Mengchen Zhang
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Caihong Wang
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Qun Xu
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Yue Feng
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Yaolong Yang
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Shan Wang
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Xiaoping Yuan
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Hanyong Yu
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Yiping Wang
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Xiaoping Chen
- Crops Research Institute, Guangdong Academy of Agricultural Sciences, South China Peanut Sub-Center of National Center of Oilseed Crops Improvement and Guangdong Provincial Key Laboratory of Crop Genetic Improvement, Guangzhou, China
| | - Xuanqiang Liang
- Crops Research Institute, Guangdong Academy of Agricultural Sciences, South China Peanut Sub-Center of National Center of Oilseed Crops Improvement and Guangdong Provincial Key Laboratory of Crop Genetic Improvement, Guangzhou, China
| | - Xinghua Wei
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
- *Correspondence: Xinghua Wei
| |
Collapse
|
54
|
Seol YJ, Won SY, Shin Y, Lee JY, Chun JS, Kim YK, Kim CK. A Multilayered Screening Method for the Identification of Regulatory Genes in Rice by Agronomic Traits. Evol Bioinform Online 2016; 12:253-262. [PMID: 27840573 PMCID: PMC5094579 DOI: 10.4137/ebo.s40622] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Revised: 09/22/2016] [Accepted: 09/30/2016] [Indexed: 12/22/2022] Open
Abstract
We developed a multilayered screening method that integrates both genome and transcriptome data to effectively identify regulatory genes in rice (Oryza sativa). We tested our method using eight rice accessions that differed in three important nutritional and agricultural traits, anthocyanin biosynthesis, amylose content, and heading date. In the genome resequencing of eight rice accessions with 24 RNA sequencing experiments, 98% of the preprocessed reads could be uniquely mapped to the reference genome, resulting in the identification of 42,699 unique transcripts. Comparison between black and white rice cultivars showed evidence of intensive selective sweeps in chromosomes 3, 10, and 12. A total of 131 genes were differentially expressed among the black rice cultivars and found to be associated with three Gene Ontology terms (secondary metabolic process, biosynthetic process, and response to stimulus). We identified nonsynonymous Single Nucleotide Polymorphism (SNP) that likely play an important role in determining the agronomic traits differences, two upregulated and three downregulated genes in the black cultivars, and two downregulated genes in the white cultivars. The three agronomic traits were clearly grouped together by the developmental stages, regardless of any other traits, suggesting that the developmental stage is the most important factor that triggers global changes in gene expression. Interestingly, glutinous and nonglutinous black rice cultivars were distinguished from one another by different heading dates.
Collapse
Affiliation(s)
- Young-Joo Seol
- Genomics Division, National Institute of Agricultural Sciences, Jeonju, Republic of Korea
| | - So Youn Won
- Genomics Division, National Institute of Agricultural Sciences, Jeonju, Republic of Korea
| | - Younhee Shin
- Codes Division, Insilicogen Inc., Suwon, Gyeonggi-do, Korea
| | - Jong-Yeol Lee
- Functional Biomaterial Division, National Academy of Agricultural Science, Jeonju, Korea
| | - Jong-Sik Chun
- School of Biological Sciences and Bioinformatics Institute, Seoul National University, Seoul, Korea
| | - Yong-Kab Kim
- School of Electrical Information Communication Engineering, Wonkwang University, Iksan, Korea
| | - Chang-Kug Kim
- Genomics Division, National Institute of Agricultural Sciences, Jeonju, Republic of Korea
| |
Collapse
|
55
|
Muto C, Ishikawa R, Olsen KM, Kawano K, Bounphanousay C, Matoh T, Sato YI. Genetic diversity of the wx flanking region in rice landraces in northern Laos. BREEDING SCIENCE 2016; 66:580-590. [PMID: 27795683 PMCID: PMC5010311 DOI: 10.1270/jsbbs.16032] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2016] [Accepted: 05/11/2016] [Indexed: 05/07/2023]
Abstract
A glutinous texture of endosperm is one of the important traits of rice (Oyza sativa L.). Northern Laos is known as a center of glutinous rice diversity. We genotyped INDEL, SSR and SNP markers in a sample of 297 rice landraces collected in northern Laos. These glutinous varieties were confirmed to share a loss-of-function mutation in Granule bound starch synthase I (Wx). INDEL markers revealed a high frequency of recombinant genotypes between indica and japonica. Principal component analysis using SSR genotypes of Wx flanking region revealed that glutinous indica landraces were scattered between non-glutinous indica and glutinous-japonica types. High ratios of heterozygosity were found especially in glutinous indica. Haplotype analysis using SNP markers around Wx locus revealed that glutinous indica landraces would have a few chromosome segments of glutinous japonica. Frequent recombinations were confirmed outside of this region in glutinous indica. This intricate genetic structure of landraces suggested that glutinous indica landraces in Laos were generated through repeated natural crossing with glutinous-japonica landraces and severe selection by local farmers.
Collapse
Affiliation(s)
- Chiaki Muto
- Genetic Resources Center, National Agriculture and Food Research Organization,
Tsukuba, Ibaraki 305-8602,
Japan
| | - Ryuji Ishikawa
- Faculty of Agriculture and Life Science, Hirosaki University,
Hirosaki, Aomori 036-8560,
Japan
- Corresponding author (e-mail: )
| | - Kenneth M. Olsen
- Biology Department, Washington University,
St. Louis 63130-4899,
USA
| | - Kazuaki Kawano
- Institute of Southern Cultural Folklore,
Kirishima, Kagoshima 899-4201,
Japan
| | - Chay Bounphanousay
- Agricultural Research Centre, National Agriculture and Forestry Research Institute,
Nongviengkham, Vientiane 7170,
Lao P.D.R
| | - Toru Matoh
- Graduate School of Agriculture, Kyoto University,
Kyoto 606-8502,
Japan
| | - Yo-Ichiro Sato
- National Institutes for the Humanities,
Minato-ku, Tokyo 105-0001,
Japan
| |
Collapse
|
56
|
Xu F, Bao J, He Q, Park YJ. Genome-wide association study of eating and cooking qualities in different subpopulations of rice (Oryza sativa L.). BMC Genomics 2016; 17:663. [PMID: 27544770 PMCID: PMC4992570 DOI: 10.1186/s12864-016-3000-z] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2016] [Accepted: 08/05/2016] [Indexed: 11/21/2022] Open
Abstract
Background Starch and protein are two major components of polished rice, and the amylose and protein contents affect eating and cooking qualities (ECQs). In the present study, genome-wide association study with high-quality re-sequencing data was performed for 10 ECQs in a panel of 227 non-glutinous rice accessions and four derived panels. Results Population structure accounted for high phenotypic variation in three routine panels and had minor effects on subspecies-based panels. Using the mixed linear model method based on the P + K model, we detected 29, 24, 16, 17, and 29 loci that were significant for ECQ parameters in each of the five panels. Some of these loci were close to starch synthesis-related genes. Two quantitative trait loci (QTLs) (chr.9: 15417525 ~ 15474876; 17538294 ~ 18443016) for several starch paste viscosity properties detected in four panels were close to the isoamylase 3 gene, one QTL (chr.1: 30627943 ~ 31668474) for consistency detected in three panels was close to the starch synthase IV-1 gene. The QTL (chr.7: 1118122 ~ 1967247) for breakdown (BD), detected in the whole panel and japonica panel, and one QTL (chr.7: 25312126 ~ 26540950) for BD and setback (SB), detected in the whole panel and indica panel, may be specific gene alleles in japonica or indica panels. One previously detected QTL (chr.11: 22240707 ~ 22563596) for protein content and one new QTL (chr.5: 7756614 ~ 8042699) for many ECQ traits detected in more than two panels, may represent valuable targets for future cloning of the underlying genes. Conclusions This study detected minor-effect QTLs affecting ECQs, and may increase our understanding of the genetic differences regulating the formation of ECQ between indica and japonica varieties. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-3000-z) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Feifei Xu
- Department of Plant Resources, College of Industrial Science, Kongju National University, Yesan, 32439, Republic of Korea.,Institute of Nuclear Agricultural Sciences, College of Agriculture and Biotechnology, Zhejiang University, Huajiachi Campus, Hangzhou, 310029, China
| | - Jinsong Bao
- Department of Plant Resources, College of Industrial Science, Kongju National University, Yesan, 32439, Republic of Korea.,Institute of Nuclear Agricultural Sciences, College of Agriculture and Biotechnology, Zhejiang University, Huajiachi Campus, Hangzhou, 310029, China
| | - Qiang He
- Department of Plant Resources, College of Industrial Science, Kongju National University, Yesan, 32439, Republic of Korea
| | - Yong-Jin Park
- Department of Plant Resources, College of Industrial Science, Kongju National University, Yesan, 32439, Republic of Korea. .,Center for crop genetic resource and breeding (CCGRB), Kongju National University, Cheonan, 31080, Republic of Korea.
| |
Collapse
|
57
|
Dang X, Liu E, Liang Y, Liu Q, Breria CM, Hong D. QTL Detection and Elite Alleles Mining for Stigma Traits in Oryza sativa by Association Mapping. FRONTIERS IN PLANT SCIENCE 2016; 7:1188. [PMID: 27555858 PMCID: PMC4977947 DOI: 10.3389/fpls.2016.01188] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2016] [Accepted: 07/22/2016] [Indexed: 05/20/2023]
Abstract
Stigma traits are very important for hybrid seed production in Oryza sativa, which is a self-pollinated crop; however, the genetic mechanism controlling the traits is poorly understood. In this study, we investigated the phenotypic data of 227 accessions across 2 years and assessed their genotypic variation with 249 simple sequence repeat (SSR) markers. By combining phenotypic and genotypic data, a genome-wide association (GWA) map was generated. Large phenotypic variations in stigma length (STL), stigma brush-shaped part length (SBPL) and stigma non-brush-shaped part length (SNBPL) were found. Significant positive correlations were identified among stigma traits. In total, 2072 alleles were detected among 227 accessions, with an average of 8.3 alleles per SSR locus. GWA mapping detected 6 quantitative trait loci (QTLs) for the STL, 2 QTLs for the SBPL and 7 QTLs for the SNBPL. Eleven, 5, and 12 elite alleles were found for the STL, SBPL, and SNBPL, respectively. Optimal cross designs were predicted for improving the target traits. The detected genetic variation in stigma traits and QTLs provides helpful information for cloning candidate STL genes and breeding rice cultivars with longer STLs in the future.
Collapse
Affiliation(s)
- Xiaojing Dang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Agriculture, Nanjing Agricultural University Nanjing, China
| | - Erbao Liu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Agriculture, Nanjing Agricultural University Nanjing, China
| | - Yinfeng Liang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Agriculture, Nanjing Agricultural University Nanjing, China
| | - Qiangming Liu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Agriculture, Nanjing Agricultural UniversityNanjing, China; Rice Research Institute, Chongqing Academy of Agricultural SciencesChongqing, China
| | - Caleb M Breria
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Agriculture, Nanjing Agricultural University Nanjing, China
| | - Delin Hong
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Agriculture, Nanjing Agricultural University Nanjing, China
| |
Collapse
|
58
|
Kumagai M, Kanehara M, Shoda S, Fujita S, Onuki S, Ueda S, Wang L. Rice Varieties in Archaic East Asia: Reduction of Its Diversity from Past to Present Times. Mol Biol Evol 2016; 33:2496-505. [PMID: 27461246 DOI: 10.1093/molbev/msw142] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
The Asian cultivated rice, Oryza sativa, is one of the most important crops feeding more than a third of global population. In spite of the studies for several decades, the origin and domestication history of rice varietal groups, japonica and indica, have not been fully unveiled. Genetic information of ancient rice remains is essential for direct and exclusive insight into the domestication history of rice. We performed ancient DNA analysis of 950- to 2,800-year-old rice remains excavated from Japan and Korea. We found the presence of both japonica- and indica-type varieties in the Yayoi period and the middle ages of Japan and the middle part of Korea Peninsula 2,000 years ago. It is popularly considered that japonica has been exclusively cultivated in northern part of East Asia including Japan and Korea. Our result disclosed unexpectedly wide diversity of rice varieties in archaic East Asia. The present results from ancient rice DNA reveal an exclusive insight for the domestication history of rice which is not provided as far as contemporary rice.
