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Kumar K, Kumari A, Durgesh K, Sevanthi AM, Sharma S, Singh NK, Gaikwad K. Identification of superior haplotypes for flowering time in pigeonpea through candidate gene-based association study of a diverse minicore collection. PLANT CELL REPORTS 2024; 43:156. [PMID: 38819495 DOI: 10.1007/s00299-024-03230-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Accepted: 05/05/2024] [Indexed: 06/01/2024]
Abstract
KEY MESSAGE In current study candidate gene (261 genes) based association mapping on 144 pigeonpea accessions for flowering time and related traits and 29 MTAs producing eight superior haplotypes were identified. In the current study, we have conducted an association analysis for flowering-associated traits in a diverse pigeonpea mini-core collection comprising 144 accessions using the SNP data of 261 flowering-related genes. In total, 13,449 SNPs were detected in the current study, which ranged from 743 (ICP10228) to 1469 (ICP6668) among the individuals. The nucleotide diversity (0.28) and Watterson estimates (0.34) reflected substantial diversity, while Tajima's D (-0.70) indicated the abundance of rare alleles in the collection. A total of 29 marker trait associations (MTAs) were identified, among which 19 were unique to days to first flowering (DOF) and/or days to fifty percent flowering (DFF), 9 to plant height (PH), and 1 to determinate (Det) growth habit using 3 years of phenotypic data. Among these MTAs, six were common to DOF and/or DFF, and four were common to DOF/DFF along with the PH, reflecting their pleiotropic action. These 29 MTAs spanned 25 genes, among which 10 genes clustered in the protein-protein network analysis, indicating their concerted involvement in floral induction. Furthermore, we identified eight haplotypes, four of which regulate late flowering, while the remaining four regulate early flowering using the MTAs. Interestingly, haplotypes conferring late flowering (H001, H002, and H008) were found to be taller, while those involved in early flowering (H003) were shorter in height. The expression pattern of these genes, as inferred from the transcriptome data, also underpinned their involvement in floral induction. The haplotypes identified will be highly useful to the pigeonpea breeding community for haplotype-based breeding.
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Affiliation(s)
- Kuldeep Kumar
- ICAR-National Institute for Plant Biotechnology, Pusa, New Delhi, India
- ICAR-Indian Institute of Pulses Research, Kanpur, Uttar Pradesh, India
- The Graduate School, ICAR-Indian Agricultural Research Institute, Pusa, New Delhi, India
| | - Anita Kumari
- Department of Botany, North Campus, University of Delhi, Delhi, New Delhi, India
| | - Kumar Durgesh
- Division of Genetics, ICAR-Indian Agricultural Research Institute, Pusa, New Delhi, India
| | | | - Sandhya Sharma
- ICAR-National Institute for Plant Biotechnology, Pusa, New Delhi, India
| | | | - Kishor Gaikwad
- ICAR-National Institute for Plant Biotechnology, Pusa, New Delhi, India.
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Zhong X, Li M, Zhang M, Feng Y, Zhang H, Tian H. Genome-wide analysis of the laccase gene family in wheat and relationship with arbuscular mycorrhizal colonization. PLANTA 2022; 257:15. [PMID: 36528718 DOI: 10.1007/s00425-022-04048-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Accepted: 12/08/2022] [Indexed: 06/17/2023]
Abstract
We identified 156 laccase genes belonging to 11 subfamilies in the wheat genome, and the natural variation of laccase genes significantly affected the development of wheat-arbuscular mycorrhizal symbiosis. Laccases (LACs) have a variety of functions in plant lignification, cell elongation and stress responses. This study aimed to reveal the phylogeny, chromosomal spatial distribution, coexpression and evolution of LAC genes in the wheat genome and to investigate the possible roles of LAC genes during arbuscular mycorrhizal (AM) symbiosis. The genomic characteristics of LAC genes were analyzed by using bioinformatics analysis methods, and the polymorphisms of LAC genes were analyzed by using a diverse wheat panel composed of 289 wheat cultivars. We identified 156 LAC genes belonging to 11 subfamilies in the wheat genome, and segmental duplication dominated the amplification of the LAC gene family in the wheat genome. LACs are dominantly located in the R2 region of wheat chromosomes. Some LACs are collinear with the characterized LACs in Arabidopsis thaliana or rice. A number of genes encoding transcription factors, kinases, and phosphatases were coexpressed with LAC genes in wheat. TaLACs may be potential targets for some miRNAs. Most TaLACs are mainly expressed in the roots and stems of plants. The expression of TaLACs could be regulated by the inoculation of Fusarium graminearum or AM fungi. The polymorphisms of TaLACs mainly accumulate by random drift instead of by selection. Through candidate gene association analysis, we found that the natural variations in TaLACs significantly affected root colonization by AM fungi. The present study provides useful information for further study of the biological functions of LAC genes in wheat, especially the roles of LAC genes during the development of AM symbiosis.
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Affiliation(s)
- Xiong Zhong
- Key Laboratory of Plant Nutrition and Agri-Environment in Northwest China, Ministry of Agriculture, College of Natural Resources and Environment, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Mengjiao Li
- Key Laboratory of Plant Nutrition and Agri-Environment in Northwest China, Ministry of Agriculture, College of Natural Resources and Environment, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Mingming Zhang
- Key Laboratory of Plant Nutrition and Agri-Environment in Northwest China, Ministry of Agriculture, College of Natural Resources and Environment, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Yang Feng
- Key Laboratory of Plant Nutrition and Agri-Environment in Northwest China, Ministry of Agriculture, College of Natural Resources and Environment, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Hui Zhang
- Key Laboratory of Plant Nutrition and Agri-Environment in Northwest China, Ministry of Agriculture, College of Natural Resources and Environment, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Hui Tian
- Key Laboratory of Plant Nutrition and Agri-Environment in Northwest China, Ministry of Agriculture, College of Natural Resources and Environment, Northwest A&F University, Yangling, 712100, Shaanxi, China.
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Chang Y, Zhang W, Ma Y, Xia M, Fan K, Jiang Z, Hu T. Transcriptome analysis of floral bud development and function analysis of a novel CO gene in Paeonia × lemoinei 'High Noon'. Sci Rep 2022; 12:17281. [PMID: 36241907 PMCID: PMC9568513 DOI: 10.1038/s41598-022-22195-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2022] [Accepted: 10/11/2022] [Indexed: 01/06/2023] Open
Abstract
Paeonia × lemoinei 'High Noon' is one of the most important cultivars in tree peony (Paeonia sect. Moutan), a traditional horticultural plant in China, with a re-blooming characteristic which was quite different from other cultivars. So, the genetic resources in 'High Noon' were incredibly valuable in flowering-time-modified molecular breeding in tree peony. However, the molecular mechanism underlying the floral bud formation of 'High Noon' was not clear yet. To explore the molecular mechanism in this process, the transcriptomes of three stages during floral bud development were deeply analyzed in this study. As a result, a total of 5816 differentially expressed genes (DEGs) were identified between the three developmental stages, and pathways including ''DNA replication'', ''metabolic pathways'', ''circadian rhythm'', and ''plant hormone signal transduction'' were mostly enriched in the functional enrichment and expression pattern analysis. Furthermore, a total of 584 genes related to the photoperiod pathway were further identified and a novel CO homolog gene PlCO was identified to be a stable hydrophilic protein, which contained both CCT domain and B-box domain. Over-expression of PlCO in Arabidopsis resulted in early flowering, which suggested a promotion role of flowering. The PlCO protein localized in nucleus and possessed a transcription activity ability, which implied that PlCO might function as a transcription factor. The transcriptome analysis revealed pathways involved in floral bud development in tree peony and provided new insight into the regulatory network underlying the floral bud development. The gene identification in 'High Noon' provided new valuable candidate genes for flowering-time-modified molecular breeding in tree peony.
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Affiliation(s)
- Yanting Chang
- grid.459618.70000 0001 0742 5632Key Laboratory of Bamboo and Rattan Science and Technology, State Forestry Administration, Institute of Horticultural Flower and Landscape, International Center for Bamboo and Rattan, Futongdong Rd, Wang Jing, Chaoyang District, Beijing, 100102 China
| | - Wenbo Zhang
- grid.459618.70000 0001 0742 5632Key Laboratory of Bamboo and Rattan Science and Technology, State Forestry Administration, Institute of Horticultural Flower and Landscape, International Center for Bamboo and Rattan, Futongdong Rd, Wang Jing, Chaoyang District, Beijing, 100102 China
| | - Yanjun Ma
- grid.459618.70000 0001 0742 5632Key Laboratory of Bamboo and Rattan Science and Technology, State Forestry Administration, Institute of Horticultural Flower and Landscape, International Center for Bamboo and Rattan, Futongdong Rd, Wang Jing, Chaoyang District, Beijing, 100102 China
| | - Mengsi Xia
- grid.459618.70000 0001 0742 5632Key Laboratory of Bamboo and Rattan Science and Technology, State Forestry Administration, Institute of Horticultural Flower and Landscape, International Center for Bamboo and Rattan, Futongdong Rd, Wang Jing, Chaoyang District, Beijing, 100102 China
| | - Keke Fan
- grid.459618.70000 0001 0742 5632Key Laboratory of Bamboo and Rattan Science and Technology, State Forestry Administration, Institute of Horticultural Flower and Landscape, International Center for Bamboo and Rattan, Futongdong Rd, Wang Jing, Chaoyang District, Beijing, 100102 China
| | - Zehui Jiang
- grid.459618.70000 0001 0742 5632Key Laboratory of Bamboo and Rattan Science and Technology, State Forestry Administration, Institute of Horticultural Flower and Landscape, International Center for Bamboo and Rattan, Futongdong Rd, Wang Jing, Chaoyang District, Beijing, 100102 China
| | - Tao Hu
- grid.459618.70000 0001 0742 5632Key Laboratory of Bamboo and Rattan Science and Technology, State Forestry Administration, Institute of Horticultural Flower and Landscape, International Center for Bamboo and Rattan, Futongdong Rd, Wang Jing, Chaoyang District, Beijing, 100102 China
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Khan SU, Saeed S, Khan MHU, Fan C, Ahmar S, Arriagada O, Shahzad R, Branca F, Mora-Poblete F. Advances and Challenges for QTL Analysis and GWAS in the Plant-Breeding of High-Yielding: A Focus on Rapeseed. Biomolecules 2021; 11:1516. [PMID: 34680149 PMCID: PMC8533950 DOI: 10.3390/biom11101516] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2021] [Revised: 10/07/2021] [Accepted: 10/11/2021] [Indexed: 12/15/2022] Open
Abstract
Yield is one of the most important agronomic traits for the breeding of rapeseed (Brassica napus L), but its genetic dissection for the formation of high yield remains enigmatic, given the rapid population growth. In the present review, we review the discovery of major loci underlying important agronomic traits and the recent advancement in the selection of complex traits. Further, we discuss the benchmark summary of high-throughput techniques for the high-resolution genetic breeding of rapeseed. Biparental linkage analysis and association mapping have become powerful strategies to comprehend the genetic architecture of complex agronomic traits in crops. The generation of improved crop varieties, especially rapeseed, is greatly urged to enhance yield productivity. In this sense, the whole-genome sequencing of rapeseed has become achievable to clone and identify quantitative trait loci (QTLs). Moreover, the generation of high-throughput sequencing and genotyping techniques has significantly enhanced the precision of QTL mapping and genome-wide association study (GWAS) methodologies. Furthermore, this study demonstrates the first attempt to identify novel QTLs of yield-related traits, specifically focusing on ovule number per pod (ON). We also highlight the recent breakthrough concerning single-locus-GWAS (SL-GWAS) and multi-locus GWAS (ML-GWAS), which aim to enhance the potential and robust control of GWAS for improved complex traits.
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Affiliation(s)
- Shahid Ullah Khan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China; (S.U.K.); (S.S.); (M.H.U.K.)
| | - Sumbul Saeed
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China; (S.U.K.); (S.S.); (M.H.U.K.)
| | - Muhammad Hafeez Ullah Khan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China; (S.U.K.); (S.S.); (M.H.U.K.)
| | - Chuchuan Fan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China; (S.U.K.); (S.S.); (M.H.U.K.)
| | - Sunny Ahmar
- Institute of Biological Sciences, University of Talca, 1 Poniente 1141, Talca 3465548, Chile;
| | - Osvin Arriagada
- Departamento de Ciencias Vegetales, Facultad de Agronomía e Ingeniería Forestal, Pontificia Universidad Católica de Chile, Santiago 7820436, Chile;
| | - Raheel Shahzad
- Department of Biotechnology, Faculty of Science & Technology, Universitas Muhammadiyah Bandung, Bandung 40614, Indonesia;
| | - Ferdinando Branca
- Department of Agriculture, Food and Environment (Di3A), University of Catania, 95123 Catania, Italy;
| | - Freddy Mora-Poblete
- Institute of Biological Sciences, University of Talca, 1 Poniente 1141, Talca 3465548, Chile;
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Meger J, Ulaszewski B, Burczyk J. Genomic signatures of natural selection at phenology-related genes in a widely distributed tree species Fagus sylvatica L. BMC Genomics 2021; 22:583. [PMID: 34332553 PMCID: PMC8325806 DOI: 10.1186/s12864-021-07907-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2021] [Accepted: 07/20/2021] [Indexed: 11/17/2022] Open
Abstract
BACKGROUND Diversity among phenology-related genes is predicted to be a contributing factor in local adaptations seen in widely distributed plant species that grow in climatically variable geographic areas, such as forest trees. European beech (Fagus sylvatica L.) is widespread, and is one of the most important broadleaved tree species in Europe; however, its potential for adaptation to climate change is a matter of uncertainty, and little is known about the molecular basis of climate change-relevant traits like bud burst. RESULTS We explored single nucleotide polymorphisms (SNP) at candidate genes related to bud burst in beech individuals sampled across 47 populations from Europe. SNP diversity was monitored for 380 candidate genes using a sequence capture approach, providing 2909 unlinked SNP loci. We used two complementary analytical methods to find loci significantly associated with geographic variables, climatic variables (expressed as principal components), or phenotypic variables (spring and autumn phenology, height, survival). Redundancy analysis (RDA) was used to detect candidate markers across two spatial scales (entire study area and within subregions). We revealed 201 candidate SNPs at the broadest scale, 53.2% of which were associated with phenotypic variables. Additive polygenic scores, which provide a measure of the cumulative signal across significant candidate SNPs, were correlated with a climate variable (first principal component, PC1) related to temperature and precipitation availability, and spring phenology. However, different genotype-environment associations were identified within Southeastern Europe as compared to the entire geographic range of European beech. CONCLUSIONS Environmental conditions play important roles as drivers of genetic diversity of phenology-related genes that could influence local adaptation in European beech. Selection in beech favors genotypes with earlier bud burst under warmer and wetter habitats within its range; however, selection pressures may differ across spatial scales.
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Affiliation(s)
- Joanna Meger
- Department of Genetics, Faculty of Biological Sciences, Kazimierz Wielki University, Chodkiewicza 30, 85-064, Bydgoszcz, Poland
| | - Bartosz Ulaszewski
- Department of Genetics, Faculty of Biological Sciences, Kazimierz Wielki University, Chodkiewicza 30, 85-064, Bydgoszcz, Poland
| | - Jaroslaw Burczyk
- Department of Genetics, Faculty of Biological Sciences, Kazimierz Wielki University, Chodkiewicza 30, 85-064, Bydgoszcz, Poland.
