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Minadakis N, Kaderli L, Horvath R, Bourgeois Y, Xu W, Thieme M, Woods DP, Roulin AC. Polygenic architecture of flowering time and its relationship with local environments in the grass Brachypodium distachyon. Genetics 2024; 227:iyae042. [PMID: 38504651 PMCID: PMC11075549 DOI: 10.1093/genetics/iyae042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Revised: 01/12/2024] [Accepted: 03/07/2024] [Indexed: 03/21/2024] Open
Abstract
Synchronizing the timing of reproduction with the environment is crucial in the wild. Among the multiple mechanisms, annual plants evolved to sense their environment, the requirement of cold-mediated vernalization is a major process that prevents individuals from flowering during winter. In many annual plants including crops, both a long and short vernalization requirement can be observed within species, resulting in so-called early-(spring) and late-(winter) flowering genotypes. Here, using the grass model Brachypodium distachyon, we explored the link between flowering-time-related traits (vernalization requirement and flowering time), environmental variation, and diversity at flowering-time genes by combining measurements under greenhouse and outdoor conditions. These experiments confirmed that B. distachyon natural accessions display large differences regarding vernalization requirements and ultimately flowering time. We underline significant, albeit quantitative effects of current environmental conditions on flowering-time-related traits. While disentangling the confounding effects of population structure on flowering-time-related traits remains challenging, population genomics analyses indicate that well-characterized flowering-time genes may contribute significantly to flowering-time variation and display signs of polygenic selection. Flowering-time genes, however, do not colocalize with genome-wide association peaks obtained with outdoor measurements, suggesting that additional genetic factors contribute to flowering-time variation in the wild. Altogether, our study fosters our understanding of the polygenic architecture of flowering time in a natural grass system and opens new avenues of research to investigate the gene-by-environment interaction at play for this trait.
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Affiliation(s)
- Nikolaos Minadakis
- Department of Plant and Microbial Biology, University of Zürich, Zollikerstr. 107, 8008 Zürich, Switzerland
| | - Lars Kaderli
- Department of Plant and Microbial Biology, University of Zürich, Zollikerstr. 107, 8008 Zürich, Switzerland
| | - Robert Horvath
- Department of Plant and Microbial Biology, University of Zürich, Zollikerstr. 107, 8008 Zürich, Switzerland
| | - Yann Bourgeois
- DIADE, University of Montpellier, CIRAD, IRD, 34 000 Montpellier, France
| | - Wenbo Xu
- Department of Plant and Microbial Biology, University of Zürich, Zollikerstr. 107, 8008 Zürich, Switzerland
| | - Michael Thieme
- Department of Plant and Microbial Biology, University of Zürich, Zollikerstr. 107, 8008 Zürich, Switzerland
| | - Daniel P Woods
- Department of Plant Sciences, University of California-Davis, 104 Robbins Hall, Davis, CA 95616, USA
- Howard Hughes Medical Institute, 4000 Jones Bridge Rd, Chevy Chase, MD 20815, USA
| | - Anne C Roulin
- Department of Plant and Microbial Biology, University of Zürich, Zollikerstr. 107, 8008 Zürich, Switzerland
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Tavares H, Readshaw A, Kania U, de Jong M, Pasam RK, McCulloch H, Ward S, Shenhav L, Forsyth E, Leyser O. Artificial selection reveals complex genetic architecture of shoot branching and its response to nitrate supply in Arabidopsis. PLoS Genet 2023; 19:e1010863. [PMID: 37616321 PMCID: PMC10482290 DOI: 10.1371/journal.pgen.1010863] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2022] [Revised: 09/06/2023] [Accepted: 07/08/2023] [Indexed: 08/26/2023] Open
Abstract
Quantitative traits may be controlled by many loci, many alleles at each locus, and subject to genotype-by-environment interactions, making them difficult to map. One example of such a complex trait is shoot branching in the model plant Arabidopsis, and its plasticity in response to nitrate. Here, we use artificial selection under contrasting nitrate supplies to dissect the genetic architecture of this complex trait, where loci identified by association mapping failed to explain heritability estimates. We found a consistent response to selection for high branching, with correlated responses in other traits such as plasticity and flowering time. Genome-wide scans for selection and simulations suggest that at least tens of loci control this trait, with a distinct genetic architecture between low and high nitrate treatments. While signals of selection could be detected in the populations selected for high branching on low nitrate, there was very little overlap in the regions selected in three independent populations. Thus the regulatory network controlling shoot branching can be tuned in different ways to give similar phenotypes.