Collapse
Affiliation(s)
- Masahiko Kumagai
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Masaaki Kanehara
- Department of Teacher Training and School Education, Nara University of Education, Nara, Japan
| | - Shin'ya Shoda
- Nara National Research Institute for Cultural Properties, Nara, Japan
| | | | - Shizuo Onuki
- Department of Archaeology, Graduate School of Humanities and Sociology, The University of Tokyo, Tokyo, Japan
| | - Shintaroh Ueda
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan School of Medicine, Hangzhou Normal University, Hangzhou, Zhejiang, China
| | - Li Wang
- School of Medicine, Hangzhou Normal University, Hangzhou, Zhejiang, China
| |
Collapse
|
59
|
Wang H, Xu X, Vieira FG, Xiao Y, Li Z, Wang J, Nielsen R, Chu C. The Power of Inbreeding: NGS-Based GWAS of Rice Reveals Convergent Evolution during Rice Domestication. MOLECULAR PLANT 2016; 9:975-85. [PMID: 27179918 DOI: 10.1016/j.molp.2016.04.018] [Citation(s) in RCA: 68] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2016] [Revised: 04/16/2016] [Accepted: 04/27/2016] [Indexed: 05/22/2023]
Abstract
Low-coverage whole-genome sequencing is an effective strategy for genome-wide association studies in humans, due to the availability of large reference panels for genotype imputation. However, it is unclear whether this strategy can be utilized in other species without reference panels. Using simulations, we show that this approach is even more relevant in inbred species such as rice (Oryza sativa L.), which are effectively haploid, allowing easy haplotype construction and imputation-based genotype calling, even without the availability of large reference panels. We sequenced 203 rice varieties with well-characterized phenotypes from the United States Department of Agriculture Rice Mini-Core Collection at an average depth of 1.5× and used the data for mapping three traits. For the first two traits, amylose content and seed length, our approach leads to direct identification of the previously identified causal SNPs in the major-effect loci. For the third trait, pericarp color, an important trait underwent selection during domestication, we identified a new major-effect locus. Although known loci can explain color variation in the varieties of two main subspecies of Asian domesticated rice, japonica and indica, the new locus identified is unique to another domesticated rice subgroup, aus, and together with existing loci, can fully explain the major variation in pericarp color in aus. Our discovery of a unique genetic basis of white pericarp in aus provides an example of convergent evolution during rice domestication and suggests that aus may have a domestication history independent of japonica and indica.
Collapse
Affiliation(s)
- Hongru Wang
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100101, China
| | - Xun Xu
- BGI-Shenzhen, Shenzhen 518083, China
| | | | - Yunhua Xiao
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100101, China
| | - Zhikang Li
- Institute of Crop Sciences/National Key Facilities for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, 12 South Zhong-Guan-Cun Street, Beijing 100081, China
| | - Jun Wang
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100101, China.
| | - Rasmus Nielsen
- Department of Integrative Biology, University of California, Berkeley, CA 94720 USA.
| | - Chengcai Chu
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China.
| |
Collapse
|
60
|
Pérez-Jaramillo JE, Mendes R, Raaijmakers JM. Impact of plant domestication on rhizosphere microbiome assembly and functions. PLANT MOLECULAR BIOLOGY 2016; 90:635-44. [PMID: 26085172 PMCID: PMC4819786 DOI: 10.1007/s11103-015-0337-7] [Citation(s) in RCA: 290] [Impact Index Per Article: 36.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Accepted: 06/04/2015] [Indexed: 05/18/2023]
Abstract
The rhizosphere microbiome is pivotal for plant health and growth, providing defence against pests and diseases, facilitating nutrient acquisition and helping plants to withstand abiotic stresses. Plants can actively recruit members of the soil microbial community for positive feedbacks, but the underlying mechanisms and plant traits that drive microbiome assembly and functions are largely unknown. Domestication of plant species has substantially contributed to human civilization, but also caused a strong decrease in the genetic diversity of modern crop cultivars that may have affected the ability of plants to establish beneficial associations with rhizosphere microbes. Here, we review how plants shape the rhizosphere microbiome and how domestication may have impacted rhizosphere microbiome assembly and functions via habitat expansion and via changes in crop management practices, root exudation, root architecture, and plant litter quality. We also propose a "back to the roots" framework that comprises the exploration of the microbiome of indigenous plants and their native habitats for the identification of plant and microbial traits with the ultimate goal to reinstate beneficial associations that may have been undermined during plant domestication.
Collapse
Affiliation(s)
- Juan E Pérez-Jaramillo
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), P.O. Box 50, 6708 PB, Wageningen, The Netherlands
- Sylvius Laboratories, Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE, Leiden, The Netherlands
| | - Rodrigo Mendes
- Laboratory of Environmental Microbiology, Brazilian Agricultural Research Corporation, Embrapa Environment, Rodovia SP 340 - km 127.5, Jaguariúna, 13820-000, Brazil
| | - Jos M Raaijmakers
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), P.O. Box 50, 6708 PB, Wageningen, The Netherlands.
- Sylvius Laboratories, Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE, Leiden, The Netherlands.
| |
Collapse
|
61
|
Zhang P, Zhong K, Shahid MQ, Tong H. Association Analysis in Rice: From Application to Utilization. FRONTIERS IN PLANT SCIENCE 2016; 7:1202. [PMID: 27582745 PMCID: PMC4987372 DOI: 10.3389/fpls.2016.01202] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2016] [Accepted: 07/28/2016] [Indexed: 05/03/2023]
Abstract
Association analysis based on linkage disequilibrium (LD) is an efficient way to dissect complex traits and to identify gene functions in rice. Although association analysis is an effective way to construct fine maps for quantitative traits, there are a few issues which need to be addressed. In this review, we will first summarize type, structure, and LD level of populations used for association analysis of rice, and then discuss the genotyping methods and statistical approaches used for association analysis in rice. Moreover, we will review current shortcomings and benefits of association analysis as well as specific types of future research to overcome these shortcomings. Furthermore, we will analyze the reasons for the underutilization of the results within association analysis in rice breeding.
Collapse
Affiliation(s)
- Peng Zhang
- State Key Laboratory of Rice Biology, China National Rice Research InstituteHangzhou, China
- *Correspondence: Peng Zhang
| | - Kaizhen Zhong
- State Key Laboratory of Rice Biology, China National Rice Research InstituteHangzhou, China
| | - Muhammad Qasim Shahid
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural UniversityGuangzhou, China
| | - Hanhua Tong
- State Key Laboratory of Rice Biology, China National Rice Research InstituteHangzhou, China
- Hanhua Tong
| |
Collapse
|
62
|
Sun L, Miao Z, Cai C, Zhang D, Zhao M, Wu Y, Zhang X, Swarm SA, Zhou L, Zhang ZJ, Nelson RL, Ma J. GmHs1-1, encoding a calcineurin-like protein, controls hard-seededness in soybean. Nat Genet 2015; 47:939-43. [PMID: 26098868 DOI: 10.1038/ng.3339] [Citation(s) in RCA: 66] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2015] [Accepted: 05/27/2015] [Indexed: 12/19/2022]
Abstract
Loss of seed-coat impermeability was essential in the domestication of many leguminous crops to promote the production of their highly nutritious seeds. Here we show that seed-coat impermeability in wild soybean is controlled by a single gene, GmHs1-1, which encodes a calcineurin-like metallophosphoesterase transmembrane protein. GmHs1-1 is primarily expressed in the Malpighian layer of the seed coat and is associated with calcium content. The transition from impermeability to permeability in domesticated soybean was caused by artificial selection of a point mutation in GmHs1-1. Interestingly, a number of soybean landraces evaded selection for permeability because of an alternative selection for seed-coat cracking that also enables seed imbibition. Despite the single origin of the mutant allele Gmhs1-1, the distribution pattern of allelic variants in the context of soybean population structure and the detected signature of genomic introgression between wild and cultivated soybeans suggest that Gmhs1-1 may have experienced reselection for seed-coat permeability.
Collapse
Affiliation(s)
- Lianjun Sun
- Department of Agronomy, Purdue University, West Lafayette, Indiana, USA
| | - Zhenyan Miao
- Department of Agronomy, Purdue University, West Lafayette, Indiana, USA
| | - Chunmei Cai
- College of Life Sciences, Qingdao Agricultural University, Qingdao, China
| | - Dajian Zhang
- Department of Agronomy, Purdue University, West Lafayette, Indiana, USA
| | - Meixia Zhao
- Department of Agronomy, Purdue University, West Lafayette, Indiana, USA
| | - Yanyan Wu
- College of Life Sciences, Qingdao Agricultural University, Qingdao, China
| | - Xueling Zhang
- College of Life Sciences, Qingdao Agricultural University, Qingdao, China
| | - Stephen A Swarm
- Department of Crop Sciences, University of Illinois, Urbana, Illinois, USA
| | - Liwen Zhou
- Plant Transformation Core Facility, Division of Plant Sciences, University of Missouri, Columbia, Missouri, USA
| | - Zhanyuan J Zhang
- Plant Transformation Core Facility, Division of Plant Sciences, University of Missouri, Columbia, Missouri, USA
| | - Randall L Nelson
- 1] Department of Crop Sciences, University of Illinois, Urbana, Illinois, USA. [2] Soybean/Maize Germplasm, Pathology, and Genetics Research Unit, US Department of Agriculture-Agricultural Research Service, Urbana, Illinois, USA
| | - Jianxin Ma
- 1] Department of Agronomy, Purdue University, West Lafayette, Indiana, USA. [2] College of Life Sciences, Qingdao Agricultural University, Qingdao, China
| |
Collapse
|
63
|
Sun L, Miao Z, Cai C, Zhang D, Zhao M, Wu Y, Zhang X, Swarm SA, Zhou L, Zhang ZJ, Nelson RL, Ma J. GmHs1-1, encoding a calcineurin-like protein, controls hard-seededness in soybean. Nat Genet 2015; 47:939-943. [PMID: 26098868 DOI: 10.1038/ng3339] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2015] [Accepted: 05/27/2015] [Indexed: 05/19/2023]
Abstract
Loss of seed-coat impermeability was essential in the domestication of many leguminous crops to promote the production of their highly nutritious seeds. Here we show that seed-coat impermeability in wild soybean is controlled by a single gene, GmHs1-1, which encodes a calcineurin-like metallophosphoesterase transmembrane protein. GmHs1-1 is primarily expressed in the Malpighian layer of the seed coat and is associated with calcium content. The transition from impermeability to permeability in domesticated soybean was caused by artificial selection of a point mutation in GmHs1-1. Interestingly, a number of soybean landraces evaded selection for permeability because of an alternative selection for seed-coat cracking that also enables seed imbibition. Despite the single origin of the mutant allele Gmhs1-1, the distribution pattern of allelic variants in the context of soybean population structure and the detected signature of genomic introgression between wild and cultivated soybeans suggest that Gmhs1-1 may have experienced reselection for seed-coat permeability.