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Identification of Candidate Gene-Based Markers for Girth Growth in Rubber Trees. PLANTS 2021; 10:plants10071440. [PMID: 34371639 PMCID: PMC8309273 DOI: 10.3390/plants10071440] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Revised: 07/08/2021] [Accepted: 07/12/2021] [Indexed: 02/01/2023]
Abstract
Girth growth is an important factor in both latex and timber production of the rubber tree. In this study, we performed candidate gene association mapping for girth growth in rubber trees using intron length polymorphism markers (ILP) in identifying the candidate genes responsible for girth growth. The COBL064_1 marker developed from the candidate gene (COBL4) regulating cellulose deposition and oriented cell expansion in the plant cell wall showed the strongest association with girth growth across two seasons in the Amazonian population and was validated in the breeding lines. We then applied single molecule real-time (SMRT) circular consensus sequencing (CCS) to analyze a wider gene region of the COBL4 to pinpoint the single nucleotide polymorphism (SNP) that best explains the association with the traits. A SNP in the 3’ UTR showing linkage disequilibrium with the COBL064_1 most associated with girth growth. This study showed that the cost-effective method of ILP gene-based markers can assist in identification of SNPs in the candidate gene associated with girth growth. The SNP markers identified in this study added useful markers for the improvement of girth growth in rubber tree breeding programs.
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Cuervo-Alarcon L, Arend M, Müller M, Sperisen C, Finkeldey R, Krutovsky KV. A candidate gene association analysis identifies SNPs potentially involved in drought tolerance in European beech (Fagus sylvatica L.). Sci Rep 2021; 11:2386. [PMID: 33504857 PMCID: PMC7840767 DOI: 10.1038/s41598-021-81594-w] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Accepted: 01/06/2021] [Indexed: 01/30/2023] Open
Abstract
Studies of genetic variation underlying traits related to drought tolerance in forest trees are of great importance for understanding their adaptive potential under a climate change scenario. In this study, using a candidate gene approach, associations between SNPs and drought related traits were assessed in saplings of European beech (Fagus sylvatica L.) representing trees growing along steep precipitation gradients. The saplings were subjected to experimentally controlled drought treatments. Response of the saplings was assessed by the evaluation of stem diameter growth (SDG) and the chlorophyll fluorescence parameters FV/FM, PIabs, and PItot. The evaluation showed that saplings from xeric sites were less affected by the drought treatment. Five SNPs (7.14%) in three candidate genes were significantly associated with the evaluated traits; saplings with particular genotypes at these SNPs showed better performance under the drought treatment. The SNPs were located in the cytosolic class I small heat-shock protein, CTR/DRE binding transcription factor, and isocitrate dehydrogenase genes and explained 5.8-13.4% of the phenotypic variance. These findings provide insight into the genetic basis of traits related to drought tolerance in European beech and could support the development of forest conservation management strategies under future climatic conditions.
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Affiliation(s)
- Laura Cuervo-Alarcon
- Department of Forest Genetics and Forest Tree Breeding, Georg-August University of Göttingen, Büsgenweg 2, 37077, Göttingen, Germany
| | - Matthias Arend
- Physiological Plant Ecology, University of Basel, Schönbeinstrasse 6, 4056, Basel, Switzerland
| | - Markus Müller
- Department of Forest Genetics and Forest Tree Breeding, Georg-August University of Göttingen, Büsgenweg 2, 37077, Göttingen, Germany
| | - Christoph Sperisen
- Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Zürcherstrasse 111, 8903, Birmensdorf, Switzerland
| | - Reiner Finkeldey
- University of Kassel, Mönchebergstrasse 19, 34109, Kassel, Germany
| | - Konstantin V Krutovsky
- Department of Forest Genetics and Forest Tree Breeding, Georg-August University of Göttingen, Büsgenweg 2, 37077, Göttingen, Germany.
- Vavilov Institute of General Genetics, Russian Academy of Sciences, 3 Gubkina Str., Moscow, Russia, 119333.
- Laboratory of Foresty Genomics, Genome Research and Education Center, Siberian Federal University, 50a/2 Akademgorodok, Krasnoyarsk, Russia, 660036.
- Department of Ecosystem Science and Management, Texas A&M University, 2138 TAMU, College Station, TX, 77843-2138, USA.
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Khanbo S, Tangphatsornruang S, Piriyapongsa J, Wirojsirasak W, Punpee P, Klomsa-Ard P, Ukoskit K. Candidate gene association of gene expression data in sugarcane contrasting for sucrose content. Genomics 2020; 113:229-237. [PMID: 33321201 DOI: 10.1016/j.ygeno.2020.12.014] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2020] [Revised: 12/03/2020] [Accepted: 12/10/2020] [Indexed: 11/19/2022]
Abstract
Association mapping of gene expression data, generated from transcriptome and proteome studies, provides a means of understanding the functional significance and trait association potential of candidate genes. In this study, we applied candidate gene association mapping to validate sugarcane genes, using data from the starch and sucrose metabolism pathway, transcriptome, and proteome. We performed multiplex PCR targeted amplicon sequencing of 109 candidate genes, using NGS technology. A range of statistical models, both single-locus and multi-locus, were compared for minimization of false positives in association mapping of four sugar-related traits with different heritability. The Fixed and random model Circulating Probability Unification model effectively suppressed false positives for both low- and high-heritability traits. We identified favorable alleles of the candidate genes involved in signalling and transcriptional regulation. The results will support genetic improvement of sugarcane and may help clarify the genetic architecture of sugar-related traits.
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Affiliation(s)
- Supaporn Khanbo
- Department of Biotechnology, Faculty of Science and Technology, Thammasat University, Rangsit Campus, Klong Luang, Pathumtani 12121, Thailand
| | - Sithichoke Tangphatsornruang
- National Science and Technology Development Agency, 113 Thailand Science Park, Khlong Luang, Pathum Thani 12120, Thailand
| | - Jittima Piriyapongsa
- National Science and Technology Development Agency, 113 Thailand Science Park, Khlong Luang, Pathum Thani 12120, Thailand
| | - Warodom Wirojsirasak
- Mitr Phol Innovation and Research Centre, 399 Moo 1, Chumphae-Phukiao Rd. Khoksa-at, Phu Khiao, Chaiyaphum 36110, Thailand
| | - Prapat Punpee
- Mitr Phol Innovation and Research Centre, 399 Moo 1, Chumphae-Phukiao Rd. Khoksa-at, Phu Khiao, Chaiyaphum 36110, Thailand
| | - Peeraya Klomsa-Ard
- Mitr Phol Innovation and Research Centre, 399 Moo 1, Chumphae-Phukiao Rd. Khoksa-at, Phu Khiao, Chaiyaphum 36110, Thailand
| | - Kittipat Ukoskit
- Department of Biotechnology, Faculty of Science and Technology, Thammasat University, Rangsit Campus, Klong Luang, Pathumtani 12121, Thailand.
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Müller LM, Mombaerts L, Pankin A, Davis SJ, Webb AAR, Goncalves J, von Korff M. Differential Effects of Day/Night Cues and the Circadian Clock on the Barley Transcriptome. PLANT PHYSIOLOGY 2020; 183:765-779. [PMID: 32229608 PMCID: PMC7271788 DOI: 10.1104/pp.19.01411] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Accepted: 03/04/2020] [Indexed: 05/05/2023]
Abstract
The circadian clock is a complex transcriptional network that regulates gene expression in anticipation of the day/night cycle and controls agronomic traits in plants. However, in crops, how the internal clock and day/night cues affect the transcriptome remains poorly understood. We analyzed the diel and circadian leaf transcriptomes in the barley (Hordeum vulgare) cultivar 'Bowman' and derived introgression lines harboring mutations in EARLY FLOWERING3 (ELF3), LUX ARRHYTHMO1 (LUX1), and EARLY MATURITY7 (EAM7). The elf3 and lux1 mutants exhibited abolished circadian transcriptome oscillations under constant conditions, whereas eam7 maintained oscillations of ≈30% of the circadian transcriptome. However, day/night cues fully restored transcript oscillations in all three mutants and thus compensated for a disrupted oscillator in the arrhythmic barley clock mutants elf3 and lux1 Nevertheless, elf3, but not lux1, affected the phase of the diel oscillating transcriptome and thus the integration of external cues into the clock. Using dynamical modeling, we predicted a structure of the barley circadian oscillator and interactions of its individual components with day/night cues. Our findings provide a valuable resource for exploring the function and output targets of the circadian clock and for further investigations into the diel and circadian control of the barley transcriptome.
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Affiliation(s)
- Lukas M Müller
- Institute for Plant Genetics, Heinrich-Heine University Düsseldorf, Düsseldorf 40225, Germany
- Max-Planck-Institute for Plant Breeding Research, Cologne 50829, Germany
| | | | - Artem Pankin
- Institute for Plant Genetics, Heinrich-Heine University Düsseldorf, Düsseldorf 40225, Germany
- Max-Planck-Institute for Plant Breeding Research, Cologne 50829, Germany
- Cluster of Excellence on Plant Sciences, "SMART Plants for Tomorrow's Needs," Heinrich-Heine University Düsseldorf, Düsseldorf 40225, Germany
| | - Seth J Davis
- Max-Planck-Institute for Plant Breeding Research, Cologne 50829, Germany
- Department of Department of Biology, University of York, York YO10 5DD, United Kingdom
- Key Laboratory of Plant Stress Biology, School of Life Sciences, Henan University, Kaifeng 15 475004, China
| | - Alex A R Webb
- Circadian Signal Transduction, Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, United Kingdom
| | - Jorge Goncalves
- Systems Control Group, University of Luxembourg, 1009 Luxembourg
| | - Maria von Korff
- Institute for Plant Genetics, Heinrich-Heine University Düsseldorf, Düsseldorf 40225, Germany
- Max-Planck-Institute for Plant Breeding Research, Cologne 50829, Germany
- Cluster of Excellence on Plant Sciences, "SMART Plants for Tomorrow's Needs," Heinrich-Heine University Düsseldorf, Düsseldorf 40225, Germany
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Xanthopoulou A, Manioudaki M, Bazakos C, Kissoudis C, Farsakoglou AM, Karagiannis E, Michailidis M, Polychroniadou C, Zambounis A, Kazantzis K, Tsaftaris A, Madesis P, Aravanopoulos F, Molassiotis A, Ganopoulos I. Whole genome re-sequencing of sweet cherry ( Prunus avium L.) yields insights into genomic diversity of a fruit species. HORTICULTURE RESEARCH 2020; 7:60. [PMID: 32377351 PMCID: PMC7193578 DOI: 10.1038/s41438-020-0281-9] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Revised: 01/17/2020] [Accepted: 02/18/2020] [Indexed: 05/30/2023]
Abstract
Sweet cherries, Prunus avium L. (Rosaceae), are gaining importance due to their perenniallity and nutritional attributes beneficial for human health. Interestingly, sweet cherry cultivars exhibit a wide range of phenotypic diversity in important agronomic traits, such as flowering time and defense reactions against pathogens. In this study, whole-genome resequencing (WGRS) was employed to characterize genetic variation, population structure and allelic variants in a panel of 20 sweet cherry and one wild cherry genotypes, embodying the majority of cultivated Greek germplasm and a representative of a local wild cherry elite phenotype. The 21 genotypes were sequenced in an average depth of coverage of 33.91×. and effective mapping depth, to the genomic reference sequence of 'Satonishiki' cultivar, between 22.21× to 36.62×. Discriminant analysis of principal components (DAPC) with SNPs revealed two clusters of genotypes. There was a rapid linkage disequilibrium decay, as the majority of SNP pairs with r2 in near complete disequilibrium (>0.8) were found at physical distances less than 10 kb. Functional analysis of the variants showed that the genomic ratio of non-synonymous/synonymous (dN/dS) changes was 1.78. The higher dN frequency in the Greek cohort of sweet cherry could be the result of artificial selection pressure imposed by breeding, in combination with the vegetative propagation of domesticated cultivars through grafting. The majority of SNPs with high impact (e.g., stop codon gaining, frameshift), were identified in genes involved in flowering time, dormancy and defense reactions against pathogens, providing promising resources for future breeding programs. Our study has established the foundation for further large scale characterization of sweet cherry germplasm, enabling breeders to incorporate diverse germplasm and allelic variants to fine tune flowering and maturity time and disease resistance in sweet cherry cultivars.
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Affiliation(s)
- Aliki Xanthopoulou
- Laboratory of Pomology, Department of Agriculture, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
| | - Maria Manioudaki
- Laboratory of Pomology, Department of Agriculture, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
| | - Christos Bazakos
- Institute of Plant Breeding and Genetic Resources, ELGO-DEMETER. Thermi, Thessaloniki, 570001 Greece
| | | | - Anna-Maria Farsakoglou
- Laboratory of Forest Genetics & Tree Breeding, Faculty of Agriculture, Forestry & Environmental Science, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Evangelos Karagiannis
- Laboratory of Pomology, Department of Agriculture, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
| | - Michail Michailidis
- Laboratory of Pomology, Department of Agriculture, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
| | - Chrysanthi Polychroniadou
- Laboratory of Pomology, Department of Agriculture, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
| | - Antonios Zambounis
- Institute of Plant Breeding and Genetic Resources, ELGO-DEMETER. Department of Deciduous Fruit Growing, Naoussa, 59035 Greece
| | - Konstantinos Kazantzis
- Institute of Plant Breeding and Genetic Resources, ELGO-DEMETER. Department of Deciduous Fruit Growing, Naoussa, 59035 Greece
| | | | - Panagiotis Madesis
- Institute of Applied Biosciences, CERTH, Thermi, Thessaloniki, 570 01 Greece
| | - Filippos Aravanopoulos
- Laboratory of Forest Genetics & Tree Breeding, Faculty of Agriculture, Forestry & Environmental Science, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Athanassios Molassiotis
- Laboratory of Pomology, Department of Agriculture, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
| | - Ioannis Ganopoulos
- Institute of Plant Breeding and Genetic Resources, ELGO-DEMETER. Thermi, Thessaloniki, 570001 Greece
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Villar L, Lienqueo I, Llanes A, Rojas P, Perez J, Correa F, Sagredo B, Masciarelli O, Luna V, Almada R. Comparative transcriptomic analysis reveals novel roles of transcription factors and hormones during the flowering induction and floral bud differentiation in sweet cherry trees (Prunus avium L. cv. Bing). PLoS One 2020; 15:e0230110. [PMID: 32163460 PMCID: PMC7067470 DOI: 10.1371/journal.pone.0230110] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2019] [Accepted: 02/22/2020] [Indexed: 12/13/2022] Open
Abstract
In sweet cherry trees, flowering is commercially important because the flowers, after fertilization, will generate the fruits. In P. avium, the flowering induction and flower organogensis are the first developmental steps towards flower formation and they occur within specialized organs known as floral buds during the summer, nine months before blooming. During this period the number of floral buds per tree and the bud fruitfulness (number of flowers per bud) are stablished affecting the potential yield of orchards and the plant architecture. The floral bud development is sensitive to any type of stress and the hotter and drier summers will interfere with this process and are calling for new adapted cultivars. A better understanding of the underlying molecular and hormonal mechanisms would be of help, but unlike the model plant Arabidopsis, very little is known about floral induction in sweet cherry. To explore the molecular mechanism of floral bud differentiation, high-throughput RNA sequencing was used to detect differences in the gene expression of P. avium floral buds at five differentiation stages. We found 2,982 differentially expressed genes during floral bud development. We identified genes associated with floral initiation or floral organ identity that appear to be useful biomarkers of floral development and several transcription factor families (ERF, MYB, bHLH, MADS-box and NAC gene family) with novel potential roles during floral transition in this species. We analyzed in deep the MADS-box gene family and we shed light about their key role during floral bud and organs development in P. avium. Furthermore, the hormonal-related signatures in the gene regulatory networks and the dynamic changes of absicic acid, zeatin and indolacetic acid contents in buds suggest an important role for these hormones during floral bud differentiation in sweet cherry. These data provide a rich source of novel informacion for functional and evolutionary studies about floral bud development in sweet cherry and new tools for biotechnology and breeding.