Collapse
Affiliation(s)
- Lianjun Sun
- Department of Agronomy, Purdue University, West Lafayette, Indiana, USA
| | - Zhenyan Miao
- Department of Agronomy, Purdue University, West Lafayette, Indiana, USA
| | - Chunmei Cai
- College of Life Sciences, Qingdao Agricultural University, Qingdao, China
| | - Dajian Zhang
- Department of Agronomy, Purdue University, West Lafayette, Indiana, USA
| | - Meixia Zhao
- Department of Agronomy, Purdue University, West Lafayette, Indiana, USA
| | - Yanyan Wu
- College of Life Sciences, Qingdao Agricultural University, Qingdao, China
| | - Xueling Zhang
- College of Life Sciences, Qingdao Agricultural University, Qingdao, China
| | - Stephen A Swarm
- Department of Crop Sciences, University of Illinois, Urbana, Illinois, USA
| | - Liwen Zhou
- Plant Transformation Core Facility, Division of Plant Sciences, University of Missouri, Columbia, Missouri, USA
| | - Zhanyuan J Zhang
- Plant Transformation Core Facility, Division of Plant Sciences, University of Missouri, Columbia, Missouri, USA
| | - Randall L Nelson
- 1] Department of Crop Sciences, University of Illinois, Urbana, Illinois, USA. [2] Soybean/Maize Germplasm, Pathology, and Genetics Research Unit, US Department of Agriculture-Agricultural Research Service, Urbana, Illinois, USA
| | - Jianxin Ma
- 1] Department of Agronomy, Purdue University, West Lafayette, Indiana, USA. [2] College of Life Sciences, Qingdao Agricultural University, Qingdao, China
| |
Collapse
|
64
|
Dang X, Giang Tran Thi T, Mawuli Edzesi W, Liang L, Liu Q, Liu E, Wang Y, Qiang S, Liu L, Hong D. Population genetic structure of Oryza sativa in East and Southeast Asia and the discovery of elite alleles for grain traits. Sci Rep 2015; 5:11254. [PMID: 26059752 PMCID: PMC4462027 DOI: 10.1038/srep11254] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2014] [Accepted: 05/05/2015] [Indexed: 01/16/2023] Open
Abstract
We investigated the nuclear simple sequence repeat (SSR) genotypes of 532 rice (Oryza sativa L.) accessions collected from East and Southeast Asia and detected abundant genetic diversity within the population. We identified 6 subpopulations and found a tendency towards directional evolution in O. sativa from low to high latitudes, with levels of linkage disequilibrium (LD) in the 6 subpopulations ranging from 10 to 30 cM. We then investigated the phenotypic data for grain length, grain width, grain thickness and 1,000-grain weight over 4 years. Using a genome-wide association analysis, we identified 17 marker-trait associations involving 14 SSR markers on 12 chromosome arms, and 8 of the 17 associations were novel. The elite alleles were mined based on the phenotypic effects of the detected quantitative trait loci (QTLs). These elite alleles could be used to improve target traits through optimal cross designs, with the expected results obtained by pyramiding or substituting the elite alleles per QTL (independent of possible epistatic effects). Together, these results provide an in-depth understanding of the genetic diversity pattern among rice-grain traits across a broad geographic scale, which has potential use in future research work, including studies related to germplasm conservation and molecular breeding by design.
Collapse
Affiliation(s)
- Xiaojing Dang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
| | - Thu Giang Tran Thi
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
- College of Agronomy, Hue University of Agriculture and Forestry, Hue University,102 Phung Hung Street, Hue City, Vietnam
| | - Wisdom Mawuli Edzesi
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
| | - Lijun Liang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
| | - Qiangming Liu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
| | - Erbao Liu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yang Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
- Department of Agricultural Resource and Environment, Heilongjiang University, Harbin, 150080, China
| | - Sheng Qiang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
| | - Linglong Liu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
| | - Delin Hong
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
| |
Collapse
|
65
|
Gaut BS. Evolution Is an Experiment: Assessing Parallelism in Crop Domestication and Experimental Evolution. Mol Biol Evol 2015; 32:1661-71. [DOI: 10.1093/molbev/msv105] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
|
66
|
Wang Y, Tan L, Fu Y, Zhu Z, Liu F, Sun C, Cai H. Molecular evolution of the Sorghum Maturity Gene Ma3. PLoS One 2015; 10:e0124435. [PMID: 25961888 PMCID: PMC4427326 DOI: 10.1371/journal.pone.0124435] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2014] [Accepted: 03/13/2015] [Indexed: 11/19/2022] Open
Abstract
Time to maturity is a critical trait in sorghum (Sorghum bicolor) breeding, as it determines whether a variety can be grown in a particular cropping system or ecosystem. Understanding the nucleotide variation and the mechanisms of molecular evolution of the maturity genes would be helpful for breeding programs. In this study, we analyzed the nucleotide diversity of Ma3, an important maturity gene in sorghum, using 252 cultivated and wild sorghum materials from all over the world. The nucleotide variation and diversity were analyzed based both on race- and usage-based groups. We also sequenced 12 genes around the Ma3 gene in 185 of these materials to search for a selective sweep and found that purifying selection was the strongest force on Ma3, as low nucleotide diversity and low-frequency amino acid variants were observed. However, a very special mutation, described as ma3R, seemed to be under positive selection, as indicated by dramatically reduced nucleotide variation not only at the loci but also in the surrounding regions among individuals carrying the mutations. In addition, in an association study using the Ma3 nucleotide variations, we detected 3 significant SNPs for the heading date at a high-latitude environment (Beijing) and 17 at a low-latitude environment (Hainan). The results of this study increases our understanding of the evolutionary mechanisms of the maturity genes in sorghum and will be useful in sorghum breeding.
Collapse
Affiliation(s)
- Yan Wang
- Department of Plant Genetics and Breeding, College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
- Beijing Key Laboratory of Crop Genetic Improvement and Genome, Ministry of Agriculture, Beijing, China
| | - Lubin Tan
- Department of Plant Genetics and Breeding, College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
- Beijing Key Laboratory of Crop Genetic Improvement and Genome, Ministry of Agriculture, Beijing, China
| | - Yongcai Fu
- Department of Plant Genetics and Breeding, College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
- Beijing Key Laboratory of Crop Genetic Improvement and Genome, Ministry of Agriculture, Beijing, China
| | - Zuofeng Zhu
- Department of Plant Genetics and Breeding, College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
- Beijing Key Laboratory of Crop Genetic Improvement and Genome, Ministry of Agriculture, Beijing, China
| | - Fengxia Liu
- Department of Plant Genetics and Breeding, College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
- Beijing Key Laboratory of Crop Genetic Improvement and Genome, Ministry of Agriculture, Beijing, China
| | - Chuanqing Sun
- Department of Plant Genetics and Breeding, College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
- Beijing Key Laboratory of Crop Genetic Improvement and Genome, Ministry of Agriculture, Beijing, China
| | - Hongwei Cai
- Department of Plant Genetics and Breeding, College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
- Beijing Key Laboratory of Crop Genetic Improvement and Genome, Ministry of Agriculture, Beijing, China
| |
Collapse
|
67
|
Takagi H, Tamiru M, Abe A, Yoshida K, Uemura A, Yaegashi H, Obara T, Oikawa K, Utsushi H, Kanzaki E, Mitsuoka C, Natsume S, Kosugi S, Kanzaki H, Matsumura H, Urasaki N, Kamoun S, Terauchi R. MutMap accelerates breeding of a salt-tolerant rice cultivar. Nat Biotechnol 2015; 33:445-9. [PMID: 25798936 DOI: 10.1038/nbt.3188] [Citation(s) in RCA: 157] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Affiliation(s)
- Hiroki Takagi
- Iwate Biotechnology Research Center, Kitakami, Iwate, Japan
| | - Muluneh Tamiru
- Iwate Biotechnology Research Center, Kitakami, Iwate, Japan
| | - Akira Abe
- Iwate Biotechnology Research Center, Kitakami, Iwate, Japan
| | - Kentaro Yoshida
- The Sainsbury Laboratory, Norwich Research Park, Norwich, UK
| | - Aiko Uemura
- Iwate Biotechnology Research Center, Kitakami, Iwate, Japan
| | | | - Tsutomu Obara
- Iwate Biotechnology Research Center, Kitakami, Iwate, Japan
| | - Kaori Oikawa
- Iwate Biotechnology Research Center, Kitakami, Iwate, Japan
| | - Hiroe Utsushi
- Iwate Biotechnology Research Center, Kitakami, Iwate, Japan
| | - Eiko Kanzaki
- Iwate Biotechnology Research Center, Kitakami, Iwate, Japan
| | | | | | | | | | - Hideo Matsumura
- Gene Research Center, Shinshu University, Ueda, Nagano, Japan
| | - Naoya Urasaki
- Okinawa Prefectural Agricultural Research Center, Itoman, Okinawa, Japan
| | - Sophien Kamoun
- The Sainsbury Laboratory, Norwich Research Park, Norwich, UK
| | | |
Collapse
|
68
|
Sun X, Jia Q, Guo Y, Zheng X, Liang K. Whole-genome analysis revealed the positively selected genes during the differentiation of indica and temperate japonica rice. PLoS One 2015; 10:e0119239. [PMID: 25774680 PMCID: PMC4361536 DOI: 10.1371/journal.pone.0119239] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2014] [Accepted: 01/11/2015] [Indexed: 11/19/2022] Open
Abstract
To investigate the selective pressures acting on the protein-coding genes during the differentiation of indica and japonica, all of the possible orthologous genes between the Nipponbare and 93–11 genomes were identified and compared with each other. Among these genes, 8,530 pairs had identical sequences, and 27,384 pairs shared more than 90% sequence identity. Only 2,678 pairs of genes displaying a Ka/Ks ratio significantly greater than one were revealed, and most of these genes contained only nonsynonymous sites. The genes without synonymous site were further analyzed with the SNP data of 1529 O. sativa and O. rufipogon accessions, and 1068 genes were identified to be under positive selection during the differentiation of indica and temperate japonica. The positively selected genes (PSGs) are unevenly distributed on 12 chromosomes, and the proteins encoded by the PSGs are dominant with binding, transferase and hydrolase activities, and especially enriched in the plant responses to stimuli, biological regulations, and transport processes. Meanwhile, the most PSGs of the known function and/or expression were involved in the regulation of biotic/abiotic stresses. The evidence of pervasive positive selection suggested that many factors drove the differentiation of indica and japonica, which has already started in wild rice but is much lower than in cultivated rice. Lower differentiation and less PSGs revealed between the Or-It and Or-IIIt wild rice groups implied that artificial selection provides greater contribution on the differentiation than natural selection. In addition, the phylogenetic tree constructed with positively selected sites showed that the japonica varieties exhibited more diversity than indica on differentiation, and Or-III of O. rufipogon exhibited more than Or-I.
Collapse
Affiliation(s)
- Xinli Sun
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Fujian Agriculture & Forestry University, Fuzhou, China
- College of Crop Science, Fujian Agriculture & Forestry University, Fuzhou, China
- * E-mail:
| | - Qi Jia
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Fujian Agriculture & Forestry University, Fuzhou, China
- College of Crop Science, Fujian Agriculture & Forestry University, Fuzhou, China
| | - Yuchun Guo
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Fujian Agriculture & Forestry University, Fuzhou, China
- College of Crop Science, Fujian Agriculture & Forestry University, Fuzhou, China
| | - Xiujuan Zheng
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Fujian Agriculture & Forestry University, Fuzhou, China
- College of Crop Science, Fujian Agriculture & Forestry University, Fuzhou, China
| | - Kangjing Liang
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Fujian Agriculture & Forestry University, Fuzhou, China
- College of Crop Science, Fujian Agriculture & Forestry University, Fuzhou, China
| |
Collapse
|
69
|
Phung NTP, Mai CD, Mournet P, Frouin J, Droc G, Ta NK, Jouannic S, Lê LT, Do VN, Gantet P, Courtois B. Characterization of a panel of Vietnamese rice varieties using DArT and SNP markers for association mapping purposes. BMC PLANT BIOLOGY 2014; 14:371. [PMID: 25524444 PMCID: PMC4279583 DOI: 10.1186/s12870-014-0371-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2014] [Accepted: 12/08/2014] [Indexed: 05/20/2023]
Abstract
BACKGROUND The development of genome-wide association studies (GWAS) in crops has made it possible to mine interesting alleles hidden in gene bank resources. However, only a small fraction of the rice genetic diversity of any given country has been exploited in the studies with worldwide sampling conducted to date. This study presents the development of a panel of rice varieties from Vietnam for GWAS purposes. RESULTS The panel, initially composed of 270 accessions, was characterized for simple agronomic traits (maturity class, grain shape and endosperm type) commonly used to classify rice varieties. We first genotyped the panel using Diversity Array Technology (DArT) markers. We analyzed the panel structure, identified two subpanels corresponding to the indica and japonica sub-species and selected 182 non-redundant accessions. However, the number of usable DArT markers (241 for an initial library of 6444 clones) was too small for GWAS purposes. Therefore, we characterized the panel of 182 accessions with 25,971 markers using genotyping by sequencing. The same indica and japonica subpanels were identified. The indica subpanel was further divided into six populations (I1 to I6) using a model-based approach. The japonica subpanel, which was more highly differentiated, was divided into 4 populations (J1 to J4), including a temperate type (J2). Passport data and phenotypic traits were used to characterize these populations. Some populations were exclusively composed of glutinous types (I3 and J2). Some of the upland rice varieties appeared to belong to indica populations, which is uncommon in this region of the world. Linkage disequilibrium decayed faster in the indica subpanel (r2 below 0.2 at 101 kb) than in the japonica subpanel (r2 below 0.2 at 425 kb), likely because of the strongest differentiation of the japonica subpanel. A matrix adapted for GWAS was built by eliminating the markers with a minor allele frequency below 5% and imputing the missing data. This matrix contained 21,814 markers. A GWAS was conducted on time to flowering to prove the utility of this panel. CONCLUSIONS This publicly available panel constitutes an important resource giving access to original allelic diversity. It will be used for GWAS on root and panicle traits.
Collapse
Affiliation(s)
- Nhung Thi Phuong Phung
- />Agricultural Genetics Institute, National Key Laboratory for Plant Cell Biotechnology, LMI RICE, Hanoi, Vietnam
| | - Chung Duc Mai
- />Agricultural Genetics Institute, National Key Laboratory for Plant Cell Biotechnology, LMI RICE, Hanoi, Vietnam
- />University of Science and Technology of Hanoi, LMI RICE, Hanoi, Vietnam
| | | | | | - Gaëtan Droc
- />Cirad, UMR-AGAP, 34398 Montpellier, France
| | - Nhung Kim Ta
- />Agricultural Genetics Institute, National Key Laboratory for Plant Cell Biotechnology, LMI RICE, Hanoi, Vietnam
- />IRD, UMR-DIADE, LMI RICE, Hanoi, Vietnam
- />Université Montpellier 2, UMR DIADE, 34095 Montpellier, France
| | | | | | - Vinh Nang Do
- />Agricultural Genetics Institute, National Key Laboratory for Plant Cell Biotechnology, LMI RICE, Hanoi, Vietnam
| | - Pascal Gantet
- />IRD, UMR-DIADE, LMI RICE, Hanoi, Vietnam
- />Université Montpellier 2, UMR DIADE, 34095 Montpellier, France
- />University of Science and Technology of Hanoi, LMI RICE, Hanoi, Vietnam
| | | |
Collapse
|
70
|
Li YH, Reif JC, Jackson SA, Ma YS, Chang RZ, Qiu LJ. Detecting SNPs underlying domestication-related traits in soybean. BMC PLANT BIOLOGY 2014; 14:251. [PMID: 25258093 PMCID: PMC4180965 DOI: 10.1186/s12870-014-0251-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2014] [Accepted: 09/18/2014] [Indexed: 05/26/2023]
Abstract
BACKGROUND Cultivated soybean (Glycine max) experienced a severe genetic bottleneck during its domestication and a further loss in diversity during its subsequent selection. Here, a panel of 65 wild (G. soja) and 353 cultivated accessions was genotyped at 552 single-nucleotide polymorphism loci to search for signals of selection during and after domestication. RESULTS The wild and cultivated populations were well differentiated from one another. Application of the Fst outlier test revealed 64 loci showing evidence for selection. Of these, 35 related to selection during domestication, while the other 29 likely gradually became monomorphic as a result of prolonged selection during post domestication. Two of the SNP locus outliers were associated with testa color. CONCLUSIONS Identifying genes controlling domestication-related traits is important for maintaining the diversity of crops. SNP locus outliers detected by a combined forward genetics and population genetics approach can provide markers with utility for the conservation of wild accessions and for trait improvement in the cultivated genepool.
Collapse
Affiliation(s)
- Ying-Hui Li
- />The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI)/Key Lab of Germplasm Utilization (MOA), Institute of Crop Science, Chinese Academy of Agricultural Sciences, 100081 Beijing, P.R. China
| | - Jochen C Reif
- />Department of Cytogenetics and Genome Analysis, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | - Scott A Jackson
- />Center for Applied Genetic Technologies, University of Georgia, Athens, GA 30602 USA
| | - Yan-Song Ma
- />The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI)/Key Lab of Germplasm Utilization (MOA), Institute of Crop Science, Chinese Academy of Agricultural Sciences, 100081 Beijing, P.R. China
- />Soybean Research Institute, Heilongjiang Academy of Agricultural Sciences, 150086 Harbin, China
| | - Ru-Zhen Chang
- />The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI)/Key Lab of Germplasm Utilization (MOA), Institute of Crop Science, Chinese Academy of Agricultural Sciences, 100081 Beijing, P.R. China
| | - Li-Juan Qiu
- />The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI)/Key Lab of Germplasm Utilization (MOA), Institute of Crop Science, Chinese Academy of Agricultural Sciences, 100081 Beijing, P.R. China
| |
Collapse
|
71
|
An Adaptive Transposable Element Insertion in the Regulatory Region of the EO Gene in the Domesticated Silkworm, Bombyx mori. Mol Biol Evol 2014; 31:3302-13. [DOI: 10.1093/molbev/msu261] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
|
72
|
Choudhury BI, Khan ML, Dayanandan S. Patterns of nucleotide diversity and phenotypes of two domestication related genes (OsC1 and Wx) in indigenous rice varieties in Northeast India. BMC Genet 2014; 15:71. [PMID: 24935343 PMCID: PMC4070345 DOI: 10.1186/1471-2156-15-71] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2013] [Accepted: 06/10/2014] [Indexed: 11/14/2022] Open
Abstract
Background During the domestication of crops, individual plants with traits desirable for human needs have been selected from their wild progenitors. Consequently, genetic and nucleotide diversity of genes associated with these selected traits in crop plants are expected to be lower than their wild progenitors. In the present study, we surveyed the pattern of nucleotide diversity of two selected trait specific genes, Wx and OsC1, which regulate amylose content and apiculus coloration respectively in cultivated rice varieties. The analyzed samples were collected from a wide geographic area in Northeast (NE) India, and included contrasting phenotypes considered to be associated with selected genes, namely glutinous and nonglutinous grains and colored and colorless apiculus. Results No statistically significant selection signatures were detected in both Wx and OsC1gene sequences. However, low level of selection that varied across the length of each gene was evident. The glutinous type varieties showed higher levels of nucleotide diversity at the Wx locus (πtot = 0.0053) than nonglutinous type varieties (πtot = 0.0043). The OsC1 gene revealed low levels of selection among the colorless apiculus varieties with lower nucleotide diversity (πtot = 0.0010) than in the colored apiculus varieties (πtot = 0.0023). Conclusions The results revealed that functional mutations at Wx and OsC1genes considered to be associated with specific phenotypes do not necessarily correspond to the phenotypes in indigenous rice varieties in NE India. This suggests that other than previously reported genomic regions may also be involved in determination of these phenotypes.
Collapse
Affiliation(s)
- Baharul Islam Choudhury
- Forest and Evolutionary Genomics Laboratory and Centre for Structural and Functional Genomics, Biology Department, Concordia University Montréal, 7141 Sherbrooke St, West, Montréal, Quebec H4B 1R6, Canada.
| | | | | |
Collapse
|
73
|
Krishnan S. G, Waters DLE, Henry RJ. Australian wild rice reveals pre-domestication origin of polymorphism deserts in rice genome. PLoS One 2014; 9:e98843. [PMID: 24905808 PMCID: PMC4048307 DOI: 10.1371/journal.pone.0098843] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2013] [Accepted: 05/08/2014] [Indexed: 12/13/2022] Open
Abstract
Background Rice is a major source of human food with a predominantly Asian production base. Domestication involved selection of traits that are desirable for agriculture and to human consumers. Wild relatives of crop plants are a source of useful variation which is of immense value for crop improvement. Australian wild rices have been isolated from the impacts of domestication in Asia and represents a source of novel diversity for global rice improvement. Oryza rufipogon is a perennial wild progenitor of cultivated rice. Oryza meridionalis is a related annual species in Australia. Results We have examined the sequence of the genomes of AA genome wild rices from Australia that are close relatives of cultivated rice through whole genome re-sequencing. Assembly of the resequencing data to the O. sativa ssp. japonica cv. Nipponbare shows that Australian wild rices possess 2.5 times more single nucleotide polymorphisms than in the Asian wild rice and cultivated O. sativa ssp. indica. Analysis of the genome of domesticated rice reveals regions of low diversity that show very little variation (polymorphism deserts). Both the perennial and annual wild rice from Australia show a high degree of conservation of sequence with that found in cultivated rice in the same 4.58Mbp region on chromosome 5, which suggests that some of the ‘polymorphism deserts’ in this and other parts of the rice genome may have originated prior to domestication due to natural selection. Conclusions Analysis of genes in the ‘polymorphism deserts’ indicates that this selection may have been due to biotic or abiotic stress in the environment of early rice relatives. Despite having closely related sequences in these genome regions, the Australian wild populations represent an invaluable source of diversity supporting rice food security.
Collapse
Affiliation(s)
- Gopala Krishnan S.
- Southern Cross Plant Science, Southern Cross University, Lismore, New South Wales, Australia
- Division of Genetics, Indian Agricultural Research Institute, New Delhi, India
| | - Daniel L. E. Waters
- Southern Cross Plant Science, Southern Cross University, Lismore, New South Wales, Australia
| | - Robert J. Henry
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, Queensland, Australia
- * E-mail:
| |
Collapse
|
74
|
The PH gene determines fruit acidity and contributes to the evolution of sweet melons. Nat Commun 2014; 5:4026. [DOI: 10.1038/ncomms5026] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2013] [Accepted: 05/02/2014] [Indexed: 12/15/2022] Open
|
75
|
Ootsuka K, Takahashi I, Tanaka K, Itani T, Tabuchi H, Yoshihashi T, Tonouchi A, Ishikawa R. Genetic polymorphisms in Japanese fragrant landraces and novel fragrant allele domesticated in northern Japan. BREEDING SCIENCE 2014; 64:115-124. [PMID: 24987297 PMCID: PMC4065318 DOI: 10.1270/jsbbs.64.115] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2013] [Accepted: 02/07/2014] [Indexed: 05/30/2023]
Abstract
Rice fragrance is an important characteristic for Southeast Asian consumers, and fragrant landraces from Japan were first recorded in the 17th century. Principal component analysis clearly showed that Japanese fragrant landraces were genetically different from non-Japanese fragrant landraces. Japanese fragrant landraces were composed of six clades, none of which carried the most common fragrance mutation, an 8-bp deletion in exon 7 of Badh2. Fragrant landraces comprised two major groups carrying different Badh2 mutations. One group carried a known SNP at exon13 and the other a SNP at the exon1-intron1 junction as splicing donor site. The latter was considered to be a potential splicing mutant group as a novel allele at Badh2. Heterozygosity (He) scores in the two fragrant groups were not significantly different from non-fragrant landraces and modern cultivars. However, lower He scores were found around the Badh2 locus in the two groups. The potential splicing mutant group showed a more extended haplotype than the E13 SNP group. A likely causal factor responsible for loss of function is a novel splicing mutation allele that may have been generated quite recently. The fragrance allele has dispersed as a result of out-crossing under local environmental conditions.