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Affiliation(s)
- Luis Villar
- Centro de Estudios Avanzados en Fruticultura (CEAF), Rengo, Chile
| | - Ixia Lienqueo
- Centro de Estudios Avanzados en Fruticultura (CEAF), Rengo, Chile
| | - Analía Llanes
- Instituto de Investigaciones Agrobiotecnológicas (INIAB-CONICET), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Universidad Nacional de Río Cuarto, Río Cuarto, Córdoba, Argentina
| | - Pamela Rojas
- Instituto de Investigaciones Agropecuarias (INIA) CRI Rayentué, Rengo, Chile
| | - Jorge Perez
- Instituto de Investigaciones Agropecuarias (INIA) CRI Rayentué, Rengo, Chile
| | - Francisco Correa
- Centro de Estudios Avanzados en Fruticultura (CEAF), Rengo, Chile
- Instituto de Investigaciones Agropecuarias (INIA) CRI Rayentué, Rengo, Chile
| | - Boris Sagredo
- Instituto de Investigaciones Agropecuarias (INIA) CRI Rayentué, Rengo, Chile
| | - Oscar Masciarelli
- Instituto de Investigaciones Agrobiotecnológicas (INIAB-CONICET), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Universidad Nacional de Río Cuarto, Río Cuarto, Córdoba, Argentina
| | - Virginia Luna
- Instituto de Investigaciones Agrobiotecnológicas (INIAB-CONICET), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Universidad Nacional de Río Cuarto, Río Cuarto, Córdoba, Argentina
| | - Rubén Almada
- Centro de Estudios Avanzados en Fruticultura (CEAF), Rengo, Chile
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12
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de Jong M, Tavares H, Pasam RK, Butler R, Ward S, George G, Melnyk CW, Challis R, Kover PX, Leyser O. Natural variation in Arabidopsis shoot branching plasticity in response to nitrate supply affects fitness. PLoS Genet 2019; 15:e1008366. [PMID: 31539368 PMCID: PMC6774567 DOI: 10.1371/journal.pgen.1008366] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Revised: 10/02/2019] [Accepted: 08/09/2019] [Indexed: 12/20/2022] Open
Abstract
The capacity of organisms to tune their development in response to environmental cues is pervasive in nature. This phenotypic plasticity is particularly striking in plants, enabled by their modular and continuous development. A good example is the activation of lateral shoot branches in Arabidopsis, which develop from axillary meristems at the base of leaves. The activity and elongation of lateral shoots depends on the integration of many signals both external (e.g. light, nutrient supply) and internal (e.g. the phytohormones auxin, strigolactone and cytokinin). Here, we characterise natural variation in plasticity of shoot branching in response to nitrate supply using two diverse panels of Arabidopsis lines. We find extensive variation in nitrate sensitivity across these lines, suggesting a genetic basis for variation in branching plasticity. High plasticity is associated with extreme branching phenotypes such that lines with the most branches on high nitrate have the fewest under nitrate deficient conditions. Conversely, low plasticity is associated with a constitutively moderate level of branching. Furthermore, variation in plasticity is associated with alternative life histories with the low plasticity lines flowering significantly earlier than high plasticity lines. In Arabidopsis, branching is highly correlated with fruit yield, and thus low plasticity lines produce more fruit than high plasticity lines under nitrate deficient conditions, whereas highly plastic lines produce more fruit under high nitrate conditions. Low and high plasticity, associated with early and late flowering respectively, can therefore be interpreted alternative escape vs mitigate strategies to low N environments. The genetic architecture of these traits appears to be highly complex, with only a small proportion of the estimated genetic variance detected in association mapping.
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Affiliation(s)
- Maaike de Jong
- Sainsbury Laboratory, University of Cambridge, Cambridge, United Kingdom
- Department of Biology, University of York, York, United Kingdom
| | - Hugo Tavares
- Sainsbury Laboratory, University of Cambridge, Cambridge, United Kingdom
| | - Raj K. Pasam
- Sainsbury Laboratory, University of Cambridge, Cambridge, United Kingdom
| | - Rebecca Butler
- Sainsbury Laboratory, University of Cambridge, Cambridge, United Kingdom
| | - Sally Ward
- Sainsbury Laboratory, University of Cambridge, Cambridge, United Kingdom
- Department of Biology, University of York, York, United Kingdom
| | - Gilu George
- Department of Biology, University of York, York, United Kingdom
| | - Charles W. Melnyk
- Sainsbury Laboratory, University of Cambridge, Cambridge, United Kingdom
| | - Richard Challis
- Department of Biology, University of York, York, United Kingdom
| | - Paula X. Kover
- Department of Biology and Biochemistry, University of Bath, Claverton Down, Bath, United Kingdom
| | - Ottoline Leyser
- Sainsbury Laboratory, University of Cambridge, Cambridge, United Kingdom
- Department of Biology, University of York, York, United Kingdom
- * E-mail:
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13
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Kamal N, Ochßner I, Schwandner A, Viehöver P, Hausmann L, Töpfer R, Weisshaar B, Holtgräwe D. Characterization of genes and alleles involved in the control of flowering time in grapevine. PLoS One 2019; 14:e0214703. [PMID: 31269026 PMCID: PMC6608932 DOI: 10.1371/journal.pone.0214703] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Accepted: 06/18/2019] [Indexed: 12/30/2022] Open
Abstract
Grapevine (Vitis vinifera) is one of the most important perennial crop plants in worldwide. Understanding of developmental processes like flowering, which impact quality and quantity of yield in this species is therefore of high interest. This gets even more important when considering some of the expected consequences of climate change. Earlier bud burst and flowering, for example, may result in yield loss due to spring frost. Berry ripening under higher temperatures will impact wine quality. Knowledge of interactions between a genotype or allele combination and the environment can be used for the breeding of genotypes that are better adapted to new climatic conditions. To this end, we have generated a list of more than 500 candidate genes that may play a role in the timing of flowering. The grapevine genome was exploited for flowering time control gene homologs on the basis of functional data from model organisms like A. thaliana. In a previous study, a mapping population derived from early flowering GF.GA-47-42 and late flowering 'Villard Blanc' was analyzed for flowering time QTLs. In a second step we have now established a workflow combining amplicon sequencing and bioinformatics to follow alleles of selected candidate genes in the F1 individuals and the parental genotypes. Allele combinations of these genes in individuals of the mapping population were correlated with early or late flowering phenotypes. Specific allele combinations of flowering time candidate genes within and outside of the QTL regions for flowering time on chromosome 1, 4, 14, 17, and 18 were found to be associated with an early flowering phenotype. In addition, expression of many of the flowering candidate genes was analyzed over consecutive stages of bud and inflorescence development indicating functional roles of these genes in the flowering control network.
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Affiliation(s)
- Nadia Kamal
- Bielefeld University, Faculty of Biology & Center for Biotechnology, Bielefeld, Germany
| | - Iris Ochßner
- Julius Kühn-Institute (JKI), Institute for Grapevine Breeding Geilweilerhof, Siebeldingen, Germany
| | - Anna Schwandner
- Julius Kühn-Institute (JKI), Institute for Grapevine Breeding Geilweilerhof, Siebeldingen, Germany
| | - Prisca Viehöver
- Bielefeld University, Faculty of Biology & Center for Biotechnology, Bielefeld, Germany
| | - Ludger Hausmann
- Julius Kühn-Institute (JKI), Institute for Grapevine Breeding Geilweilerhof, Siebeldingen, Germany
| | - Reinhard Töpfer
- Julius Kühn-Institute (JKI), Institute for Grapevine Breeding Geilweilerhof, Siebeldingen, Germany
| | - Bernd Weisshaar
- Bielefeld University, Faculty of Biology & Center for Biotechnology, Bielefeld, Germany
| | - Daniela Holtgräwe
- Bielefeld University, Faculty of Biology & Center for Biotechnology, Bielefeld, Germany
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14
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Salentijn EMJ, Petit J, Trindade LM. The Complex Interactions Between Flowering Behavior and Fiber Quality in Hemp. FRONTIERS IN PLANT SCIENCE 2019; 10:614. [PMID: 31156677 PMCID: PMC6532435 DOI: 10.3389/fpls.2019.00614] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Accepted: 04/25/2019] [Indexed: 05/05/2023]
Abstract
Hemp, Cannabis sativa L., is a sustainable multipurpose fiber crop with high nutrient and water use efficiency and with biomass of excellent quality for textile fibers and construction materials. The yield and quality of hemp biomass are largely determined by the genetic background of the hemp cultivar but are also strongly affected by environmental factors, such as temperature and photoperiod. Hemp is a facultative short-day plant, characterized by a strong adaptation to photoperiod and a great influence of environmental factors on important agronomic traits such as "flowering-time" and "sex determination." This sensitivity of hemp can cause a considerable degree of heterogeneity, leading to unforeseen yield reductions. Fiber quality for instance is influenced by the developmental stage of hemp at harvest. Also, male and female plants differ in stature and produce fibers with different properties and quality. Next to these causes, there is evidence for specific genotypic variation in fiber quality among hemp accessions. Before improved hemp cultivars can be developed, with specific flowering-times and fiber qualities, and adapted to different geographical regions, a better understanding of the molecular mechanisms controlling important phenological traits such as "flowering-time" and "sex determination" in relation to fiber quality in hemp is required. It is well known that genetic factors play a major role in the outcome of both phenological traits, but the major molecular factors involved in this mechanism are not characterized in hemp. Genome sequences and transcriptome data are available but their analysis mainly focused on the cannabinoid pathway for medical purposes. Herein, we review the current knowledge of phenotypic and genetic data available for "flowering-time," "sex determination," and "fiber quality" in short-day and dioecious crops, respectively, and compare them with the situation in hemp. A picture emerges for several controlling key genes, for which natural genetic variation may lead to desired flowering behavior, including examples of pleiotropic effects on yield quality and on carbon partitioning. Finally, we discuss the prospects for using this knowledge for the molecular breeding of this sustainable crop via a candidate gene approach.
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15
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Zhou R, Liu P, Li D, Zhang X, Wei X. Photoperiod response-related gene SiCOL1 contributes to flowering in sesame. BMC PLANT BIOLOGY 2018; 18:343. [PMID: 30526484 PMCID: PMC6288898 DOI: 10.1186/s12870-018-1583-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Accepted: 11/30/2018] [Indexed: 05/20/2023]
Abstract
BACKGROUND Sesame is a major oilseed crop which is widely cultivated all around the world. Flowering, the timing of transition from vegetative to reproductive growth, is one of the most important events in the life cycle of sesame. Sesame is a typical short-day (SD) plant and its flowering is largely affected by photoperiod. However, the flowering mechanism in sesame at the molecular level is still not very clear. Previous studies showed that the CONSTANS (CO) gene is the crucial photoperiod response gene which plays a center role in duration of the plant vegetative growth. RESULTS In this study, the CO-like (COL) genes were identified and characterized in the sesame genome. Two homologs of the CO gene in the SiCOLs, SiCOL1 and SiCOL2, were recognized and comprehensively analyzed. However, sequence analysis showed that SiCOL2 lacked one of the B-box motifs. In addition, the flowering time of the transgenic Arabidopsis lines with overexpressed SiCOL2 were longer than that of SiCOL1, indicating that SiCOL1 was more likely to be the potential functional homologue of CO in sesame. Expression analysis revealed that SiCOL1 had high expressed levels before flowering in leaves and exhibited diurnal rhythmic expression in both SD and long-day (LD) conditions. In total, 16 haplotypes of SiCOL1 were discovered in the sesame collections from Asia. However, the mutated haplotypes did not express under both SD and LD conditions and was regarded as a nonfunctional allele. Notably, the sesame landraces from high-latitude regions harboring nonfunctional alleles of SiCOL1 flowered much earlier than landraces from low-latitude regions under LD condition, and adapted to the northernmost regions of sesame cultivation. The result indicated that sesame landraces from high-latitude regions might have undergone artificial selection to adapt to the LD environment. CONCLUSIONS Our results suggested that SiCOL1 might contribute to regulation of flowering in sesame and natural variations in SiCOL1 were probably related to the expansion of sesame cultivation to high-latitude regions. The results could be used in sesame breeding and in broadening adaptation of sesame varieties to new regions.
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Affiliation(s)
- Rong Zhou
- Key Laboratory of Biology and Genetic Improvement of Oil Crops of the Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, 430062 China
| | - Pan Liu
- Key Laboratory of Biology and Genetic Improvement of Oil Crops of the Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, 430062 China
| | - Donghua Li
- Key Laboratory of Biology and Genetic Improvement of Oil Crops of the Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, 430062 China
| | - Xiurong Zhang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops of the Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, 430062 China
| | - Xin Wei
- Key Laboratory of Biology and Genetic Improvement of Oil Crops of the Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, 430062 China
- College of Life Sciences, Shanghai Normal University, Shanghai, 200234 China
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16
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Li B, Zhao W, Li D, Chao H, Zhao X, Ta N, Li Y, Guan Z, Guo L, Zhang L, Li S, Wang H, Li M. Genetic dissection of the mechanism of flowering time based on an environmentally stable and specific QTL in Brassica napus. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2018; 277:296-310. [PMID: 30466595 DOI: 10.1016/j.plantsci.2018.10.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Revised: 10/02/2018] [Accepted: 10/04/2018] [Indexed: 05/02/2023]
Abstract
Flowering time is an important agronomic trait that is highly influenced by the environment. To elucidate the genetic mechanism of flowering time in rapeseed (Brassica napus L.), a genome-wide QTL analysis was performed in a doubled haploid population grown in winter, semi-winter and spring ecological conditions. Fifty-five consensus QTLs were identified after combining phenotype and genomic data, including 12 environment-stable QTLs and 43 environment-specific QTLs. Importantly, six major QTLs for flowering time were identified, of which two were considered environment-specific QTLs in spring ecological condition and four were considered environment-stable QTLs in winter and semi-winter ecological conditions. Through QTL comparison, 18 QTLs were colocalized with QTLs from six other published studies. Combining the candidate genes with their functional annotation, in 49 of 55 consensus QTLs, 151 candidate genes in B. napus corresponding to 95 homologous genes in Arabidopsis thaliana related to flowering were identified, including BnaC03g32910D (CO), BnaA02g12130D (FT) and BnaA03g13630D (FLC). Most of the candidate genes were involved in different flowering regulatory pathways. Based on re-sequencing and differences in sequence annotation between the two parents, we found that regions containing some candidate genes have numerous non-frameshift InDels and many non- synonymous mutations, which might directly lead to gene functional variation. Flowering time was negativly correlated with seed yield and thousand seed weight based on a QTL comparison of flowering time and seed yield traits, which has implications in breeding new early-maturing varieties of B. napus. Moreover, a putative flowering regulatory network was constructed, including the photoperiod, circadian clock, vernalization, autonomous and gibberellin pathways. Multiple copies of genes led to functional difference among the different copies of homologous genes, which also increased the complexity of the flowering regulatory networks. Taken together, the present results not only provide new insights into the genetic regulatory network underlying the control of flowering time but also improve our understanding of flowering time regulatory pathways in rapeseed.
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Affiliation(s)
- Baojun Li
- Hybrid Rape Research Center of Shaanxi Province, Shaanxi Rapeseed Branch of National Centre for Oil Crops Genetic Improvement, Yangling, China; Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China.
| | - Weiguo Zhao
- Hybrid Rape Research Center of Shaanxi Province, Shaanxi Rapeseed Branch of National Centre for Oil Crops Genetic Improvement, Yangling, China; Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China.
| | - Dianrong Li
- Hybrid Rape Research Center of Shaanxi Province, Shaanxi Rapeseed Branch of National Centre for Oil Crops Genetic Improvement, Yangling, China.
| | - Hongbo Chao
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China.
| | - Xiaoping Zhao
- Hybrid Rape Research Center of Shaanxi Province, Shaanxi Rapeseed Branch of National Centre for Oil Crops Genetic Improvement, Yangling, China.
| | - Na Ta
- Hybrid Rape Research Center of Shaanxi Province, Shaanxi Rapeseed Branch of National Centre for Oil Crops Genetic Improvement, Yangling, China.
| | - Yonghong Li
- Hybrid Rape Research Center of Shaanxi Province, Shaanxi Rapeseed Branch of National Centre for Oil Crops Genetic Improvement, Yangling, China.
| | - Zhoubo Guan
- Hybrid Rape Research Center of Shaanxi Province, Shaanxi Rapeseed Branch of National Centre for Oil Crops Genetic Improvement, Yangling, China.
| | - Liangxing Guo
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China.
| | - Lina Zhang
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China.
| | - Shisheng Li
- Hubei Key Laboratory of Economic Forest Germplasm Improvement and Resources Comprehensive Utilization, Hubei Collaborative Innovation Center for the Characteristic Resources Exploitation of Dabie Mountains, Huanggang Normal University, Huanggang, China.
| | - Hao Wang
- Hybrid Rape Research Center of Shaanxi Province, Shaanxi Rapeseed Branch of National Centre for Oil Crops Genetic Improvement, Yangling, China.
| | - Maoteng Li
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China; Hubei Key Laboratory of Economic Forest Germplasm Improvement and Resources Comprehensive Utilization, Hubei Collaborative Innovation Center for the Characteristic Resources Exploitation of Dabie Mountains, Huanggang Normal University, Huanggang, China.
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17
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Rahman H, Bennett RA, Kebede B. Molecular mapping of QTL alleles of Brassica oleracea affecting days to flowering and photosensitivity in spring Brassica napus. PLoS One 2018; 13:e0189723. [PMID: 29320498 PMCID: PMC5761838 DOI: 10.1371/journal.pone.0189723] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Accepted: 11/30/2017] [Indexed: 12/29/2022] Open
Abstract
Earliness of flowering and maturity are important traits in spring Brassica napus canola–whether grown under long- or short-day condition. By use of a spring B. napus mapping population carrying the genome content of B. oleracea and testing this population under 10 to 18 h photoperiod and 18 to 20 0C (day) temperature conditions, we identified a major QTL on the chromosome C1 affecting flowering time without being influenced by photoperiod and temperature, and a major QTL on C9 affecting flowering time under a short photoperiod (10 h); in both cases, the QTL alleles reducing the number of days to flowering in B. napus were introgressed from the late flowering species B. oleracea. Additive effect of the C1 QTL allele at 14 to18 h photoperiod was 1.1 to 2.9 days; however, the same QTL allele exerted an additive effect of 6.2 days at 10 h photoperiod. Additive effect of the C9 QTL at 10 h photoperiod was 2.8 days. These two QTL also showed significant interaction in the control of flowering only under a short-day (10 h photoperiod) condition with an effect of 2.3 days. A few additional QTL were also detected on the chromosomes C2 and C8; however, none of these QTL could be detected under all photoperiod and temperature conditions. BLASTn search identified several putative flowering time genes on the chromosomes C1 and C9 and located the physical position of the QTL markers in the Brassica genome; however, only a few of these genes were found within the QTL region. Thus, the molecular markers and the genomic regions identified in this research could potentially be used in breeding for the development of early flowering photoinsensitive B. napus canola cultivars, as well as for identification of candidate genes involved in flowering time variation and photosensitivity.
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Affiliation(s)
- Habibur Rahman
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Canada
- * E-mail:
| | - Rick A. Bennett
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Canada
| | - Berisso Kebede
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Canada
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Bloomer RH, Dean C. Fine-tuning timing: natural variation informs the mechanistic basis of the switch to flowering in Arabidopsis thaliana. JOURNAL OF EXPERIMENTAL BOTANY 2017; 68:5439-5452. [PMID: 28992087 DOI: 10.1093/jxb/erx270] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
The evolution of diverse life history strategies has allowed Arabidopsis thaliana to adapt to worldwide locations, spanning a range of latitudinal and environmental conditions. Arabidopsis thaliana accessions are either vernalization-requiring winter annuals or rapid cyclers, with extensive natural variation in vernalization requirement and response. Genetic and molecular analysis of this variation has enhanced our understanding of the mechanisms involved in life history determination, with translation to both natural and crop systems in the Brassicaceae and beyond.
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Affiliation(s)
- R H Bloomer
- John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - C Dean
- John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
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Long photoperiod affects the maize transition from vegetative to reproductive stages: a proteomic comparison between photoperiod-sensitive inbred line and its recurrent parent. Amino Acids 2017; 50:149-161. [PMID: 29030729 DOI: 10.1007/s00726-017-2501-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Accepted: 09/30/2017] [Indexed: 01/20/2023]
Abstract
Maize (Zea mays L.) is a typical short-day plant that is produced as an important food product and industrial material. The photoperiod is one of the most important evolutionary mechanisms enabling the adaptation of plant developmental phases to changes in climate conditions. There are differences in the photoperiod sensitivity of maize inbred lines from tropical to temperate regions. In this study, to identify the maize proteins responsive to a long photoperiod (LP), the photoperiod-insensitive inbred line HZ4 and its near-isogenic line H496, which is sensitive to LP conditions, were analyzed under long-day conditions using isobaric tags for relative and absolute quantitation. We identified 5259 proteins in maize leaves exposed to the LP condition between the vegetative and reproductive stages. These proteins included 579 and 576 differentially accumulated proteins in H496 and HZ4 leaves, respectively. The differentially accumulated proteins (e.g., membrane, defense, and energy- and ribosome-related proteins) exhibited the opposite trends in HZ4 and H496 plants during the transition from the vegetative stage to the reproductive stage. These results suggest that the photoperiod-associated fragment in H496 plants considerably influences various proteins to respond to the photoperiod sensitivity. Overall, our data provide new insights into the effects of long-day treatments on the maize proteome, and may be useful for the development of new germplasm.
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Genome-Wide Linkage-Disequilibrium Mapping to the Candidate Gene Level in Melon (Cucumis melo). Sci Rep 2017; 7:9770. [PMID: 28852011 PMCID: PMC5575340 DOI: 10.1038/s41598-017-09987-4] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2017] [Accepted: 08/01/2017] [Indexed: 12/22/2022] Open
Abstract
Cucumis melo is highly diverse for fruit traits providing wide breeding and genetic research opportunities, including genome-wide association (GWA) analysis. We used a collection of 177 accessions representing the two C. melo subspecies and 11 horticultural groups for detailed characterization of fruit traits variation and evaluation of the potential of GWA for trait mapping in melon. Through genotyping-by-sequencing, 23,931 informative SNPs were selected for genome-wide analyses. We found that linkage-disequilibrium decays at ~100 Kb in this collection and that population structure effect on association results varies between traits. We mapped several monogenic traits to narrow intervals overlapping with known causative genes, demonstrating the potential of diverse collections and GWA for mapping Mendelian traits to a candidate-gene level in melon. We further report on mapping of fruit shape quantitative trait loci (QTLs) and comparison with multiple previous QTL studies. Expansion of sample size and a more balanced representation of taxonomic groups might improve efficiency for simple traits dissection. But, as in other plant species, integrated linkage-association multi-allelic approaches are likely to produce better combination of statistical power, diversity capture and mapping resolution in melon. Our data can be utilized for selection of the most appropriate accessions for such approaches.
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Kumar J, Gupta DS, Gupta S, Dubey S, Gupta P, Kumar S. Quantitative trait loci from identification to exploitation for crop improvement. PLANT CELL REPORTS 2017; 36:1187-1213. [PMID: 28352970 DOI: 10.1007/s00299-017-2127-y] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2016] [Accepted: 03/09/2017] [Indexed: 05/24/2023]
Abstract
Advancement in the field of genetics and genomics after the discovery of Mendel's laws of inheritance has led to map the genes controlling qualitative and quantitative traits in crop plant species. Mapping of genomic regions controlling the variation of quantitatively inherited traits has become routine after the advent of different types of molecular markers. Recently, the next generation sequencing methods have accelerated the research on QTL analysis. These efforts have led to the identification of more closely linked molecular markers with gene/QTLs and also identified markers even within gene/QTL controlling the trait of interest. Efforts have also been made towards cloning gene/QTLs or identification of potential candidate genes responsible for a trait. Further new concepts like crop QTLome and QTL prioritization have accelerated precise application of QTLs for genetic improvement of complex traits. In the past years, efforts have also been made in exploitation of a number of QTL for improving grain yield or other agronomic traits in various crops through markers assisted selection leading to cultivation of these improved varieties at farmers' field. In present article, we reviewed QTLs from their identification to exploitation in plant breeding programs and also reviewed that how improved cultivars developed through introgression of QTLs have improved the yield productivity in many crops.
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Affiliation(s)
- Jitendra Kumar
- Division of Crop Improvement, ICAR-Indian Institute of Pulses Research, Kanpur, India.
| | - Debjyoti Sen Gupta
- Division of Crop Improvement, ICAR-Indian Institute of Pulses Research, Kanpur, India
| | - Sunanda Gupta
- Division of Crop Improvement, ICAR-Indian Institute of Pulses Research, Kanpur, India
| | - Sonali Dubey
- Division of Crop Improvement, ICAR-Indian Institute of Pulses Research, Kanpur, India
| | - Priyanka Gupta
- Division of Crop Improvement, ICAR-Indian Institute of Pulses Research, Kanpur, India
| | - Shiv Kumar
- International Center for Agricultural Research in the Dry Areas (ICARDA), Rabat-Institutes, B.P. 6299, Rabat, Morocco
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Cheng Z, Ge W, Li L, Hou D, Ma Y, Liu J, Bai Q, Li X, Mu S, Gao J. Analysis of MADS-Box Gene Family Reveals Conservation in Floral Organ ABCDE Model of Moso Bamboo ( Phyllostachys edulis). FRONTIERS IN PLANT SCIENCE 2017; 8:656. [PMID: 28515730 PMCID: PMC5413564 DOI: 10.3389/fpls.2017.00656] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2017] [Accepted: 04/10/2017] [Indexed: 05/05/2023]
Abstract
Mini chromosome maintenance 1, agamous, deficiens, and serum response factor (MADS)-box genes are transcription factors which play fundamental roles in flower development and regulation of floral organ identity. However, till date, identification and functions of MADS-box genes remain largely unclear in Phyllostachys edulis. In view of this, we performed a whole-genome survey and identified 34 MADS-box genes in P. edulis, and based on phylogeny, they were classified as MIKCC, MIKC∗, Mα, and Mβ. The detailed analysis about gene structure and motifs, phylogenetic classification, comparison of gene divergence and duplication are provided. Interestingly, expression patterns for most genes were found similar to those of Arabidopsis and rice, indicating that the well-established ABCDE model can be applied to P. edulis. Moreover, we overexpressed PheMADS15, an AP1-like gene, in Arabidopsis, and found that the transgenic plants have early flowering phenotype, suggesting that PheMADS15 might be a regulator of flowering transition in P. edulis. Taken together, this study provides not only insightful comprehension but also useful information for understanding the functions of MADS-box genes in P. edulis.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Jian Gao
- Key Laboratory of Bamboo and Rattan Science and Technology of the State Forestry Administration, International Centre for Bamboo and RattanBeijing, China
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Ou CG, Mao JH, Liu LJ, Li CJ, Ren HF, Zhao ZW, Zhuang FY. Characterising genes associated with flowering time in carrot (Daucus carota L.) using transcriptome analysis. PLANT BIOLOGY (STUTTGART, GERMANY) 2017; 19:286-297. [PMID: 27775866 DOI: 10.1111/plb.12519] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2016] [Accepted: 10/19/2016] [Indexed: 05/24/2023]
Abstract
Carrot is generally regarded as a biennial plant with an obligatory vernalization requirement. Early spring cultivation makes plants vulnerable to premature bolting, which results in a loss of commercial value. However, our knowledge of flowering time genes and flowering mechanisms in carrot remain limited. Bolting behavior of D. carota ssp. carota 'Songzi', a wild species sensitive to flower induction by vernalization and photoperiod, and orange cultivar 'Amsterdam forcing', and their offspring were investigated in different growing conditions. We performed RNA-seq to identify the flowering time genes, and digital gene expression (DGE) analysis to examine their expression levels. The circadian patterns of related genes were identified by qPCR. The results showed bolting behavior of carrot was influenced by low temperature, illumination intensity and photoperiod. A total of 45 flowering time-related unigenes were identified, which were classified into five categories including photoperiod, vernalization, autonomous and gibberellin pathway, and floral integrators. Homologs of LATE ELONGATED HYPOCOTYL (LHY) and CONSTANS-LIKE 2 (COL2) were more highly expressed under short day condition than under long day condition. Homologs of COL2, CONSTANS-LIKE 5 (COL5), SUPPRESSION OF OVEREXPRESSION OF CONSTANS 1 (SOC1), FLOWERING LOCUS C (FLC) and GIBBERELLIC ACID INSENSITIVE (GAI) were differentially expressed between 'Songzi' and 'Amsterdam forcing'. The homolog of COL2 (Dct43207) was repressed by light, but that of COL5 (Dct20940) was induced. A preliminary model of genetic network controlling flowering time was constructed by associating the results of DGE analysis with correlation coefficients between genes. This study provides useful information for further investigating the genetic mechanism of flowering in carrot.