Collapse
Affiliation(s)
- Kenta Ootsuka
- Faculty of Agriculture and Life Science, Hirosaki University,
Hirosaki, Aomori 036-8561,
Japan
| | - Ikuya Takahashi
- Faculty of Agriculture and Life Science, Hirosaki University,
Hirosaki, Aomori 036-8561,
Japan
| | - Katsunori Tanaka
- Faculty of Humanity, Hirosaki University,
Hirosaki, Aomori 036-8561,
Japan
| | - Tomio Itani
- Faculty of Life and Environmental Sciences, Prefectural University of Hiroshima,
Shobara, Hiroshima 727-0023,
Japan
| | - Hiroaki Tabuchi
- Upland Farming Research Division, Miyakonojo Research Station, NARO Kyushu Okinawa Agricultural Research Center,
6651-2 Yokoichi, Miyakonojo, Miyazaki 885-0091,
Japan
| | - Tadashi Yoshihashi
- Post harvest Science and Technology Division, Japan International Research Center for Agricultural Sciences,
Tsukuba, Ibaraki 305-8686,
Japan
| | - Akio Tonouchi
- Faculty of Agriculture and Life Science, Hirosaki University,
Hirosaki, Aomori 036-8561,
Japan
| | - Ryuji Ishikawa
- Faculty of Agriculture and Life Science, Hirosaki University,
Hirosaki, Aomori 036-8561,
Japan
| |
Collapse
|
76
|
Dang X, Thi TGT, Dong G, Wang H, Edzesi WM, Hong D. Genetic diversity and association mapping of seed vigor in rice (Oryza sativa L.). PLANTA 2014; 239:1309-19. [PMID: 24668487 DOI: 10.1007/s00425-014-2060-z] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2013] [Accepted: 03/06/2014] [Indexed: 05/20/2023]
Abstract
Seed vigor is closely related to direct seeding in rice (Oryza sativa L.). Previous quantitative trait locus (QTL) studies for seed vigor were mainly derived from bi-parental segregating populations and no report from natural populations. In this study, association mapping for seed vigor was performed on a selected sample of 540 rice cultivars (419 from China and 121 from Vietnam). Population structure was estimated on the basis of 262 simple sequence repeat (SSR) markers. Seed vigor was evaluated by root length (RL), shoot length (SL) and shoot dry weight in 2011 and 2012. Abundant phenotypic and genetic diversities were found in the studied population. The population was divided into seven subpopulations, and the levels of linkage disequilibrium (LD) ranged from 10 to 80 cM. We identified 27 marker-trait associations involving 18 SSR markers for three traits. According to phenotypic effects for alleles of the detected QTLs, elite alleles were mined. These elite alleles could be used to design parental combinations and the expected results would be obtained by pyramiding or substituting the elite alleles per QTL (apart from possible epistatic effects). Our results demonstrate that association mapping can complement and enhance previous QTL information for marker-assisted selection and breeding by design.
Collapse
Affiliation(s)
- Xiaojing Dang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
| | | | | | | | | | | |
Collapse
|
77
|
Abstract
Rice (Oryza sativa) is one of the most important cereal grains in the world today and serves as a staple food source for more than half of the world's population. Research into when, where, and how rice was brought into cultivation and eventually domesticated, along with its development into a staple food source, is thus essential. These questions have been a point of nearly continuous research in both archaeology and genetics, and new information has continually come to light as theory, data acquisition, and analytical techniques have advanced over time. Here, we review the broad history of our scientific understanding of the rice domestication process from both an archaeological and genetic perspective and examine in detail the information that has come to light in both of these fields in the last 10 y. Current findings from genetics and archaeology are consistent with the domestication of O. sativa japonica in the Yangtze River valley of southern China. Interestingly, although it appears rice was cultivated in the area by as early 8000 BP, the key domestication trait of nonshattering was not fixed for another 1,000 y or perhaps longer. Rice was also cultivated in India as early as 5000 BP, but the domesticated indica subspecies currently appears to be a product of the introgression of favorable alleles from japonica. These findings are reshaping our understanding of rice domestication and also have implications for understanding the complex evolutionary process of plant domestication.
Collapse
|
78
|
Adetunji I, Willems G, Tschoep H, Bürkholz A, Barnes S, Boer M, Malosetti M, Horemans S, van Eeuwijk F. Genetic diversity and linkage disequilibrium analysis in elite sugar beet breeding lines and wild beet accessions. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2014; 127:559-571. [PMID: 24292512 DOI: 10.1007/s00122-013-2239-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2013] [Accepted: 11/20/2013] [Indexed: 06/02/2023]
Abstract
Linkage disequilibrium decay in sugar beet is strongly affected by the breeding history, and varies extensively between and along chromosomes, allowing identification of known and unknown signatures of selection. Genetic diversity and linkage disequilibrium (LD) patterns were investigated in 233 elite sugar beet breeding lines and 91 wild beet accessions, using 454 single nucleotide polymorphisms (SNPs) and 418 SNPs, respectively. Principal coordinate analysis suggested the existence of three groups of germplasm, corresponding to the wild beets, the seed parent and the pollen parent breeding pool. LD was investigated in each of these groups, with and without correction for genetic relatedness. Without correction for genetic relatedness, in the pollen as well as the seed parent pool, LD persisted beyond 50 centiMorgan (cM) on four (2, 3, 4 and 5) and three chromosomes (2, 4 and 6), respectively; after correction for genetic relatedness, LD decayed after <6 cM on all chromosomes in both pools. In the wild beet accessions, there was a strong LD decay: on average LD disappeared after 1 cM when LD was calculated with a correction for genetic relatedness. Persistence of LD was not only observed between distant SNPs on the same chromosome, but also between SNPs on different chromosomes. Regions on chromosomes 3 and 4 that harbor disease resistance and monogermy loci showed strong genetic differentiation between the pollen and seed parent pools. Other regions, on chromosomes 8 and 9, for which no a priori information was available with respect to their contribution to the phenotype, still contributed to clustering of lines in the elite breeding material.
Collapse
|
79
|
Pearl SA, Bowers JE, Reyes-Chin-Wo S, Michelmore RW, Burke JM. Genetic analysis of safflower domestication. BMC PLANT BIOLOGY 2014; 14:43. [PMID: 24502326 PMCID: PMC3925122 DOI: 10.1186/1471-2229-14-43] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2013] [Accepted: 01/28/2014] [Indexed: 05/31/2023]
Abstract
BACKGROUND Safflower (Carthamus tinctorius L.) is an oilseed crop in the Compositae (a.k.a. Asteraceae) that is valued for its oils rich in unsaturated fatty acids. Here, we present an analysis of the genetic architecture of safflower domestication and compare our findings to those from sunflower (Helianthus annuus L.), an independently domesticated oilseed crop within the same family.We mapped quantitative trait loci (QTL) underlying 24 domestication-related traits in progeny from a cross between safflower and its wild progenitor, Carthamus palaestinus Eig. Also, we compared QTL positions in safflower against those that have been previously identified in cultivated x wild sunflower crosses to identify instances of colocalization. RESULTS We mapped 61 QTL, the vast majority of which (59) exhibited minor or moderate phenotypic effects. The two large-effect QTL corresponded to one each for flower color and leaf spininess. A total of 14 safflower QTL colocalized with previously reported sunflower QTL for the same traits. Of these, QTL for three traits (days to flower, achene length, and number of selfed seed) had cultivar alleles that conferred effects in the same direction in both species. CONCLUSIONS As has been observed in sunflower, and unlike many other crops, our results suggest that the genetics of safflower domestication is quite complex. Moreover, our comparative mapping results indicate that safflower and sunflower exhibit numerous instances of QTL colocalization, suggesting that parallel trait transitions during domestication may have been driven, at least in part, by parallel genotypic evolution at some of the same underlying genes.
Collapse
Affiliation(s)
- Stephanie A Pearl
- Department of Plant Biology, Miller Plant Sciences, University of Georgia, Athens, GA 30602, USA
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA 30602, USA
| | - John E Bowers
- Department of Plant Biology, Miller Plant Sciences, University of Georgia, Athens, GA 30602, USA
| | | | | | - John M Burke
- Department of Plant Biology, Miller Plant Sciences, University of Georgia, Athens, GA 30602, USA
| |
Collapse
|
80
|
Meyer RS, Purugganan MD. Evolution of crop species: genetics of domestication and diversification. Nat Rev Genet 2014; 14:840-52. [PMID: 24240513 DOI: 10.1038/nrg3605] [Citation(s) in RCA: 582] [Impact Index Per Article: 58.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Domestication is a good model for the study of evolutionary processes because of the recent evolution of crop species (<12,000 years ago), the key role of selection in their origins, and good archaeological and historical data on their spread and diversification. Recent studies, such as quantitative trait locus mapping, genome-wide association studies and whole-genome resequencing studies, have identified genes that are associated with the initial domestication and subsequent diversification of crops. Together, these studies reveal the functions of genes that are involved in the evolution of crops that are under domestication, the types of mutations that occur during this process and the parallelism of mutations that occur in the same pathways and proteins, as well as the selective forces that are acting on these mutations and that are associated with geographical adaptation of crop species.
Collapse
Affiliation(s)
- Rachel S Meyer
- Center for Genomics and Systems Biology, Department of Biology, 12 Waverly Place, New York University, New York 10003, USA
| | | |
Collapse
|
81
|
Beckles DM, Thitisaksakul M. How environmental stress affects starch composition and functionality in cereal endosperm. STARCH-STARKE 2013. [DOI: 10.1002/star.201300212] [Citation(s) in RCA: 89] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Diane M. Beckles
- Department of Plant Sciences; University of California; Davis CA USA
| | | |
Collapse
|
82
|
Zheng H, Wang H, Yang H, Wu J, Shi B, Cai R, Xu Y, Wu A, Luo L. Genetic diversity and molecular evolution of Chinese waxy maize germplasm. PLoS One 2013; 8:e66606. [PMID: 23818949 PMCID: PMC3688585 DOI: 10.1371/journal.pone.0066606] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2013] [Accepted: 05/07/2013] [Indexed: 02/02/2023] Open
Abstract
Waxy maize (Zea mays L. var. certaina Kulesh), with many excellent characters in terms of starch composition and economic value, has grown in China for a long history and its production has increased dramatically in recent decades. However, the evolution and origin of waxy maize still remains unclear. We studied the genetic diversity of Chinese waxy maize including typical landraces and inbred lines by SSR analysis and the results showed a wide genetic diversity in the Chinese waxy maize germplasm. We analyzed the origin and evolution of waxy maize by sequencing 108 samples, and downloading 52 sequences from GenBank for the waxy locus in a number of accessions from genus Zea. A sharp reduction of nucleotide diversity and significant neutrality tests (Tajima's D and Fu and Li's F*) were observed at the waxy locus in Chinese waxy maize but not in nonglutinous maize. Phylogenetic analysis indicated that Chinese waxy maize originated from the cultivated flint maize and most of the modern waxy maize inbred lines showed a distinct independent origin and evolution process compared with the germplasm from Southwest China. The results indicated that an agronomic trait can be quickly improved to meet production demand by selection.
Collapse
Affiliation(s)
- Hongjian Zheng
- Shanghai Academy of Agricultural Sciences, Shanghai, China
- Shanghai Agrobiological Gene Center, Shanghai, China
| | - Hui Wang
- Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Hua Yang
- Shanghai Academy of Agricultural Sciences, Shanghai, China
- Shanghai Agrobiological Gene Center, Shanghai, China
| | - Jinhong Wu
- Shanghai Academy of Agricultural Sciences, Shanghai, China
- Shanghai Agrobiological Gene Center, Shanghai, China
| | - Biao Shi
- Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Run Cai
- School of Agriculture and Biology, Shanghai Jiaotong University, Shanghai, China
| | - Yunbi Xu
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
- International Maize and Wheat Improvement Center (CIMMYT), Texcoco, Mexico
| | - Aizhong Wu
- Shanghai Academy of Agricultural Sciences, Shanghai, China
- * E-mail: (AW); (LL)
| | - Lijun Luo
- Shanghai Academy of Agricultural Sciences, Shanghai, China
- Shanghai Agrobiological Gene Center, Shanghai, China
- * E-mail: (AW); (LL)
| |
Collapse
|
83
|
Mandel JR, Nambeesan S, Bowers JE, Marek LF, Ebert D, Rieseberg LH, Knapp SJ, Burke JM. Association mapping and the genomic consequences of selection in sunflower. PLoS Genet 2013; 9:e1003378. [PMID: 23555290 PMCID: PMC3605098 DOI: 10.1371/journal.pgen.1003378] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2012] [Accepted: 01/29/2013] [Indexed: 11/18/2022] Open
Abstract
The combination of large-scale population genomic analyses and trait-based mapping approaches has the potential to provide novel insights into the evolutionary history and genome organization of crop plants. Here, we describe the detailed genotypic and phenotypic analysis of a sunflower (Helianthus annuus L.) association mapping population that captures nearly 90% of the allelic diversity present within the cultivated sunflower germplasm collection. We used these data to characterize overall patterns of genomic diversity and to perform association analyses on plant architecture (i.e., branching) and flowering time, successfully identifying numerous associations underlying these agronomically and evolutionarily important traits. Overall, we found variable levels of linkage disequilibrium (LD) across the genome. In general, islands of elevated LD correspond to genomic regions underlying traits that are known to have been targeted by selection during the evolution of cultivated sunflower. In many cases, these regions also showed significantly elevated levels of differentiation between the two major sunflower breeding groups, consistent with the occurrence of divergence due to strong selection. One of these regions, which harbors a major branching locus, spans a surprisingly long genetic interval (ca. 25 cM), indicating the occurrence of an extended selective sweep in an otherwise recombinogenic interval.
Collapse
Affiliation(s)
- Jennifer R. Mandel
- Department of Plant Biology, Miller Plant Sciences, University of Georgia, Athens, Georgia, United States of America
| | - Savithri Nambeesan
- Department of Plant Biology, Miller Plant Sciences, University of Georgia, Athens, Georgia, United States of America
| | - John E. Bowers
- Department of Plant Biology, Miller Plant Sciences, University of Georgia, Athens, Georgia, United States of America
| | - Laura F. Marek
- North Central Regional Plant Introduction Station, USDA–ARS, Ames, Iowa, United States of America
| | - Daniel Ebert
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
| | - Loren H. Rieseberg
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Biology, Indiana University, Bloomington, Indiana, United States of America
| | - Steven J. Knapp
- Monsanto Company, Woodland, California, United States of America
| | - John M. Burke
- Department of Plant Biology, Miller Plant Sciences, University of Georgia, Athens, Georgia, United States of America
- * E-mail:
| |
Collapse
|
84
|
Wang SY, Luo J, Murphy RW, Wu SF, Zhu CL, Gao Y, Zhang YP. Origin of Chinese goldfish and sequential loss of genetic diversity accompanies new breeds. PLoS One 2013; 8:e59571. [PMID: 23527220 PMCID: PMC3602300 DOI: 10.1371/journal.pone.0059571] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2012] [Accepted: 02/19/2013] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Goldfish, Carassius auratus, have experienced strong anthropogenic selection during their evolutionary history, generating a tremendous extent of morphological variation relative to that in native Carassius. To locate the geographic origin of goldfish, we analyzed nucleotide sequences from part of the control region (CR) and the entire cytochrome b (Cytb) mitochondrial DNA genes for 234 goldfish and a large series of native specimens. Four important morphological characteristics used in goldfish taxonomy-body shape, dorsal fin, eye shape, and tailfin-were selected for hypothesis-testing to identify those that better correspond to evolutionary history. PRINCIPAL FINDING Haplotypes of goldfish rooted in two sublineages (C5 and C6), which contained the haplotypes of native C. a. auratus from southern China. Values of F(ST) and N(m) revealed a close relationship between goldfish and native C. a. auratus from the lower Yangtze River. An extraordinary, stepwise loss of genetic diversity was detected from native fish to goldfish and from Grass-goldfish relative to other breeds. Significantly negative results for the tests of Tajima's D and Fu and Li's D* and F* were identified in goldfish, including the Grass breed. The results identified eye-shape as being the least informative character for grouping goldfish with respect to their evolutionary history. Fisher's exact test identified matrilineal constraints on domestication. CONCLUSIONS Chinese goldfish have a matrilineal origin from native southern Chinese C. a. auratus, especially the lineages from the lower Yangtze River. Anthropogenic selection of the native Carassius eliminated aesthetically unappealing goldfish and this action appeared to be responsible for the stepwise decrease in genetic diversity of domesticated goldfish, a process similar to that reported for the domestication of pigs, rice, and maize. The three-breed taxonomy--Grass-goldfish, Egg-goldfish, and Wen-goldfish--better reflected the history of domestication.
Collapse
Affiliation(s)
- Shu-Yan Wang
- State Key Laboratory of Genetic Resources and Evolution, and Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, the Chinese Academy of Sciences, Kunming, China
- School of Life Sciences, University of Science and Technology of China, Hefei, China
| | - Jing Luo
- Laboratory for Conservation and Utilization of Bio-resources, College of Life Sciences, Yunnan University, Kunming, China
| | - Robert W. Murphy
- State Key Laboratory of Genetic Resources and Evolution, and Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, the Chinese Academy of Sciences, Kunming, China
- Centre for Biodiversity and Conservation Biology, Royal Ontario Museum, Toronto, Canada
| | - Shi-Fang Wu
- State Key Laboratory of Genetic Resources and Evolution, and Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, the Chinese Academy of Sciences, Kunming, China
| | - Chun-Ling Zhu
- State Key Laboratory of Genetic Resources and Evolution, and Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, the Chinese Academy of Sciences, Kunming, China
| | - Yun Gao
- State Key Laboratory of Genetic Resources and Evolution, and Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, the Chinese Academy of Sciences, Kunming, China
- * E-mail: (YG); (Y-PZ)
| | - Ya-Ping Zhang
- State Key Laboratory of Genetic Resources and Evolution, and Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, the Chinese Academy of Sciences, Kunming, China
- Laboratory for Conservation and Utilization of Bio-resources, College of Life Sciences, Yunnan University, Kunming, China
- * E-mail: (YG); (Y-PZ)
| |
Collapse
|
85
|
Screen for Footprints of Selection during Domestication/Captive Breeding of Atlantic Salmon. Comp Funct Genomics 2012; 2012:628204. [PMID: 23326209 PMCID: PMC3544263 DOI: 10.1155/2012/628204] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2012] [Revised: 10/29/2012] [Accepted: 11/09/2012] [Indexed: 11/28/2022] Open
Abstract
Domesticated animals provide a unique opportunity to identify genomic targets of artificial selection to the captive environment. Here, we screened three independent domesticated/captive Atlantic salmon (Salmo salar) strains and their wild progenitor populations in an effort to detect potential signals of domestication selection by typing of 261 SNPs and 70 microsatellite loci. By combining information from four different neutrality tests, in total ten genomic regions showed signs of directional selection based on multiple sources of evidence. Most of the identified candidate regions were rather small ranging from zero to a few centimorgans (cM) in the female Atlantic salmon linkage map. We also evaluated how adaptation from standing variation affects adjacent SNP and microsatellite variation along the chromosomes and, by using forward simulations with strong selection, we were able to generate genetic differentiation patterns comparable to the observed data. This study highlights the significance of standing genetic variation during the early stages of adaptation and represents a useful step towards identifying functional variants involved in domestication of Atlantic salmon.
Collapse
|
86
|
Huang L, Jiang H, Ren X, Chen Y, Xiao Y, Zhao X, Tang M, Huang J, Upadhyaya HD, Liao B. Abundant microsatellite diversity and oil content in wild Arachis species. PLoS One 2012; 7:e50002. [PMID: 23185514 PMCID: PMC3502184 DOI: 10.1371/journal.pone.0050002] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2012] [Accepted: 10/15/2012] [Indexed: 01/05/2023] Open
Abstract
The peanut (Arachis hypogaea) is an important oil crop. Breeding for high oil content is becoming increasingly important. Wild Arachis species have been reported to harbor genes for many valuable traits that may enable the improvement of cultivated Arachis hypogaea, such as resistance to pests and disease. However, only limited information is available on variation in oil content. In the present study, a collection of 72 wild Arachis accessions representing 19 species and 3 cultivated peanut accessions were genotyped using 136 genome-wide SSR markers and phenotyped for oil content over three growing seasons. The wild Arachis accessions showed abundant diversity across the 19 species. A. duranensis exhibited the highest diversity, with a Shannon-Weaver diversity index of 0.35. A total of 129 unique alleles were detected in the species studied. A. rigonii exhibited the largest number of unique alleles (75), indicating that this species is highly differentiated. AMOVA and genetic distance analyses confirmed the genetic differentiation between the wild Arachis species. The majority of SSR alleles were detected exclusively in the wild species and not in A. hypogaea, indicating that directional selection or the hitchhiking effect has played an important role in the domestication of the cultivated peanut. The 75 accessions were grouped into three clusters based on population structure and phylogenic analysis, consistent with their taxonomic sections, species and genome types. A. villosa and A. batizocoi were grouped with A. hypogaea, suggesting the close relationship between these two diploid wild species and the cultivated peanut. Considerable phenotypic variation in oil content was observed among different sections and species. Nine alleles were identified as associated with oil content based on association analysis, of these, three alleles were associated with higher oil content but were absent in the cultivated peanut. The results demonstrated that there is great potential to increase the oil content in A. hypogaea by using the wild Arachis germplasm.
Collapse
Affiliation(s)
- Li Huang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Huifang Jiang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Xiaoping Ren
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Yuning Chen
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Yingjie Xiao
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, China
| | - Xinyan Zhao
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Mei Tang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Jiaquan Huang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Hari D. Upadhyaya
- International Crops Research Institute for the Semi-Arid Tropics, Patancheru, Andhra Pradesh, India
| | - Boshou Liao
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| |
Collapse
|
87
|
Sun J, Liu D, Wang JY, Ma DR, Tang L, Gao H, Xu ZJ, Chen WF. The contribution of intersubspecific hybridization to the breeding of super-high-yielding japonica rice in northeast China. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2012; 125:1149-57. [PMID: 22660631 DOI: 10.1007/s00122-012-1901-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2011] [Accepted: 05/19/2012] [Indexed: 05/16/2023]
Abstract
Hybridization between indica and japonica rice combined with utilization of ideal plant type has led to the development of high-yielding japonica rice in northern China. However, the contribution at the genomic level of intersubspecific hybridization to the increased yield of northern Chinese japonica rice is uncertain. In this study, we analyzed the genomic pedigree of descendants of hybridization between indica and japonica rice grown in northeastern China between 1963 and 2008. Simple sequence repeat markers indicated that since 1990 the genetic diversity among northern japonica cultivars was enriched. Genome-wide analysis with subspecies-specific indel and intron length polymorphism markers showed indica-allele frequencies were significantly increased in cultivars bred after 1990, and were significantly positively correlated with spikelet number per panicle and significantly negatively correlated with panicle number per plant. Among eight genes controlling agronomic traits, GN1a and GS3 were partially fixed in the genome of northern japonica cultivars. In contrast, Waxy and qSH1 were eliminated, whereas DEP1 and qSW5 were retained. Indica germplasm is an important contributor to the increased yield of northern japonica rice. Breeding for high yield and grain quality in combination is a complicated process and difficult to achieve when relying on only one or several functional genes, thus the selection expertise of the breeder remains critical.