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Affiliation(s)
- C-G Ou
- Key Laboratory of Horticultural Crop Biology and Germplasm Innovation, Ministry of Agriculture, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Science, Beijing, China
| | - J-H Mao
- Key Laboratory of Horticultural Crop Biology and Germplasm Innovation, Ministry of Agriculture, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Science, Beijing, China
| | - L-J Liu
- Key Laboratory of Horticultural Crop Biology and Germplasm Innovation, Ministry of Agriculture, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Science, Beijing, China
| | - C-J Li
- Suzhou Academy of Agricultural Science, Suzhou, Anhui, China
| | - H-F Ren
- Suzhou Academy of Agricultural Science, Suzhou, Anhui, China
| | - Z-W Zhao
- Key Laboratory of Horticultural Crop Biology and Germplasm Innovation, Ministry of Agriculture, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Science, Beijing, China
| | - F-Y Zhuang
- Key Laboratory of Horticultural Crop Biology and Germplasm Innovation, Ministry of Agriculture, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Science, Beijing, China
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24
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Daware AV, Srivastava R, Singh AK, Parida SK, Tyagi AK. Regional Association Analysis of MetaQTLs Delineates Candidate Grain Size Genes in Rice. FRONTIERS IN PLANT SCIENCE 2017; 8:807. [PMID: 28611791 PMCID: PMC5447001 DOI: 10.3389/fpls.2017.00807] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Accepted: 04/29/2017] [Indexed: 05/20/2023]
Abstract
Molecular mapping studies which aim to identify genetic basis of diverse agronomic traits are vital for marker-assisted crop improvement. Numerous Quantitative Trait Loci (QTLs) mapped in rice span long genomic intervals with hundreds to thousands of genes, which limits their utilization for marker-assisted genetic enhancement of rice. Although potent, fine mapping of QTLs is challenging task as it requires screening of large number of segregants to identify suitable recombination events. Association mapping offers much higher resolution as compared to QTL mapping, but detects considerable number of spurious QTLs. Therefore, combined use of QTL and association mapping strategies can provide advantages associated with both these methods. In the current study, we utilized meta-analysis approach to identify metaQTLs associated with grain size/weight in diverse Indian indica and aromatic rice accessions. Subsequently, attempt has been made to narrow-down identified grain size/weight metaQTLs through individual SNP- as well as haplotype-based regional association analysis. The study identified six different metaQTL regions, three of which were successfully revalidated, and substantially scaled-down along with GS3 QTL interval (positive control) by regional association analysis. Consequently, two potential candidate genes within two reduced metaQTLs were identified based on their differential expression profiles in different tissues/stages of rice accessions during seed development. The developed strategy has broader practical utility for rapid delineation of candidate genes and natural alleles underlying QTLs associated with complex agronomic traits in rice as well as major crop plants enriched with useful genetic and genomic information.
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Affiliation(s)
| | | | - Ashok K. Singh
- Division of Genetics, Indian Agricultural Research InstituteNew Delhi, India
| | - Swarup K. Parida
- National Institute of Plant Genome ResearchNew Delhi, India
- *Correspondence: Akhilesh K. Tyagi, Swarup K. Parida, ;
| | - Akhilesh K. Tyagi
- National Institute of Plant Genome ResearchNew Delhi, India
- Department of Plant Molecular Biology, University of Delhi South CampusNew Delhi, India
- *Correspondence: Akhilesh K. Tyagi, Swarup K. Parida, ;
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25
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Feng Y, Lu Q, Zhai R, Zhang M, Xu Q, Yang Y, Wang S, Yuan X, Yu H, Wang Y, Wei X. Genome wide association mapping for grain shape traits in indica rice. PLANTA 2016; 244:819-30. [PMID: 27198135 PMCID: PMC5018019 DOI: 10.1007/s00425-016-2548-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2016] [Accepted: 05/06/2016] [Indexed: 05/20/2023]
Abstract
Using genome-wide association mapping, 47 SNPs within 27 significant loci were identified for four grain shape traits, and 424 candidate genes were predicted from public database. Grain shape is a key determinant of grain yield and quality in rice (Oryza sativa L.). However, our knowledge of genes controlling rice grain shape remains limited. Genome-wide association mapping based on linkage disequilibrium (LD) has recently emerged as an effective approach for identifying genes or quantitative trait loci (QTL) underlying complex traits in plants. In this study, association mapping based on 5291 single nucleotide polymorphisms (SNPs) was conducted to identify significant loci associated with grain shape traits in a global collection of 469 diverse rice accessions. A total of 47 SNPs were located in 27 significant loci for four grain traits, and explained ~44.93-65.90 % of the phenotypic variation for each trait. In total, 424 candidate genes within a 200 kb extension region (±100 kb of each locus) of these loci were predicted. Of them, the cloned genes GS3 and qSW5 showed very strong effects on grain length and grain width in our study. Comparing with previously reported QTLs for grain shape traits, we found 11 novel loci, including 3, 3, 2 and 3 loci for grain length, grain width, grain length-width ratio and thousand grain weight, respectively. Validation of these new loci would be performed in the future studies. These results revealed that besides GS3 and qSW5, multiple novel loci and mechanisms were involved in determining rice grain shape. These findings provided valuable information for understanding of the genetic control of grain shape and molecular marker assistant selection (MAS) breeding in rice.
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Affiliation(s)
- Yue Feng
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, Zhejiang, China
| | - Qing Lu
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, Zhejiang, China
| | - Rongrong Zhai
- Institute of Crop and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, Zhejiang, China
| | - Mengchen Zhang
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, Zhejiang, China
| | - Qun Xu
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, Zhejiang, China
| | - Yaolong Yang
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, Zhejiang, China
| | - Shan Wang
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, Zhejiang, China
| | - Xiaoping Yuan
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, Zhejiang, China
| | - Hanyong Yu
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, Zhejiang, China
| | - Yiping Wang
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, Zhejiang, China
| | - Xinghua Wei
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, Zhejiang, China.
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26
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Yuan W, Flowers JM, Sahraie DJ, Ehrenreich IM, Purugganan MD. Extreme QTL mapping of germination speed in Arabidopsis thaliana. Mol Ecol 2016; 25:4177-96. [DOI: 10.1111/mec.13768] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2015] [Revised: 07/01/2016] [Accepted: 07/06/2016] [Indexed: 12/21/2022]
Affiliation(s)
- Wei Yuan
- Department of Biology; Center for Genomics and Systems Biology; New York University; 12 Waverly Place New York NY 10003 USA
| | - Jonathan M. Flowers
- Department of Biology; Center for Genomics and Systems Biology; New York University; 12 Waverly Place New York NY 10003 USA
- Center for Genomics and Systems Biology; NYU Abu Dhabi Research Institute; New York University Abu Dhabi; Saadiyat Island Abu Dhabi United Arab Emirates
| | - Dustin J. Sahraie
- Department of Biology; Center for Genomics and Systems Biology; New York University; 12 Waverly Place New York NY 10003 USA
| | - Ian M. Ehrenreich
- Molecular and Computational Biology Section; University of Southern California; Ray R. Irani Hall 201 Los Angeles CA 90089-2910 USA
| | - Michael D. Purugganan
- Department of Biology; Center for Genomics and Systems Biology; New York University; 12 Waverly Place New York NY 10003 USA
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27
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Holmes MW, Hammond TT, Wogan GOU, Walsh RE, LaBarbera K, Wommack EA, Martins FM, Crawford JC, Mack KL, Bloch LM, Nachman MW. Natural history collections as windows on evolutionary processes. Mol Ecol 2016; 25:864-81. [PMID: 26757135 DOI: 10.1111/mec.13529] [Citation(s) in RCA: 139] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2015] [Revised: 11/30/2015] [Accepted: 12/27/2015] [Indexed: 12/14/2022]
Abstract
Natural history collections provide an immense record of biodiversity on Earth. These repositories have traditionally been used to address fundamental questions in biogeography, systematics and conservation. However, they also hold the potential for studying evolution directly. While some of the best direct observations of evolution have come from long-term field studies or from experimental studies in the laboratory, natural history collections are providing new insights into evolutionary change in natural populations. By comparing phenotypic and genotypic changes in populations through time, natural history collections provide a window into evolutionary processes. Recent studies utilizing this approach have revealed some dramatic instances of phenotypic change over short timescales in response to presumably strong selective pressures. In some instances, evolutionary change can be paired with environmental change, providing a context for potential selective forces. Moreover, in a few cases, the genetic basis of phenotypic change is well understood, allowing for insight into adaptive change at multiple levels. These kinds of studies open the door to a wide range of previously intractable questions by enabling the study of evolution through time, analogous to experimental studies in the laboratory, but amenable to a diversity of species over longer timescales in natural populations.
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Affiliation(s)
- Michael W Holmes
- Museum of Vertebrate Zoology and Department of Integrative Biology, University of California, Berkeley, CA, 97420-3140, USA.,Department of Biology, Coastal Carolina University, Conway, SC, 29528, USA
| | - Talisin T Hammond
- Museum of Vertebrate Zoology and Department of Integrative Biology, University of California, Berkeley, CA, 97420-3140, USA
| | - Guinevere O U Wogan
- Museum of Vertebrate Zoology and Department of Integrative Biology, University of California, Berkeley, CA, 97420-3140, USA
| | - Rachel E Walsh
- Museum of Vertebrate Zoology and Department of Integrative Biology, University of California, Berkeley, CA, 97420-3140, USA
| | - Katie LaBarbera
- Museum of Vertebrate Zoology and Department of Integrative Biology, University of California, Berkeley, CA, 97420-3140, USA
| | - Elizabeth A Wommack
- Museum of Vertebrate Zoology and Department of Integrative Biology, University of California, Berkeley, CA, 97420-3140, USA.,Department of Zoology and Physiology, University of Wyoming Museum of Vertebrates, Laramie, WY, 82071, USA
| | - Felipe M Martins
- Museum of Vertebrate Zoology and Department of Integrative Biology, University of California, Berkeley, CA, 97420-3140, USA
| | - Jeremy C Crawford
- Museum of Vertebrate Zoology and Department of Integrative Biology, University of California, Berkeley, CA, 97420-3140, USA
| | - Katya L Mack
- Museum of Vertebrate Zoology and Department of Integrative Biology, University of California, Berkeley, CA, 97420-3140, USA
| | - Luke M Bloch
- Museum of Vertebrate Zoology and Department of Integrative Biology, University of California, Berkeley, CA, 97420-3140, USA
| | - Michael W Nachman
- Museum of Vertebrate Zoology and Department of Integrative Biology, University of California, Berkeley, CA, 97420-3140, USA
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28
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Meng L, Guo L, Ponce K, Zhao X, Ye G. Characterization of Three Rice Multiparent Advanced Generation Intercross (MAGIC) Populations for Quantitative Trait Loci Identification. THE PLANT GENOME 2016; 9. [PMID: 27898805 DOI: 10.3835/plantgenome2015.10.0109] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Three new rice ( L.) multiparent advanced generation intercross (MAGIC) populations were developed using eight elite rice varieties from different breeding programs. These three populations were two recombinant inbred line (RIL) populations derived from two 4-way crosses, DC1 and DC2, and one RIL population derived from an 8-way cross. These populations were genotyped using an Illumina Infinium rice 6K SNP chip. The potential of the three MAGIC populations in identifying marker-trait associations was demonstrated using the plant height (PH) and heading date (HD) measured in 2014. A population of 248 IRRI breeding lines and a population of 323 Chinese breeding lines were also included to compare genetic diversity and linkage disequilibrium (LD) pattern. Our study discovered that (i) the 8-way population had a higher gene diversity than the DC1, DC2, and IRRI populations; (ii) all three MAGIC populations showed no clear population structure; (iii) LD decayed to < 0.2 at about 2.5, 2.5, 1.25, 1.75, and 4.0 Mb for the DC1, DC2, 8-way, IRRI, and Chinese populations, respectively; and (iv) the 8-way population was more powerful than the DC1, DC2, and IRRI populations on QTL identification. The association analysis identified two and three QTL for PH and HD, respectively. Four of the five QTL had peak markers close to known genes. A novel QTL for PH was identified on chromosome 12 using the 8-way population. Therefore, our study suggests that the three new MAGIC populations are valuable resources for QTL identification.
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29
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Burgarella C, Chantret N, Gay L, Prosperi J, Bonhomme M, Tiffin P, Young ND, Ronfort J. Adaptation to climate through flowering phenology: a case study in
Medicago truncatula. Mol Ecol 2016; 25:3397-415. [DOI: 10.1111/mec.13683] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2015] [Revised: 04/26/2016] [Accepted: 04/27/2016] [Indexed: 12/30/2022]
Affiliation(s)
- Concetta Burgarella
- UMR 232 DIADE/DYNADIV Institut de Recherche pour le Developpement (IRD) 911 avenue Agropolis BP 64501, 34394 Montpellier France
- UMR AGAP, Equipe Génomique évolutive et gestion des populations Institut national de Recherche Agronomique (INRA) 34060 Montpellier France
| | - Nathalie Chantret
- UMR AGAP, Equipe Génomique évolutive et gestion des populations Institut national de Recherche Agronomique (INRA) 34060 Montpellier France
| | - Laurène Gay
- UMR AGAP, Equipe Génomique évolutive et gestion des populations Institut national de Recherche Agronomique (INRA) 34060 Montpellier France
| | - Jean‐Marie Prosperi
- UMR AGAP, Equipe Génomique évolutive et gestion des populations Institut national de Recherche Agronomique (INRA) 34060 Montpellier France
| | - Maxime Bonhomme
- UPS Laboratoire de Recherche en Sciences Végétales Université de Toulouse BP42617, Auzeville F‐31326 Castanet‐Tolosan France
- Laboratoire de Recherche en Sciences Végétales CNRS BP42617, Auzeville F‐31326 Castanet‐Tolosan France
| | - Peter Tiffin
- Department of Plant Biology University of Minnesota St. Paul MN 55108 USA
| | - Nevin D. Young
- Department of Plant Biology University of Minnesota St. Paul MN 55108 USA
- Department of Plant Pathology University of Minnesota St. Paul MN 55108 USA
| | - Joelle Ronfort
- UMR AGAP, Equipe Génomique évolutive et gestion des populations Institut national de Recherche Agronomique (INRA) 34060 Montpellier France
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30
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Li YX, Li C, Bradbury PJ, Liu X, Lu F, Romay CM, Glaubitz JC, Wu X, Peng B, Shi Y, Song Y, Zhang D, Buckler ES, Zhang Z, Li Y, Wang T. Identification of genetic variants associated with maize flowering time using an extremely large multi-genetic background population. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2016; 86:391-402. [PMID: 27012534 DOI: 10.1111/tpj.13174] [Citation(s) in RCA: 72] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2015] [Revised: 03/17/2016] [Accepted: 03/18/2016] [Indexed: 05/04/2023]
Abstract
Flowering time is one of the major adaptive traits in domestication of maize and an important selection criterion in breeding. To detect more maize flowering time variants we evaluated flowering time traits using an extremely large multi- genetic background population that contained more than 8000 lines under multiple Sino-United States environments. The population included two nested association mapping (NAM) panels and a natural association panel. Nearly 1 million single-nucleotide polymorphisms (SNPs) were used in the analyses. Through the parallel linkage analysis of the two NAM panels, both common and unique flowering time regions were detected. Genome wide, a total of 90 flowering time regions were identified. One-third of these regions were connected to traits associated with the environmental sensitivity of maize flowering time. The genome-wide association study of the three panels identified nearly 1000 flowering time-associated SNPs, mainly distributed around 220 candidate genes (within a distance of 1 Mb). Interestingly, two types of regions were significantly enriched for these associated SNPs - one was the candidate gene regions and the other was the approximately 5 kb regions away from the candidate genes. Moreover, the associated SNPs exhibited high accuracy for predicting flowering time.
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Affiliation(s)
- Yong-Xiang Li
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 10008, China
| | - Chunhui Li
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 10008, China
| | - Peter J Bradbury
- Institute for Genomic Diversity, Cornell University, Ithaca, NY, 14853, USA
| | - Xiaolei Liu
- Institute for Genomic Diversity, Cornell University, Ithaca, NY, 14853, USA
| | - Fei Lu
- Institute for Genomic Diversity, Cornell University, Ithaca, NY, 14853, USA
| | - Cinta M Romay
- Institute for Genomic Diversity, Cornell University, Ithaca, NY, 14853, USA
| | - Jeffrey C Glaubitz
- Institute for Genomic Diversity, Cornell University, Ithaca, NY, 14853, USA
| | - Xun Wu
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 10008, China
| | - Bo Peng
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 10008, China
| | - Yunsu Shi
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 10008, China
| | - Yanchun Song
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 10008, China
| | - Dengfeng Zhang
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 10008, China
| | - Edward S Buckler
- Institute for Genomic Diversity, Cornell University, Ithaca, NY, 14853, USA
- United States Department of Agriculture-Agricultural Research Service, Ithaca, NY, 14853, USA
| | - Zhiwu Zhang
- Department of Animal Science, Northeast Agricultural University, Harbin, Heilongjiang, 150030, China
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA, 99164, USA
| | - Yu Li
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 10008, China
| | - Tianyu Wang
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 10008, China
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Predicting the evolutionary dynamics of seasonal adaptation to novel climates in Arabidopsis thaliana. Proc Natl Acad Sci U S A 2016; 113:E2812-21. [PMID: 27140640 DOI: 10.1073/pnas.1517456113] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Predicting whether and how populations will adapt to rapid climate change is a critical goal for evolutionary biology. To examine the genetic basis of fitness and predict adaptive evolution in novel climates with seasonal variation, we grew a diverse panel of the annual plant Arabidopsis thaliana (multiparent advanced generation intercross lines) in controlled conditions simulating four climates: a present-day reference climate, an increased-temperature climate, a winter-warming only climate, and a poleward-migration climate with increased photoperiod amplitude. In each climate, four successive seasonal cohorts experienced dynamic daily temperature and photoperiod variation over a year. We measured 12 traits and developed a genomic prediction model for fitness evolution in each seasonal environment. This model was used to simulate evolutionary trajectories of the base population over 50 y in each climate, as well as 100-y scenarios of gradual climate change following adaptation to a reference climate. Patterns of plastic and evolutionary fitness response varied across seasons and climates. The increased-temperature climate promoted genetic divergence of subpopulations across seasons, whereas in the winter-warming and poleward-migration climates, seasonal genetic differentiation was reduced. In silico "resurrection experiments" showed limited evolutionary rescue compared with the plastic response of fitness to seasonal climate change. The genetic basis of adaptation and, consequently, the dynamics of evolutionary change differed qualitatively among scenarios. Populations with fewer founding genotypes and populations with genetic diversity reduced by prior selection adapted less well to novel conditions, demonstrating that adaptation to rapid climate change requires the maintenance of sufficient standing variation.
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Niedzicka M, Fijarczyk A, Dudek K, Stuglik M, Babik W. Molecular Inversion Probes for targeted resequencing in non-model organisms. Sci Rep 2016; 6:24051. [PMID: 27046329 PMCID: PMC4820773 DOI: 10.1038/srep24051] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2015] [Accepted: 03/18/2016] [Indexed: 12/21/2022] Open
Abstract
Applications that require resequencing of hundreds or thousands of predefined genomic regions in numerous samples are common in studies of non-model organisms. However few approaches at the scale intermediate between multiplex PCR and sequence capture methods are available. Here we explored the utility of Molecular Inversion Probes (MIPs) for the medium-scale targeted resequencing in a non-model system. Markers targeting 112 bp of exonic sequence were designed from transcriptome of Lissotriton newts. We assessed performance of 248 MIP markers in a sample of 85 individuals. Among the 234 (94.4%) successfully amplified markers 80% had median coverage within one order of magnitude, indicating relatively uniform performance; coverage uniformity across individuals was also high. In the analysis of polymorphism and segregation within family, 77% of 248 tested MIPs were confirmed as single copy Mendelian markers. Genotyping concordance assessed using replicate samples exceeded 99%. MIP markers for targeted resequencing have a number of advantages: high specificity, high multiplexing level, low sample requirement, straightforward laboratory protocol, no need for preparation of genomic libraries and no ascertainment bias. We conclude that MIP markers provide an effective solution for resequencing targets of tens or hundreds of kb in any organism and in a large number of samples.
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Affiliation(s)
- M Niedzicka
- Institute of Environmental Sciences, Jagiellonian University, Gronostajowa 7, 30-387 Kraków, Poland
| | - A Fijarczyk
- Institute of Environmental Sciences, Jagiellonian University, Gronostajowa 7, 30-387 Kraków, Poland
| | - K Dudek
- Institute of Environmental Sciences, Jagiellonian University, Gronostajowa 7, 30-387 Kraków, Poland
| | - M Stuglik
- Institute of Environmental Sciences, Jagiellonian University, Gronostajowa 7, 30-387 Kraków, Poland
| | - W Babik
- Institute of Environmental Sciences, Jagiellonian University, Gronostajowa 7, 30-387 Kraków, Poland
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Li Q, Yan W, Chen H, Tan C, Han Z, Yao W, Li G, Yuan M, Xing Y. Duplication of OsHAP family genes and their association with heading date in rice. JOURNAL OF EXPERIMENTAL BOTANY 2016; 67:1759-68. [PMID: 26798026 PMCID: PMC4783360 DOI: 10.1093/jxb/erv566] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Heterotrimeric Heme Activator Protein (HAP) family genes are involved in the regulation of flowering in plants. It is not clear how many HAP genes regulate heading date in rice. In this study, we identified 35 HAP genes, including seven newly identified genes, and performed gene duplication and candidate gene-based association analyses. Analyses showed that segmental duplication and tandem duplication are the main mechanisms of HAP gene duplication. Expression profiling and functional identification indicated that duplication probably diversifies the functions of HAP genes. A nucleotide diversity analysis revealed that 13 HAP genes underwent selection. A candidate gene-based association analysis detected four HAP genes related to heading date. An investigation of transgenic plants or mutants of 23 HAP genes confirmed that overexpression of at least four genes delayed heading date under long-day conditions, including the previously cloned Ghd8/OsHAP3H. Our results indicate that the large number of HAP genes in rice was mainly produced by gene duplication, and a few HAP genes function to regulate heading date. Selection of HAP genes is probably caused by their diverse functions rather than regulation of heading.
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Affiliation(s)
- Qiuping Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Wenhao Yan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Huaxia Chen
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Cong Tan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Zhongmin Han
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Wen Yao
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Guangwei Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Mengqi Yuan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Yongzhong Xing
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China Hubei Collaborative Innovation Center for Grain Industry , China
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Liu Y, Wang L, Deng M, Li Z, Lu Y, Wang J, Wei Y, Zheng Y. Genome-wide association study of phosphorus-deficiency-tolerance traits in Aegilops tauschii. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2015; 128:2203-12. [PMID: 26187748 DOI: 10.1007/s00122-015-2578-x] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2015] [Accepted: 07/01/2015] [Indexed: 05/19/2023]
Abstract
Using GWAS, 13 significant SNPs distributed on six of the seven Aegilops tauschii chromosomes (all but 5D) were identified, and several candidate P-deficiency-responsive genes were proposed from searches of public databases. Aegilops tauschii, the wheat (Triticum aestivum) D-genome progenitor, possesses numerous genes for stress resistance, including genes for tolerance of phosphorus (P) deficiency. Investigation of the genetic architecture of A. tauschii will help in developing P-deficiency-tolerant varieties of wheat. We evaluated nine traits in a population of 380 A. tauschii specimens under conditions with and without P application, and we performed genome-wide association studies for these traits using single nucleotide polymorphism (SNP) chips containing 7185 markers. Using a general linear model, we identified 119 SNPs that were significantly associated with all nine traits, and a mixed linear model revealed 18 SNPs associated with all traits. Both models detected 13 significant markers distributed on six of the seven A. tauschii chromosomes (all but 5D). Searches of public databases revealed several candidate/flanking genes related to P-deficiency tolerance. These genes were grouped in five categories by the types of proteins they encoded: defense response proteins, enzymes, promoters and transcription factors, storage proteins, or proteins triggered by P deficiency. The identified SNPs and genes contain essential information for cloning genes related to P-deficiency tolerance in A. tauschii and wheat, and they provide a foundation for breeding P-deficiency tolerant wheat cultivars.
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Affiliation(s)
- Yaxi Liu
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, China.
| | - Lang Wang
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, China.
| | - Mei Deng
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, China.
| | - Zhanyi Li
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, China.
| | - Yanli Lu
- Maize Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, China.
| | - Jirui Wang
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, China.
| | - Yuming Wei
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, China.
| | - Youliang Zheng
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, China.
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35
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Upadhyaya HD, Bajaj D, Das S, Saxena MS, Badoni S, Kumar V, Tripathi S, Gowda CLL, Sharma S, Tyagi AK, Parida SK. A genome-scale integrated approach aids in genetic dissection of complex flowering time trait in chickpea. PLANT MOLECULAR BIOLOGY 2015; 89:403-20. [PMID: 26394865 DOI: 10.1007/s11103-015-0377-z] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2015] [Accepted: 09/02/2015] [Indexed: 05/08/2023]
Abstract
A combinatorial approach of candidate gene-based association analysis and genome-wide association study (GWAS) integrated with QTL mapping, differential gene expression profiling and molecular haplotyping was deployed in the present study for quantitative dissection of complex flowering time trait in chickpea. Candidate gene-based association mapping in a flowering time association panel (92 diverse desi and kabuli accessions) was performed by employing the genotyping information of 5724 SNPs discovered from 82 known flowering chickpea gene orthologs of Arabidopsis and legumes as well as 832 gene-encoding transcripts that are differentially expressed during flower development in chickpea. GWAS using both genome-wide GBS- and candidate gene-based genotyping data of 30,129 SNPs in a structured population of 92 sequenced accessions (with 200-250 kb LD decay) detected eight maximum effect genomic SNP loci (genes) associated (34% combined PVE) with flowering time. Six flowering time-associated major genomic loci harbouring five robust QTLs mapped on a high-resolution intra-specific genetic linkage map were validated (11.6-27.3% PVE at 5.4-11.7 LOD) further by traditional QTL mapping. The flower-specific expression, including differential up- and down-regulation (>three folds) of eight flowering time-associated genes (including six genes validated by QTL mapping) especially in early flowering than late flowering contrasting chickpea accessions/mapping individuals during flower development was evident. The gene haplotype-based LD mapping discovered diverse novel natural allelic variants and haplotypes in eight genes with high trait association potential (41% combined PVE) for flowering time differentiation in cultivated and wild chickpea. Taken together, eight potential known/candidate flowering time-regulating genes [efl1 (early flowering 1), FLD (Flowering locus D), GI (GIGANTEA), Myb (Myeloblastosis), SFH3 (SEC14-like 3), bZIP (basic-leucine zipper), bHLH (basic helix-loop-helix) and SBP (SQUAMOSA promoter binding protein)], including novel markers, QTLs, alleles and haplotypes delineated by aforesaid genome-wide integrated approach have potential for marker-assisted genetic improvement and unravelling the domestication pattern of flowering time in chickpea.
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Affiliation(s)
- Hari D Upadhyaya
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Telangana, 502324, India
| | - Deepak Bajaj
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Shouvik Das
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Maneesha S Saxena
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Saurabh Badoni
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Vinod Kumar
- National Research Centre on Plant Biotechnology (NRCPB), New Delhi, 110012, India
| | - Shailesh Tripathi
- Division of Genetics, Indian Agricultural Research Institute (IARI), New Delhi, 110012, India
| | - C L L Gowda
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Telangana, 502324, India
| | - Shivali Sharma
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Telangana, 502324, India
| | - Akhilesh K Tyagi
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Swarup K Parida
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India.
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Ma B, Liao L, Zheng H, Chen J, Wu B, Ogutu C, Li S, Korban SS, Han Y. Genes Encoding Aluminum-Activated Malate Transporter II and their Association with Fruit Acidity in Apple. THE PLANT GENOME 2015; 8:eplantgenome2015.03.0016. [PMID: 33228269 DOI: 10.3835/plantgenome2015.03.0016] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2015] [Accepted: 05/27/2015] [Indexed: 05/25/2023]
Abstract
A gene encoding aluminum-activated malate transporter (ALMT) was previously reported as a candidate for the Ma locus controlling acidity in apple (Malus × domestica Borkh.). In this study, we found that apple ALMT genes can be divided into three families and the Ma1 gene belongs to the ALMTII family. Duplication of ALMTII genes in apple is related to the polyploid origin of the apple genome. Divergence in expression has occurred between the Ma1 gene and its homologs in the ALMTII family and only the Ma1 gene is significantly associated with malic acid content. The Ma locus consists of two alleles, Ma1 and ma1. Ma1 resides in the tonoplast and its ectopic expression in yeast was found to increase the influx of malic acid into yeast cells significantly, suggesting it may function as a vacuolar malate channel. In contrast, ma1 encodes a truncated protein because of a single nucleotide substitution of G with A in the last exon. As this truncated protein resides within the cell membrane, it is deemed to be nonfunctional as a vacuolar malate channel. The frequency of the Ma1Ma1 genotype is very low in apple cultivars but is high in wild relatives, which suggests that apple domestication may be accompanied by selection for the Ma1 gene. In addition, variations in the malic acid content of mature fruits were also observed between accessions with the same genotype in the Ma locus. This suggests that the Ma gene is not the only genetic determinant of fruit acidity in apple.
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Affiliation(s)
- Baiquan Ma
- Key Lab. of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden of the Chinese Academy of Sciences, Wuhan, 430074, P.R. China
- Graduate Univ. of Chinese Academy of Sciences, 19A Yuquanlu, Beijing, 100049, P.R. China
| | - Liao Liao
- Key Lab. of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden of the Chinese Academy of Sciences, Wuhan, 430074, P.R. China
| | - Hongyu Zheng
- Key Lab. of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden of the Chinese Academy of Sciences, Wuhan, 430074, P.R. China
- Graduate Univ. of Chinese Academy of Sciences, 19A Yuquanlu, Beijing, 100049, P.R. China
| | - Jie Chen
- Beijing Key Lab. of Grape Sciences and Enology, and Key Lab. of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- Graduate Univ. of Chinese Academy of Sciences, 19A Yuquanlu, Beijing, 100049, P.R. China
| | - Benhong Wu
- Beijing Key Lab. of Grape Sciences and Enology, and Key Lab. of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Collins Ogutu
- Key Lab. of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden of the Chinese Academy of Sciences, Wuhan, 430074, P.R. China
- Graduate Univ. of Chinese Academy of Sciences, 19A Yuquanlu, Beijing, 100049, P.R. China
| | - Shaohua Li
- Key Lab. of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden of the Chinese Academy of Sciences, Wuhan, 430074, P.R. China
| | - Schuyler S Korban
- Dep. of Biology, Univ. of Massachusetts-Boston, Boston, MA, 02184, USA
| | - Yuepeng Han
- Key Lab. of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden of the Chinese Academy of Sciences, Wuhan, 430074, P.R. China
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37
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Qin P, Wang L, Liu K, Mao S, Li Z, Gao S, Shi H, Liu Y. Genomewide association study of Aegilops tauschii traits under seedling-stage cadmium stress. ACTA ACUST UNITED AC 2015. [DOI: 10.1016/j.cj.2015.04.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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38
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Manzaneda AJ, Rey PJ, Anderson JT, Raskin E, Weiss-Lehman C, Mitchell-Olds T. Natural variation, differentiation, and genetic trade-offs of ecophysiological traits in response to water limitation in Brachypodium distachyon and its descendent allotetraploid B. hybridum (Poaceae). Evolution 2015; 69:2689-704. [PMID: 26377138 DOI: 10.1111/evo.12776] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2013] [Revised: 07/02/2015] [Accepted: 08/25/2015] [Indexed: 11/30/2022]
Abstract
Differences in tolerance to water stress may underlie ecological divergence of closely related ploidy lineages. However, the mechanistic basis of physiological variation governing ecogeographical cytotype segregation is not well understood. Here, using Brachypodium distachyon and its derived allotetraploid B. hybridum as model, we test the hypothesis that, for heteroploid annuals, ecological divergence of polyploids in drier environments is based on trait differentiation enabling drought escape. We demonstrate that under water limitation allotetraploids maintain higher photosynthesis and stomatal conductance and show earlier flowering than diploids, concordant with a drought-escape strategy to cope with water stress. Increased heterozygosity and greater genetic variability and plasticity of polyploids could confer a superior adaptive capability. Consistent with these predictions, we document (1) greater standing within-population genetic variation in water-use efficiency (WUE) and flowering time in allotetraploids, and (2) the existence of (nonlinear) environmental clines in physiology across allotetraploid populations. Increased gas exchange and diminished WUE occurred at the driest end of the gradient, consistent with a drought-escape strategy. Finally, we found that allotetraploids showed weaker genetic correlations than diploids congruous with the expectation of relaxed pleiotropic constraints in polyploids. Our results suggest evolutionary divergence of ecophysiological traits in each ploidy lineage.