Collapse
Affiliation(s)
- Jian Sun
- Key Laboratory of Northeast Rice Biology and Breeding, Ministry of Agriculture, Rice Research Institute, Shenyang Agricultural University, Dongling Road 120, Shenyang, 110866, China
| | | | | | | | | | | | | | | |
Collapse
|
88
|
Vanniarajan C, Vinod KK, Pereira A. Molecular evaluation of genetic diversity and association studies in rice (Oryza sativa L.). J Genet 2012; 91:9-19. [PMID: 22546822 DOI: 10.1007/s12041-012-0146-6] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
In the present study, we tested rice genotypes that included un(der)exploited landraces of Tamil Nadu along with indica and japonica test cultivars to ascertain their genetic diversity structure. Highly polymorphic microsatellite markers were used for generating marker segregation data. A novel measure, allele discrimination index, was used to determine subpopulation differentiation power of each marker. Phenotypic data were collected for yield and component traits. Pattern of molecular differentiation separated indica and japonica genotypes; indica genotypes had two subpopulations within. Landraces were found to have indica genome, but formed a separate subgroup with low linkage disequilibrium. The landraces further separated into distinct group in both hierarchical clustering analysis using neighbour-joining method as well as in the model based population structure analysis. Japonica and the remaining indica cultivars formed two other distinct groups. Linkage disequilibrium observed in the whole population was considerably reduced in subpopulations. Low linkage disequilibrium of landforms suggests their narrow adaptation in local geographical niche. Many population specific alleles could be identified particularly for japonica cultivars and landraces. Association analysis revealed nine marker-trait associations with three agronomic traits, of which 67% were previously reported. Although the testing landraces together with known cultivars had permitted genomewide association mapping, the experiment offers scope to study more landraces collected from the entire geographical region for drawing more reliable information.
Collapse
Affiliation(s)
- C Vanniarajan
- Plant Research International, Wageningen University and Research Centre, 6700 AA Wageningen, The Netherlands
| | | | | |
Collapse
|
89
|
Chapman MA, Burke JM. Evidence of selection on fatty acid biosynthetic genes during the evolution of cultivated sunflower. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2012; 125:897-907. [PMID: 22580969 DOI: 10.1007/s00122-012-1881-z] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2012] [Accepted: 04/19/2012] [Indexed: 05/21/2023]
Abstract
The identification of genes underlying the phenotypic transitions that took place during crop evolution, as well as the genomic extent of resultant selective sweeps, is of great interest to both evolutionary biologists and applied plant scientists. In this study, we report the results of a molecular evolutionary analysis of 11 genes that underlie fatty acid biosynthesis and metabolism in wild and cultivated sunflower (Helianthus annuus). Seven of these 11 genes showed evidence of selection at the nucleotide level, with 1 (FAD7) having experienced selection prior to domestication, 2 (FAD2-3 and FAD3) having experienced selection during domestication, and 4 (FAB1, FAD2-1, FAD6, and FATB) having experienced selection during the subsequent period of improvement. Sequencing of a subset of these genes from an extended panel of sunflower cultivars revealed little additional variation, and an analysis of the genomic region surrounding one of these genes (FAD2-1) revealed the occurrence of an extensive selective sweep affecting a region spanning at least ca. 100 kb. Given that previous population genetic analyses have revealed a relatively rapid decay of linkage disequilibrium in sunflower, this finding indicates the occurrence of strong selection and a rapid sweep.
Collapse
Affiliation(s)
- Mark A Chapman
- Department of Plant Biology, University of Georgia, Miller Plant Sciences Bldg., Athens, GA 30602, USA.
| | | |
Collapse
|
90
|
Comparative population genomics of maize domestication and improvement. Nat Genet 2012; 44:808-11. [PMID: 22660546 DOI: 10.1038/ng.2309] [Citation(s) in RCA: 563] [Impact Index Per Article: 46.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2011] [Accepted: 05/04/2012] [Indexed: 12/20/2022]
Abstract
Domestication and plant breeding are ongoing 10,000-year-old evolutionary experiments that have radically altered wild species to meet human needs. Maize has undergone a particularly striking transformation. Researchers have sought for decades to identify the genes underlying maize evolution, but these efforts have been limited in scope. Here, we report a comprehensive assessment of the evolution of modern maize based on the genome-wide resequencing of 75 wild, landrace and improved maize lines. We find evidence of recovery of diversity after domestication, likely introgression from wild relatives, and evidence for stronger selection during domestication than improvement. We identify a number of genes with stronger signals of selection than those previously shown to underlie major morphological changes. Finally, through transcriptome-wide analysis of gene expression, we find evidence both consistent with removal of cis-acting variation during maize domestication and improvement and suggestive of modern breeding having increased dominance in expression while targeting highly expressed genes.
Collapse
|
91
|
Hufford MB, Xu X, van Heerwaarden J, Pyhäjärvi T, Chia JM, Cartwright RA, Elshire RJ, Glaubitz JC, Guill KE, Kaeppler SM, Lai J, Morrell PL, Shannon LM, Song C, Springer NM, Swanson-Wagner RA, Tiffin P, Wang J, Zhang G, Doebley J, McMullen MD, Ware D, Buckler ES, Yang S, Ross-Ibarra J. Comparative population genomics of maize domestication and improvement. Nat Genet 2012. [PMID: 22660546 DOI: 10.1038/ng2309] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/10/2023]
Abstract
Domestication and plant breeding are ongoing 10,000-year-old evolutionary experiments that have radically altered wild species to meet human needs. Maize has undergone a particularly striking transformation. Researchers have sought for decades to identify the genes underlying maize evolution, but these efforts have been limited in scope. Here, we report a comprehensive assessment of the evolution of modern maize based on the genome-wide resequencing of 75 wild, landrace and improved maize lines. We find evidence of recovery of diversity after domestication, likely introgression from wild relatives, and evidence for stronger selection during domestication than improvement. We identify a number of genes with stronger signals of selection than those previously shown to underlie major morphological changes. Finally, through transcriptome-wide analysis of gene expression, we find evidence both consistent with removal of cis-acting variation during maize domestication and improvement and suggestive of modern breeding having increased dominance in expression while targeting highly expressed genes.
Collapse
Affiliation(s)
- Matthew B Hufford
- Department of Plant Sciences, University of California, Davis, California, USA
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
92
|
Huang CL, Hung CY, Chiang YC, Hwang CC, Hsu TW, Huang CC, Hung KH, Tsai KC, Wang KH, Osada N, Schaal BA, Chiang TY. Footprints of natural and artificial selection for photoperiod pathway genes in Oryza. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2012; 70:769-82. [PMID: 22268451 DOI: 10.1111/j.1365-313x.2012.04915.x] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Asian rice, Oryza sativa, consists of two major subspecies, indica and japonica, which are physiologically differentiated and adapted to different latitudes. Genes for photoperiod sensitivity are likely targets of selection along latitude. We examined the footprints of natural and artificial selections for four major genes of the photoperiod pathway, namely PHYTOCHROME B (PhyB), HEADING DATE 1 (Hd1), HEADING DATE 3a (Hd3a), and EARLY HEADING DATE 1 (Ehd1), by investigation of the patterns of nucleotide polymorphisms in cultivated and wild rice. Geographical subdivision between tropical and subtropical O. rufipogon was found for all of the photoperiod genes in plants divided by the Tropic of Cancer (TOC). All of these genes, except for PhyB, were characterized by the existence of clades that split a long time ago and that corresponded to latitudinal subdivisions, and revealed a likely diversifying selection. Ssp. indica showed close affinity to tropical O. rufipogon for all genes, while ssp. japonica, which has a much wider range of distribution, displayed complex patterns of differentiation from O. rufipogon, which reflected various agricultural needs in relation to crop yield. In japonica, all genes, except Hd3a, were genetically differentiated at the TOC, while geographical subdivision occurred at 31°N in Hd3a, probably the result of varying photoperiods. Many other features of the photoperiod genes revealed domestication signatures, which included high linkage disequilibrium (LD) within genes, the occurrence of frequent and recurrent non-functional Hd1 mutants in cultivated rice, crossovers between subtropical and tropical alleles of Hd1, and significant LD between Hd1 and Hd3a in japonica and indica.
Collapse
Affiliation(s)
- Chao-Li Huang
- Department of Life Sciences, National Cheng Kung University, Tainan 701, Taiwan
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
93
|
Lu L, Yan W, Xue W, Shao D, Xing Y. Evolution and association analysis of Ghd7 in rice. PLoS One 2012; 7:e34021. [PMID: 22666315 PMCID: PMC3364234 DOI: 10.1371/journal.pone.0034021] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2011] [Accepted: 02/20/2012] [Indexed: 11/19/2022] Open
Abstract
Plant height, heading date, and yield are the main targets for rice genetic improvement. Ghd7 is a pleiotropic gene that controls the aforementioned traits simultaneously. In this study, a rice germplasm collection of 104 accessions (Oryza sativa) and 3 wild rice varieties (O.rufipogon) was used to analyze the evolution and association of Ghd7 with plant height, heading date, and yield. Among the 104 accessions, 76 single nucleotide polymorphisms (SNPs) and six insertions and deletions were found within a 3932-bp DNA fragment of Ghd7. A higher pairwise π and θ in the promoter indicated a highly diversified promoter of Ghd7. Sixteen haplotypes and 8 types of Ghd7 protein were detected. SNP changes between haplotypes indicated that Ghd7 evolved from two distinct ancestral gene pools, and independent domestication processes were detected in indica and japonica varietals respectively. In addition to the previously reported premature stop mutation in the first exon of Ghd7, which caused phenotypic changes of multiple traits, we found another functional C/T mutation (SNP S_555) by structure-based association analysis. SNP S_555 is located in the promoter and was related to plant height probably by altering gene expression. Moreover, another seven SNP mutations in complete linkage were found to be associated with the number of spikelets per panicle, regardless of the photoperiod. These associations provide the potential for flexibility of Ghd7 application in rice breeding programs.
Collapse
Affiliation(s)
- Li Lu
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, China
| | - Wenhao Yan
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, China
| | - Weiya Xue
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, China
| | - Di Shao
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, China
| | - Yongzhong Xing
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, China
- * E-mail:
| |
Collapse
|
94
|
Frankham R. How closely does genetic diversity in finite populations conform to predictions of neutral theory? Large deficits in regions of low recombination. Heredity (Edinb) 2012; 108:167-78. [PMID: 21878983 PMCID: PMC3282390 DOI: 10.1038/hdy.2011.66] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2010] [Revised: 06/21/2011] [Accepted: 06/27/2011] [Indexed: 11/09/2022] Open
Abstract
Levels of genetic diversity in finite populations are crucial in conservation and evolutionary biology. Genetic diversity is required for populations to evolve and its loss is related to inbreeding in random mating populations, and thus to reduced population fitness and increased extinction risk. Neutral theory is widely used to predict levels of genetic diversity. I review levels of genetic diversity in finite populations in relation to predictions of neutral theory. Positive associations between genetic diversity and population size, as predicted by neutral theory, are observed for microsatellites, allozymes, quantitative genetic variation and usually for mitochondrial DNA (mtDNA). However, there are frequently significant deviations from neutral theory owing to indirect selection at linked loci caused by balancing selection, selective sweeps and background selection. Substantially lower genetic diversity than predicted under neutrality was found for chromosomes with low recombination rates and high linkage disequilibrium (compared with 'normally' recombining chromosomes within species and adjusted for different copy numbers and mutation rates), including W (median 100% lower) and Y (89% lower) chromosomes, dot fourth chromosomes in Drosophila (94% lower) and mtDNA (67% lower). Further, microsatellite genetic and allelic diversity were lost at 12 and 33% faster rates than expected in populations adapting to captivity, owing to widespread selective sweeps. Overall, neither neutral theory nor most versions of the genetic draft hypothesis are compatible with all empirical results.