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Affiliation(s)
- Antonio J Manzaneda
- Departamento Biología Animal, Biología Vegetal y Ecología, Universidad de Jaén, Paraje las Lagunillas s/n, 23071, Jaén, Spain. .,Institute for Genome Sciences and Policy, Department of Biology, Duke University, P.O. Box 90338, Durham, North Carolina, 27708.
| | - Pedro J Rey
- Departamento Biología Animal, Biología Vegetal y Ecología, Universidad de Jaén, Paraje las Lagunillas s/n, 23071, Jaén, Spain
| | - Jill T Anderson
- Department of Genetics, University of Georgia, Athens, Georgia, 30602
| | - Evan Raskin
- Institute for Genome Sciences and Policy, Department of Biology, Duke University, P.O. Box 90338, Durham, North Carolina, 27708
| | - Christopher Weiss-Lehman
- Department of Ecology and Evolutionary Biology, Biofrontiers Institute, University of Colorado, Boulder, Colarado, 80309
| | - Thomas Mitchell-Olds
- Institute for Genome Sciences and Policy, Department of Biology, Duke University, P.O. Box 90338, Durham, North Carolina, 27708
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Grover CE, Gallagher JP, Wendel JF. Candidate Gene Identification of Flowering Time Genes in Cotton. THE PLANT GENOME 2015; 8:eplantgenome2014.12.0098. [PMID: 33228302 DOI: 10.3835/plantgenome2014.12.0098] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2014] [Accepted: 02/11/2015] [Indexed: 06/11/2023]
Abstract
Flowering time control is critically important to all sexually reproducing angiosperms in both natural ecological and agronomic settings. Accordingly, there is much interest in defining the genes involved in the complex flowering-time network and how these respond to natural and artificial selection, the latter often entailing transitions in day-length responses. Here we describe a candidate gene analysis in the cotton genus Gossypium, which uses homologs from the well-described Arabidopsis flowering network to bioinformatically and phylogenetically identify orthologs in the published genome sequence from G. raimondii Ulbr., one of the two model diploid progenitors of the commercially important allopolyploid cottons, G. hirsutum L. and G. barbadense L. Presence and patterns of expression were evaluated from 13 aboveground tissues related to flowering for each of the candidate genes using allopolyploid G. hirsutum as a model. Furthermore, we use a comparative context to determine copy number variability of each key gene family across 10 published angiosperm genomes. Data suggest a pattern of repeated loss of duplicates following ancient whole-genome doubling events in diverse lineages. The data presented here provide a foundation for understanding both the parallel evolution of day-length neutrality in domesticated cottons and the flowering-time network, in general, in this important crop plant.
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Affiliation(s)
- Corrinne E Grover
- Department of Ecology, Evolution, and Organismal Biology, Iowa State Univ., Ames, IA, 50011
| | - Joseph P Gallagher
- Department of Ecology, Evolution, and Organismal Biology, Iowa State Univ., Ames, IA, 50011
| | - Jonathan F Wendel
- Department of Ecology, Evolution, and Organismal Biology, Iowa State Univ., Ames, IA, 50011
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Singh BP, Jayaswal PK, Singh B, Singh PK, Kumar V, Mishra S, Singh N, Panda K, Singh NK. Natural allelic diversity in OsDREB1F gene in the Indian wild rice germplasm led to ascertain its association with drought tolerance. PLANT CELL REPORTS 2015; 34:993-1004. [PMID: 25693492 DOI: 10.1007/s00299-015-1760-6] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2014] [Revised: 12/27/2014] [Accepted: 01/12/2015] [Indexed: 05/17/2023]
Abstract
Three coding SNPs and one haplotype identified in the OsDREB1F gene have potential to be associated with drought tolerance in rice. Drought is a serious constraint to rice production worldwide, that can be addressed by deployment of drought tolerant genes. OsDREB1F, one of the most potent drought tolerance transcription activator genes, was re-sequenced for allele mining and association study in a set of 136 wild rice accessions and four cultivated rice. This analysis led to identify 22 SNPs with eight haplotypes based on allelic variations in the accessions used. The nucleotide variation-based neutrality tests suggested that the OsDREB1F gene has been subjected to purifying selection in the studied set of rice germplasm. Six different OsDREB1F protein variants were identified on the basis of translated amino acid residues amongst the orthologues. Five protein variants were truncated due to deletions in coding region and found susceptible to drought stress. Association study revealed that three coding SNPs of this gene were significantly associated with drought tolerance. One OsDREB1F variant in the activation domain of OsDREB1F gene which led to conversion of aspartate amino acid to glutamate was found to be associated with drought tolerance. Three-dimensional homology modeling assisted to understand the functional significance of this identified potential allele for drought tolerance in rice. The natural allelic variants mined in the OsDREB1F gene can be further used in translational genomics for improving the water use efficiency in rice.
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Affiliation(s)
- Bikram Pratap Singh
- National Research Center on Plant Biotechnology, IARI, New Delhi, 110012, India
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41
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Kooyers NJ. The evolution of drought escape and avoidance in natural herbaceous populations. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2015; 234:155-62. [PMID: 25804818 DOI: 10.1016/j.plantsci.2015.02.012] [Citation(s) in RCA: 177] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2014] [Revised: 02/04/2015] [Accepted: 02/19/2015] [Indexed: 05/03/2023]
Abstract
While the functional genetics and physiological mechanisms controlling drought resistance in crop plants have been intensely studied, less research has examined the genetic basis of adaptation to drought stress in natural populations. Drought resistance adaptations in nature reflect natural rather than human-mediated selection and may identify novel mechanisms for stress tolerance. Adaptations conferring drought resistance have historically been divided into alternative strategies including drought escape (rapid development to complete a life cycle before drought) and drought avoidance (reducing water loss to prevent dehydration). Recent studies in genetic model systems such as Arabidopsis, Mimulus, and Panicum have begun to elucidate the genes, expression profiles, and physiological changes responsible for ecologically important variation in drought resistance. Similar to most crop plants, variation in drought escape and avoidance is complex, underlain by many QTL of small effect, and pervasive gene by environment interactions. Recently identified major-effect alleles point to a significant role for genetic constraints in limiting the concurrent evolution of both drought escape and avoidance strategies, although these constraints are not universally found. This progress suggests that understanding the mechanistic basic and fitness consequences of gene by environment interactions will be critical for crop improvement and forecasting population persistence in unpredictable environments.
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Affiliation(s)
- Nicholas J Kooyers
- Department of Biology, University of Virginia, Charlottesville, VA 22904, USA.
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42
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Tamang P, Neupane A, Mamidi S, Friesen T, Brueggeman R. Association mapping of seedling resistance to spot form net blotch in a worldwide collection of barley. PHYTOPATHOLOGY 2015; 105:500-8. [PMID: 25870925 DOI: 10.1094/phyto-04-14-0106-r] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Spot form net blotch (SFNB), caused by the necrotrophic fungal pathogen Pyrenophora teres f. maculata, is an important foliar disease of barley in major production regions around the world. Deployment of adequate host resistance is challenging because the virulence of P. teres f. maculata is highly variable and characterized minor-effect resistances are typically ineffective against the diverse pathogen populations. A world barley core collection consisting of 2,062 barley accessions of diverse origin and genotype were phenotyped at the seedling stage with four P. teres f. maculata isolates collected from the United States (FGO), New Zealand (NZKF2), Australia (SG1), and Denmark (DEN 2.6). Of the 2,062 barley accessions phenotyped, 1,480 were genotyped with the Illumina barley iSelect chip and passed the quality controls with 5,954 polymorphic markers used for further association mapping analysis. Genome-wide association mapping was utilized to identify and map resistance loci from the seedling disease response data and the single nucleotide polymorphism (SNP) marker data. The best among six different regression models was identified for each isolate and association analysis was performed separately for each. A total of 138 significant (-log10P value>3.0) marker-trait associations (MTA) were detected. Using a 5 cM cutoff, a total of 10, 8, 13, and 10 quantitative trait loci (QTL) associated with SFNB resistance were identified for the FGO, SG1, NZKF2, and DEN 2.6 isolates, respectively. Loci containing from 1 to 34 MTA were identified on all seven barley chromosomes with one locus at 66 to 69 cM on chromosome 2H common to all four isolates. Six distinct loci were identified by the association mapping (AM) analysis that corresponded to previously characterized SFNB resistance QTL identified by biparental population analysis (QRpt4, QRpt6, Rpt4, Rpt6, Rpt7, and a QTL on 4H that was not given a provisional gene or QTL nomenclature). The 21 putative novel loci identified may represent a broad spectrum of resistance and or susceptibility loci. This is the first comprehensive AM study to characterize SFNB resistance loci underlying broad populations of the barley host and P. teres f. maculata pathogen.
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Affiliation(s)
- Prabin Tamang
- First, second, fourth, and fifth authors: Department of Plant Pathology, North Dakota State University, Fargo, ND 58108-6050; third author: Department of Plant Science, North Dakota State University, Fargo, ND 58108-6050; and fourth author: U.S. Department of Agriculture-Agriculture Research Service, Red River Valley Agricultural Research Center, Cereal Crops Research Unit, Fargo, ND 58102-2765
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Hamilton JA, Okada M, Korves T, Schmitt J. The role of climate adaptation in colonization success inArabidopsis thaliana. Mol Ecol 2015; 24:2253-63. [DOI: 10.1111/mec.13099] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2014] [Revised: 01/15/2015] [Accepted: 01/19/2015] [Indexed: 12/25/2022]
Affiliation(s)
- Jill A. Hamilton
- Department of Evolution and Ecology; University of California; Davis CA 95616 USA
| | - Miki Okada
- Department of Evolution and Ecology; University of California; Davis CA 95616 USA
| | - Tonia Korves
- Data Analytics Department; The MITRE Corporation; 202 Burlington Rd, Bedford MA 01730 USA
| | - Johanna Schmitt
- Department of Evolution and Ecology; University of California; Davis CA 95616 USA
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Jourdan M, Gagné S, Dubois-Laurent C, Maghraoui M, Huet S, Suel A, Hamama L, Briard M, Peltier D, Geoffriau E. Carotenoid content and root color of cultivated carrot: a candidate-gene association study using an original broad unstructured population. PLoS One 2015; 10:e0116674. [PMID: 25614987 PMCID: PMC4304819 DOI: 10.1371/journal.pone.0116674] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2014] [Accepted: 12/11/2014] [Indexed: 02/01/2023] Open
Abstract
Accumulated in large amounts in carrot, carotenoids are an important product quality attribute and therefore a major breeding trait. However, the knowledge of carotenoid accumulation genetic control in this root vegetable is still limited. In order to identify the genetic variants linked to this character, we performed an association mapping study with a candidate gene approach. We developed an original unstructured population with a broad genetic basis to avoid the pitfall of false positive detection due to population stratification. We genotyped 109 SNPs located in 17 candidate genes – mostly carotenoid biosynthesis genes – on 380 individuals, and tested the association with carotenoid contents and color components. Total carotenoids and β-carotene contents were significantly associated with genes zeaxanthin epoxydase (ZEP), phytoene desaturase (PDS) and carotenoid isomerase (CRTISO) while α-carotene was associated with CRTISO and plastid terminal oxidase (PTOX) genes. Color components were associated most significantly with ZEP. Our results suggest the involvement of the couple PDS/PTOX and ZEP in carotenoid accumulation, as the result of the metabolic and catabolic activities respectively. This study brings new insights in the understanding of the carotenoid pathway in non-photosynthetic organs.
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Affiliation(s)
- Matthieu Jourdan
- Agrocampus Ouest, UMR1345 Institut de Recherche en Horticulture et Semences, Angers, France
- Université d’Angers, UMR1345 Institut de Recherche en Horticulture et Semences, Angers, France
- INRA, UMR1345 Institut de Recherche en Horticulture et Semences, Beaucouzé, France
| | - Séverine Gagné
- Agrocampus Ouest, UMR1345 Institut de Recherche en Horticulture et Semences, Angers, France
- Université d’Angers, UMR1345 Institut de Recherche en Horticulture et Semences, Angers, France
- INRA, UMR1345 Institut de Recherche en Horticulture et Semences, Beaucouzé, France
| | - Cécile Dubois-Laurent
- Agrocampus Ouest, UMR1345 Institut de Recherche en Horticulture et Semences, Angers, France
- Université d’Angers, UMR1345 Institut de Recherche en Horticulture et Semences, Angers, France
- INRA, UMR1345 Institut de Recherche en Horticulture et Semences, Beaucouzé, France
| | - Mohamed Maghraoui
- Agrocampus Ouest, UMR1345 Institut de Recherche en Horticulture et Semences, Angers, France
- Université d’Angers, UMR1345 Institut de Recherche en Horticulture et Semences, Angers, France
- INRA, UMR1345 Institut de Recherche en Horticulture et Semences, Beaucouzé, France
| | - Sébastien Huet
- Agrocampus Ouest, UMR1345 Institut de Recherche en Horticulture et Semences, Angers, France
- Université d’Angers, UMR1345 Institut de Recherche en Horticulture et Semences, Angers, France
- INRA, UMR1345 Institut de Recherche en Horticulture et Semences, Beaucouzé, France
| | - Anita Suel
- Agrocampus Ouest, UMR1345 Institut de Recherche en Horticulture et Semences, Angers, France
- Université d’Angers, UMR1345 Institut de Recherche en Horticulture et Semences, Angers, France
- INRA, UMR1345 Institut de Recherche en Horticulture et Semences, Beaucouzé, France
| | - Latifa Hamama
- Agrocampus Ouest, UMR1345 Institut de Recherche en Horticulture et Semences, Angers, France
- Université d’Angers, UMR1345 Institut de Recherche en Horticulture et Semences, Angers, France
- INRA, UMR1345 Institut de Recherche en Horticulture et Semences, Beaucouzé, France
| | - Mathilde Briard
- Agrocampus Ouest, UMR1345 Institut de Recherche en Horticulture et Semences, Angers, France
- Université d’Angers, UMR1345 Institut de Recherche en Horticulture et Semences, Angers, France
- INRA, UMR1345 Institut de Recherche en Horticulture et Semences, Beaucouzé, France
| | - Didier Peltier
- Agrocampus Ouest, UMR1345 Institut de Recherche en Horticulture et Semences, Angers, France
- Université d’Angers, UMR1345 Institut de Recherche en Horticulture et Semences, Angers, France
- INRA, UMR1345 Institut de Recherche en Horticulture et Semences, Beaucouzé, France
| | - Emmanuel Geoffriau
- Agrocampus Ouest, UMR1345 Institut de Recherche en Horticulture et Semences, Angers, France
- Université d’Angers, UMR1345 Institut de Recherche en Horticulture et Semences, Angers, France
- INRA, UMR1345 Institut de Recherche en Horticulture et Semences, Beaucouzé, France
- * E-mail:
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Suter L, Rüegg M, Zemp N, Hennig L, Widmer A. Gene regulatory variation mediates flowering responses to vernalization along an altitudinal gradient in Arabidopsis. PLANT PHYSIOLOGY 2014; 166:1928-42. [PMID: 25339407 PMCID: PMC4256870 DOI: 10.1104/pp.114.247346] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Steep environmental gradients provide ideal settings for studies of potentially adaptive phenotypic and genetic variation in plants. The accurate timing of flowering is crucial for reproductive success and is regulated by several pathways, including the vernalization pathway. Among the numerous genes known to enable flowering in response to vernalization, the most prominent is FLOWERING LOCUS C (FLC). FLC and other genes of the vernalization pathway vary extensively among natural populations and are thus candidates for the adaptation of flowering time to environmental gradients such as altitude. We used 15 natural Arabidopsis (Arabidopsis thaliana) genotypes originating from an altitudinal gradient (800-2,700 m above sea level) in the Swiss Alps to test whether flowering time correlated with altitude under different vernalization scenarios. Additionally, we measured the expression of 12 genes of the vernalization pathway and its downstream targets. Flowering time correlated with altitude in a nonlinear manner for vernalized plants. Flowering time could be explained by the expression and regulation of the vernalization pathway, most notably by AGAMOUS LIKE19 (AGL19), FLOWERING LOCUS T (FT), and FLC. The expression of AGL19, FT, and VERNALIZATION INSENSITIVE3 was associated with altitude, and the regulation of MADS AFFECTING FLOWERING2 (MAF2) and MAF3 differed between low- and high-altitude genotypes. In conclusion, we found clinal variation across an altitudinal gradient both in flowering time and the expression and regulation of genes in the flowering time control network, often independent of FLC, suggesting that the timing of flowering may contribute to altitudinal adaptation.
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Affiliation(s)
- Léonie Suter
- Eidgenössisch Technische Hochschule Zürich, Institute of Integrative Biology, 8092 Zurich, Switzerland (L.S., M.R., N.Z., A.W.); andDepartment of Plant Biology, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, SE-75007 Uppsala, Sweden (L.H.)
| | - Marlene Rüegg
- Eidgenössisch Technische Hochschule Zürich, Institute of Integrative Biology, 8092 Zurich, Switzerland (L.S., M.R., N.Z., A.W.); andDepartment of Plant Biology, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, SE-75007 Uppsala, Sweden (L.H.)
| | - Niklaus Zemp
- Eidgenössisch Technische Hochschule Zürich, Institute of Integrative Biology, 8092 Zurich, Switzerland (L.S., M.R., N.Z., A.W.); andDepartment of Plant Biology, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, SE-75007 Uppsala, Sweden (L.H.)
| | - Lars Hennig
- Eidgenössisch Technische Hochschule Zürich, Institute of Integrative Biology, 8092 Zurich, Switzerland (L.S., M.R., N.Z., A.W.); andDepartment of Plant Biology, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, SE-75007 Uppsala, Sweden (L.H.)
| | - Alex Widmer
- Eidgenössisch Technische Hochschule Zürich, Institute of Integrative Biology, 8092 Zurich, Switzerland (L.S., M.R., N.Z., A.W.); andDepartment of Plant Biology, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, SE-75007 Uppsala, Sweden (L.H.)
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Ye J, Liu P, Zhu C, Qu J, Wang X, Sun Y, Sun F, Jiang Y, Yue G, Wang C. Identification of candidate genes JcARF19 and JcIAA9 associated with seed size traits in Jatropha. Funct Integr Genomics 2014; 14:757-66. [PMID: 25228410 DOI: 10.1007/s10142-014-0400-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2014] [Revised: 09/02/2014] [Accepted: 09/07/2014] [Indexed: 11/25/2022]
Abstract
Jatropha curcas is a new promising bioenergy crop due to the high oil content in its seeds that can be converted into biodiesel. Seed size, a major determinant of Jatropha oil yield, is a target trait for Jatropha breeding. Due to the vital roles of phytohormone auxin in controlling seed and fruit development, we screened key genes in auxin pathway including ARF and IAA families and downstream effectors to identify candidate genes controlling seed size in Jatropha. As a result, JcARF19 was mapped in the major quantitative trait locus (QTL) region and significantly associated with seed length. By using expression QTL (eQTL) analysis to link variants with functional candidate genes, we provided evidences that seed traits were affected by the interaction of JcARF19 and JcIAA9. ARF19 and IAA9, involved in auxin signal transduction, were conserved in higher plants. These data including the single-nucleotide polymorphisms (SNPs) in the two genes could lead to utilization of the genes by integrating favored alleles into elite varieties through marker-assisted selection.
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Affiliation(s)
- Jian Ye
- Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, 117604, Singapore, Singapore
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Fechter I, Hausmann L, Zyprian E, Daum M, Holtgräwe D, Weisshaar B, Töpfer R. QTL analysis of flowering time and ripening traits suggests an impact of a genomic region on linkage group 1 in Vitis. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2014; 127:1857-72. [PMID: 25112201 PMCID: PMC4145202 DOI: 10.1007/s00122-014-2310-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2013] [Accepted: 04/05/2014] [Indexed: 05/21/2023]
Abstract
In the recent past, genetic analyses of grapevine focused mainly on the identification of resistance loci for major diseases such as powdery and downy mildew. Currently, breeding programs make intensive use of these results by applying molecular markers linked to the resistance traits. However, modern genetics also allows to address additional agronomic traits that have considerable impact on the selection of grapevine cultivars. In this study, we have used linkage mapping for the identification and characterization of flowering time and ripening traits in a mapping population from a cross of V3125 ('Schiava Grossa' × 'Riesling') and the interspecific rootstock cultivar 'Börner' (Vitis riparia × Vitis cinerea). Comparison of the flowering time QTL mapping with data derived from a second independent segregating population identified several common QTLs. Especially a large region on linkage group 1 proved to be of special interest given the genetic divergence of the parents of the two populations. The proximity of the QTL region contains two CONSTANS-like genes. In accordance with data from other plants such as Arabidopsis thaliana and Oryza sativa, we hypothesize that these genes are major contributors to control the time of flowering in Vitis.
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Affiliation(s)
- Iris Fechter
- Institute for Grapevine Breeding, Julius Kuehn-Institute, Federal Research Centre for Cultivated Plants, Geilweilerhof, 76833, Siebeldingen, Germany,
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Schmalenbach I, Zhang L, Ryngajllo M, Jiménez-Gómez JM. Functional analysis of the Landsberg erecta allele of FRIGIDA. BMC PLANT BIOLOGY 2014; 14:218. [PMID: 25207670 PMCID: PMC4158083 DOI: 10.1186/s12870-014-0218-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2014] [Accepted: 08/04/2014] [Indexed: 05/08/2023]
Abstract
BACKGROUND Most of the natural variation in flowering time in Arabidopsis thaliana can be attributed to allelic variation at the gene FRIGIDA (FRI, AT4G00650), which activates expression of the floral repressor FLOWERING LOCUS C (FLC, AT5G10140). Usually, late-flowering accessions carry functional FRI alleles (FRI-wt), whereas early flowering accessions contain non-functional alleles. The two most frequent alleles found in early flowering accessions are the ones present in the commonly used lab strains Columbia (FRI-Col) and Landsberg erecta (FRI-Ler), which contain a premature stop codon and a deletion of the start codon respectively. RESULTS Analysis of flowering time data from various Arabidopsis natural accessions indicated that the FRI-Ler allele retains some functionality. We generated transgenic lines carrying the FRI-Col or FRI-Ler allele in order to compare their effect on flowering time, vernalization response and FLC expression in the same genetic background. We characterize their modes of regulation through allele-specific expression and their relevance in nature through re-analysis of published datasets. We demonstrate that the FRI-Ler allele induces FLC expression, delays flowering time and confers sensitivity to vernalization in contrast to the true null FRI-Col allele. Nevertheless, the FRI-Ler allele revealed a weaker effect when compared to the fully functional FRI-wt allele, mainly due to reduced expression. CONCLUSIONS The present study defines for the first time the existence of a new class of Arabidopsis accessions with an intermediate phenotype between slow and rapid cycling types. Although using available data from a common garden experiment we cannot observe fitness differences between accessions carrying the FRI-Ler or the FRI-Col allele, the phenotypic changes observed in the lab suggest that variation in these alleles could play a role in adaptation to specific natural environments.
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Affiliation(s)
- Inga Schmalenbach
- />Department of Plant Breeding and Genetics, Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829 Cologne, Germany
| | - Lei Zhang
- />Department of Plant Breeding and Genetics, Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829 Cologne, Germany
| | - Malgorzata Ryngajllo
- />Department of Plant Breeding and Genetics, Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829 Cologne, Germany
| | - José M Jiménez-Gómez
- />Department of Plant Breeding and Genetics, Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829 Cologne, Germany
- />INRA, UMR1318, Institut Jean-Pierre Bourgin, RD10, F-78000 Versailles, France
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Gao J, Zhang Y, Zhang C, Qi F, Li X, Mu S, Peng Z. Characterization of the floral transcriptome of Moso bamboo (Phyllostachys edulis) at different flowering developmental stages by transcriptome sequencing and RNA-seq analysis. PLoS One 2014; 9:e98910. [PMID: 24915141 PMCID: PMC4051636 DOI: 10.1371/journal.pone.0098910] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2013] [Accepted: 05/07/2014] [Indexed: 01/09/2023] Open
Abstract
Background As an arborescent and perennial plant, Moso bamboo (Phyllostachys edulis (Carrière) J. Houzeau, synonym Phyllostachys heterocycla Carrière) is characterized by its infrequent sexual reproduction with flowering intervals ranging from several to more than a hundred years. However, little bamboo genomic research has been conducted on this due to a variety of reasons. Here, for the first time, we investigated the transcriptome of developing flowers in Moso bamboo by using high-throughput Illumina GAII sequencing and mapping short reads to the Moso bamboo genome and reference genes. We performed RNA-seq analysis on four important stages of flower development, and obtained extensive gene and transcript abundance data for the floral transcriptome of this key bamboo species. Results We constructed a cDNA library using equal amounts of RNA from Moso bamboo leaf samples from non-flowering plants (CK) and mixed flower samples (F) of four flower development stages. We generated more than 67 million reads from each of the CK and F samples. About 70% of the reads could be uniquely mapped to the Moso bamboo genome and the reference genes. Genes detected at each stage were categorized to putative functional categories based on their expression patterns. The analysis of RNA-seq data of bamboo flowering tissues at different developmental stages reveals key gene expression properties during the flower development of bamboo. Conclusion We showed that a combination of transcriptome sequencing and RNA-seq analysis was a powerful approach to identifying candidate genes related to floral transition and flower development in bamboo species. The results give a better insight into the mechanisms of Moso bamboo flowering and ageing. This transcriptomic data also provides an important gene resource for improving breeding for Moso bamboo.
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Affiliation(s)
- Jian Gao
- International Center for Bamboo and Rattan, Key Laboratory of Bamboo and Rattan Science and Technology, State Forestry Administration, Beijing, People's Republic of China
- * E-mail: (JG); (ZP)
| | - Ying Zhang
- International Center for Bamboo and Rattan, Key Laboratory of Bamboo and Rattan Science and Technology, State Forestry Administration, Beijing, People's Republic of China
| | - Chunling Zhang
- International Center for Bamboo and Rattan, Key Laboratory of Bamboo and Rattan Science and Technology, State Forestry Administration, Beijing, People's Republic of China
| | - Feiyan Qi
- International Center for Bamboo and Rattan, Key Laboratory of Bamboo and Rattan Science and Technology, State Forestry Administration, Beijing, People's Republic of China
| | - Xueping Li
- International Center for Bamboo and Rattan, Key Laboratory of Bamboo and Rattan Science and Technology, State Forestry Administration, Beijing, People's Republic of China
| | - Shaohua Mu
- International Center for Bamboo and Rattan, Key Laboratory of Bamboo and Rattan Science and Technology, State Forestry Administration, Beijing, People's Republic of China
| | - Zhenhua Peng
- International Center for Bamboo and Rattan, Key Laboratory of Bamboo and Rattan Science and Technology, State Forestry Administration, Beijing, People's Republic of China
- * E-mail: (JG); (ZP)
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Wilczek AM, Cooper MD, Korves TM, Schmitt J. Lagging adaptation to warming climate in Arabidopsis thaliana. Proc Natl Acad Sci U S A 2014; 111:7906-13. [PMID: 24843140 PMCID: PMC4050579 DOI: 10.1073/pnas.1406314111] [Citation(s) in RCA: 108] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
If climate change outpaces the rate of adaptive evolution within a site, populations previously well adapted to local conditions may decline or disappear, and banked seeds from those populations will be unsuitable for restoring them. However, if such adaptational lag has occurred, immigrants from historically warmer climates will outperform natives and may provide genetic potential for evolutionary rescue. We tested for lagging adaptation to warming climate using banked seeds of the annual weed Arabidopsis thaliana in common garden experiments in four sites across the species' native European range: Valencia, Spain; Norwich, United Kingdom; Halle, Germany; and Oulu, Finland. Genotypes originating from geographic regions near the planting site had high relative fitness in each site, direct evidence for broad-scale geographic adaptation in this model species. However, genotypes originating in sites historically warmer than the planting site had higher average relative fitness than local genotypes in every site, especially at the northern range limit in Finland. This result suggests that local adaptive optima have shifted rapidly with recent warming across the species' native range. Climatic optima also differed among seasonal germination cohorts within the Norwich site, suggesting that populations occurring where summer germination is common may have greater evolutionary potential to persist under future warming. If adaptational lag has occurred over just a few decades in banked seeds of an annual species, it may be an important consideration for managing longer-lived species, as well as for attempts to conserve threatened populations through ex situ preservation.
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Affiliation(s)
- Amity M Wilczek
- Department of Ecology and Evolutionary Biology, Brown University, Providence, RI 02912;Department of Natural Sciences, Deep Springs College, Big Pine, CA 93513
| | - Martha D Cooper
- Department of Ecology and Evolutionary Biology, Brown University, Providence, RI 02912
| | - Tonia M Korves
- Department of Ecology and Evolutionary Biology, Brown University, Providence, RI 02912;Data Analytics Department, The MITRE Corporation, Bedford, MA 01730-1420; and
| | - Johanna Schmitt
- Department of Ecology and Evolutionary Biology, Brown University, Providence, RI 02912;Department of Evolution and Ecology, University of California, Davis, CA 95616
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