Collapse
Affiliation(s)
- R Frankham
- Department of Biological Sciences, Macquarie University, Sydney, New South Wales, Australia.
| |
Collapse
|
95
|
Singh D, Singh PK, Chaudhary S, Mehla K, Kumar S. Exome sequencing and advances in crop improvement. ADVANCES IN GENETICS 2012; 79:87-121. [PMID: 22989766 DOI: 10.1016/b978-0-12-394395-8.00003-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Next-generation sequencing strategies have opened new vistas for molecular plant breeding. The sequence information obtained by the advent of next-generation sequencing provides a valuable tool not only for improving domesticated crops but also for investigating the natural evolution of crops. Such information provides an enormous potential for sustainable agriculture. In this review, we discuss how such sequencing approaches have transformed exome sequencing into a practical utility that has enormous potential for crop improvement in agriculture. Furthermore, we also describe the future of crop improvement beyond the exome sequencing strategies.
Collapse
Affiliation(s)
- Devi Singh
- Molecular Biology Laboratory, Department of Genetics and Plant Breeding, Sardar Vallabhbhai Patel University of Agriculture and Technology, Meerut, UP, India
| | | | | | | | | |
Collapse
|
96
|
Zhang P, Li J, Li X, Liu X, Zhao X, Lu Y. Population structure and genetic diversity in a rice core collection (Oryza sativa L.) investigated with SSR markers. PLoS One 2011; 6:e27565. [PMID: 22164211 PMCID: PMC3229487 DOI: 10.1371/journal.pone.0027565] [Citation(s) in RCA: 116] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2011] [Accepted: 10/19/2011] [Indexed: 11/19/2022] Open
Abstract
The assessment of genetic diversity and population structure of a core collection would benefit to make use of these germplasm as well as applying them in association mapping. The objective of this study were to (1) examine the population structure of a rice core collection; (2) investigate the genetic diversity within and among subgroups of the rice core collection; (3) identify the extent of linkage disequilibrium (LD) of the rice core collection. A rice core collection consisting of 150 varieties which was established from 2260 varieties of Ting's collection of rice germplasm were genotyped with 274 SSR markers and used in this study. Two distinct subgroups (i.e. SG 1 and SG 2) were detected within the entire population by different statistical methods, which is in accordance with the differentiation of indica and japonica rice. MCLUST analysis might be an alternative method to STRUCTURE for population structure analysis. A percentage of 26% of the total markers could detect the population structure as the whole SSR marker set did with similar precision. Gene diversity and MRD between the two subspecies varied considerably across the genome, which might be used to identify candidate genes for the traits under domestication and artificial selection of indica and japonica rice. The percentage of SSR loci pairs in significant (P<0.05) LD is 46.8% in the entire population and the ratio of linked to unlinked loci pairs in LD is 1.06. Across the entire population as well as the subgroups and sub-subgroups, LD decays with genetic distance, indicating that linkage is one main cause of LD. The results of this study would provide valuable information for association mapping using the rice core collection in future.
Collapse
Affiliation(s)
- Peng Zhang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, China
| | - Jinquan Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, China
- * E-mail: (JL); (YL)
| | - Xiaoling Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, China
| | - Xiangdong Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, China
| | - Xingjuan Zhao
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, China
| | - Yonggen Lu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, China
- * E-mail: (JL); (YL)
| |
Collapse
|
97
|
Sunflower domestication alleles support single domestication center in eastern North America. Proc Natl Acad Sci U S A 2011; 108:14360-5. [PMID: 21844335 DOI: 10.1073/pnas.1104853108] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Phylogenetic analyses of genes with demonstrated involvement in evolutionary transitions can be an important means of resolving conflicting hypotheses about evolutionary history or process. In sunflower, two genes have previously been shown to have experienced selective sweeps during its early domestication. In the present study, we identified a third candidate early domestication gene and conducted haplotype analyses of all three genes to address a recent, controversial hypothesis about the origin of cultivated sunflower. Although the scientific consensus had long been that sunflower was domesticated once in eastern North America, the discovery of pre-Columbian sunflower remains at archaeological sites in Mexico led to the proposal of a second domestication center in southern Mexico. Previous molecular studies with neutral markers were consistent with the former hypothesis. However, only two indigenous Mexican cultivars were included in these studies, and their provenance and genetic purity have been questioned. Therefore, we sequenced regions of the three candidate domestication genes containing SNPs diagnostic for domestication from large, newly collected samples of Mexican sunflower landraces and Mexican wild populations from a broad geographic range. The new germplasm also was genotyped for 12 microsatellite loci. Our evidence from multiple evolutionarily important loci and from neutral markers supports a single domestication event for extant cultivated sunflower in eastern North America.
Collapse
|
98
|
Famoso AN, Zhao K, Clark RT, Tung CW, Wright MH, Bustamante C, Kochian LV, McCouch SR. Genetic architecture of aluminum tolerance in rice (Oryza sativa) determined through genome-wide association analysis and QTL mapping. PLoS Genet 2011; 7:e1002221. [PMID: 21829395 PMCID: PMC3150440 DOI: 10.1371/journal.pgen.1002221] [Citation(s) in RCA: 233] [Impact Index Per Article: 17.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2011] [Accepted: 06/21/2011] [Indexed: 01/22/2023] Open
Abstract
Aluminum (Al) toxicity is a primary limitation to crop productivity on acid soils, and rice has been demonstrated to be significantly more Al tolerant than other cereal crops. However, the mechanisms of rice Al tolerance are largely unknown, and no genes underlying natural variation have been reported. We screened 383 diverse rice accessions, conducted a genome-wide association (GWA) study, and conducted QTL mapping in two bi-parental populations using three estimates of Al tolerance based on root growth. Subpopulation structure explained 57% of the phenotypic variation, and the mean Al tolerance in Japonica was twice that of Indica. Forty-eight regions associated with Al tolerance were identified by GWA analysis, most of which were subpopulation-specific. Four of these regions co-localized with a priori candidate genes, and two highly significant regions co-localized with previously identified QTLs. Three regions corresponding to induced Al-sensitive rice mutants (ART1, STAR2, Nrat1) were identified through bi-parental QTL mapping or GWA to be involved in natural variation for Al tolerance. Haplotype analysis around the Nrat1 gene identified susceptible and tolerant haplotypes explaining 40% of the Al tolerance variation within the aus subpopulation, and sequence analysis of Nrat1 identified a trio of non-synonymous mutations predictive of Al sensitivity in our diversity panel. GWA analysis discovered more phenotype-genotype associations and provided higher resolution, but QTL mapping identified critical rare and/or subpopulation-specific alleles not detected by GWA analysis. Mapping using Indica/Japonica populations identified QTLs associated with transgressive variation where alleles from a susceptible aus or indica parent enhanced Al tolerance in a tolerant Japonica background. This work supports the hypothesis that selectively introgressing alleles across subpopulations is an efficient approach for trait enhancement in plant breeding programs and demonstrates the fundamental importance of subpopulation in interpreting and manipulating the genetics of complex traits in rice.
Collapse
Affiliation(s)
- Adam N. Famoso
- Department of Plant Breeding and Genetics, Cornell University, Ithaca, New York, United States of America
| | - Keyan Zhao
- Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, New York, United States of America
| | - Randy T. Clark
- Robert W. Holley Center for Agriculture and Health, Agricultural Research Service, US Department of Agriculture, Cornell University, Ithaca, New York, United States of America
| | - Chih-Wei Tung
- Department of Plant Breeding and Genetics, Cornell University, Ithaca, New York, United States of America
| | - Mark H. Wright
- Department of Plant Breeding and Genetics, Cornell University, Ithaca, New York, United States of America
- Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, New York, United States of America
| | - Carlos Bustamante
- Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, New York, United States of America
| | - Leon V. Kochian
- Robert W. Holley Center for Agriculture and Health, Agricultural Research Service, US Department of Agriculture, Cornell University, 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
- * E-mail:
| |
Collapse
|
99
|
Li X, Yan W, Agrama H, Jia L, Shen X, Jackson A, Moldenhauer K, Yeater K, McClung A, Wu D. Mapping QTLs for improving grain yield using the USDA rice mini-core collection. PLANTA 2011; 234:347-61. [PMID: 21479810 DOI: 10.1007/s00425-011-1405-0] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2011] [Accepted: 03/23/2011] [Indexed: 05/20/2023]
Abstract
Yield is the most important and complex trait for genetic improvement in crops, and marker-assisted selection enhances the improvement efficiency. The USDA rice mini-core collection derived from over 18,000 accessions of global origins is an ideal panel for association mapping. We phenotyped 203 O. sativa accessions for 14 agronomic traits and identified 5 that were highly and significantly correlated with grain yield per plant: plant height, plant weight, tillers, panicle length, and kernels/branch. Genotyping with 155 genome-wide molecular markers demonstrated 5 main cluster groups. Linkage disequilibrium (LD) decayed at least 20 cM and marker pairs with significant LD ranged from 4.64 to 6.06% in four main groups. Model comparisons revealed that different dimensions of principal component analysis affected yield and its correlated traits for mapping accuracy, and kinship did not improve the mapping in this collection. Thirty marker-trait associations were highly significant, 4 for yield, 3 for plant height, 6 for plant weight, 9 for tillers, 5 for panicle length and 3 for kernels/branch. Twenty-one markers contributed to the 30 associations, because 8 markers were co-associated with 2 or more traits. Allelic analysis of OSR13, RM471 and RM7003 for their co-associations with yield traits demonstrated that allele 126 bp of RM471 and 108 bp of RM7003 should receive greater attention, because they had the greatest positive effect on yield traits. Tagging the QTLs responsible for multiple yield traits may simultaneously help dissect the complex yield traits and elevate the efficiency to improve grain yield using marker-assisted selection in rice.
Collapse
Affiliation(s)
- Xiaobai Li
- State Key Lab of Rice Biology, IAEA Collaborating Center, Zhejiang University, Hangzhou, China
| | | | | | | | | | | | | | | | | | | |
Collapse
|
100
|
Xie X, Molina J, Hernandez R, Reynolds A, Boyko AR, Bustamante CD, Purugganan MD. Levels and patterns of nucleotide variation in domestication QTL regions on rice chromosome 3 suggest lineage-specific selection. PLoS One 2011; 6:e20670. [PMID: 21674010 PMCID: PMC3108957 DOI: 10.1371/journal.pone.0020670] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2011] [Accepted: 05/08/2011] [Indexed: 02/03/2023] Open
Abstract
Oryza sativa or Asian cultivated rice is one of the major cereal grass species domesticated for human food use during the Neolithic. Domestication of this species from the wild grass Oryza rufipogon was accompanied by changes in several traits, including seed shattering, percent seed set, tillering, grain weight, and flowering time. Quantitative trait locus (QTL) mapping has identified three genomic regions in chromosome 3 that appear to be associated with these traits. We would like to study whether these regions show signatures of selection and whether the same genetic basis underlies the domestication of different rice varieties. Fragments of 88 genes spanning these three genomic regions were sequenced from multiple accessions of two major varietal groups in O. sativa--indica and tropical japonica--as well as the ancestral wild rice species O. rufipogon. In tropical japonica, the levels of nucleotide variation in these three QTL regions are significantly lower compared to genome-wide levels, and coalescent simulations based on a complex demographic model of rice domestication indicate that these patterns are consistent with selection. In contrast, there is no significant reduction in nucleotide diversity in the homologous regions in indica rice. These results suggest that there are differences in the genetic and selective basis for domestication between these two Asian rice varietal groups.
Collapse
Affiliation(s)
- Xianfa Xie
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, New York, United States of America.
| | | | | | | | | | | | | |
Collapse
|