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Affiliation(s)
- Hugo Tavares
- Sainsbury Laboratory, University of Cambridge, Cambridge, United Kingdom
| | - Anne Readshaw
- Department of Biology, University of York, York, United Kingdom
| | - Urszula Kania
- Sainsbury Laboratory, University of Cambridge, Cambridge, United Kingdom
| | - Maaike de Jong
- Sainsbury Laboratory, University of Cambridge, Cambridge, United Kingdom
| | - Raj K. Pasam
- Sainsbury Laboratory, University of Cambridge, Cambridge, United Kingdom
| | - Hayley McCulloch
- 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
| | - Liron Shenhav
- Sainsbury Laboratory, University of Cambridge, Cambridge, United Kingdom
| | - Elizabeth Forsyth
- Sainsbury Laboratory, University of Cambridge, Cambridge, United Kingdom
| | - Ottoline Leyser
- Sainsbury Laboratory, University of Cambridge, Cambridge, United Kingdom
- Department of Biology, University of York, York, United Kingdom
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3
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Tong Z, Xu M, Zhang Q, Lin F, Fang D, Chen X, Zhu T, Liu Y, Xu H, Xiao B. Construction of a high-density genetic map and dissection of genetic architecture of six agronomic traits in tobacco ( Nicotiana tabacum L.). FRONTIERS IN PLANT SCIENCE 2023; 14:1126529. [PMID: 36875609 PMCID: PMC9975568 DOI: 10.3389/fpls.2023.1126529] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/18/2022] [Accepted: 01/26/2023] [Indexed: 06/18/2023]
Abstract
Tobacco (Nicotiana tabacum L.) is an economic crop and a model organism for studies on plant biology and genetics. A population of 271 recombinant inbred lines (RIL) derived from K326 and Y3, two elite flue-cured tobacco parents, has been constructed to investigate the genetic basis of agronomic traits in tobacco. Six agronomic traits including natural plant height (nPH), natural leaf number (nLN), stem girth (SG), inter-node length (IL), length of the largest leaf (LL) and width of the largest leaf (LW) were measured in seven environments, spanning the period between 2018 and 2021. We firstly developed an integrated SNP-indel-SSR linkage map with 43,301 SNPs, 2,086 indels and 937 SSRs, which contained 7,107 bin markers mapped on 24 LGs and covered 3334.88 cM with an average genetic distance of 0.469cM. Based on this high-density genetic map, a total of 70 novel QTLs were detected for six agronomic traits by a full QTL model using the software QTLNetwork, of which 32 QTLs showed significant additive effects, 18 QTLs showed significant additive-by-environment interaction effects, 17 pairs showed significant additive-by-additive epistatic effects and 13 pairs showed significant epistasis-by-environment interaction effects. In addition to additive effect as a major contributor to genetic variation, both epistasis effects and genotype-by-environment interaction effects played an important role in explaining phenotypic variation for each trait. In particular, qnLN6-1 was detected with considerably large main effect and high heritability ( h a 2 =34.80%). Finally, four genes including Nt16g00284.1, Nt16g00767.1, Nt16g00853.1, Nt16g00877.1 were predicted as pleiotropic candidate genes for five traits.
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Affiliation(s)
- Zhijun Tong
- Key Laboratory of Tobacco Biotechnological Breeding, National Tobacco Genetic Engineering Research Center, Yunnan Academy of Tobacco Agricultural Sciences, Kunming, Yunnan, China
| | - Manling Xu
- Institute of Bioinformatics and Institute of Crop Science, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, Zhejiang, China
| | - Qixin Zhang
- Institute of Bioinformatics and Institute of Crop Science, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, Zhejiang, China
| | - Feng Lin
- Institute of Bioinformatics and Institute of Crop Science, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, Zhejiang, China
| | - Dunhuang Fang
- Key Laboratory of Tobacco Biotechnological Breeding, National Tobacco Genetic Engineering Research Center, Yunnan Academy of Tobacco Agricultural Sciences, Kunming, Yunnan, China
| | - Xuejun Chen
- Key Laboratory of Tobacco Biotechnological Breeding, National Tobacco Genetic Engineering Research Center, Yunnan Academy of Tobacco Agricultural Sciences, Kunming, Yunnan, China
| | - Tianneng Zhu
- Institute of Bioinformatics and Institute of Crop Science, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, Zhejiang, China
| | - Yingchao Liu
- Institute of Bioinformatics and Institute of Crop Science, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, Zhejiang, China
| | - Haiming Xu
- Institute of Bioinformatics and Institute of Crop Science, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, Zhejiang, China
| | - Bingguang Xiao
- Key Laboratory of Tobacco Biotechnological Breeding, National Tobacco Genetic Engineering Research Center, Yunnan Academy of Tobacco Agricultural Sciences, Kunming, Yunnan, China
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4
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Huang S, Zhang Y, Ren H, Li X, Zhang X, Zhang Z, Zhang C, Liu S, Wang X, Zeng Q, Wang Q, Singh RP, Bhavani S, Wu J, Han D, Kang Z. Epistatic interaction effect between chromosome 1BL (Yr29) and a novel locus on 2AL facilitating resistance to stripe rust in Chinese wheat Changwu 357-9. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:2501-2513. [PMID: 35723707 DOI: 10.1007/s00122-022-04133-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Accepted: 05/18/2022] [Indexed: 06/15/2023]
Abstract
Four stable QTL for adult plant resistance were identified in wheat line Changwu 357-9, including a new QTL on 2AL showing significant interaction with Yr29 to reduce stripe rust severity. Stripe rust (yellow rust) is a serious disease of bread wheat (Triticum aestivum L.) worldwide. Genetic resistance is considered the most economical, effective and environmentally friendly method to control the disease and to minimize the use of fungicides. The current study focused on characterizing the components of stripe rust resistance and understanding the interactions in Changwu 357-9 (CW357-9)/Avocet S RIL population. A genetic linkage map constructed using a new GenoBaits Wheat 16K Panel and the 660K SNP array had 5104 polymorphic SNP markers spanning 3533.11 cM. Four stable QTL, consistently identified across five environments, were detected on chromosome arms 1BL, 2AL, 3DS, and 6BS in Changwu357-9. The most effective QTL QYrCW357-1BL was Yr29. The 6BS QTL was identified as Yr78, which has been combined with the 1BL QTL in many wheat cultivars and breeding lines. The novel QTL on 2AL with moderate effect showed a stable and significant epistatic interaction with Yr29. The QTL on 3DL should be same as QYrsn.nwafu-3DL and enriches the overall stripe rust resistance gene pool for breeding. Polymorphisms of flanking AQP markers AX-110020417 (for QYrCW357-1BL), AX-110974948 (for QYrCW357-2AL), AX-109466386 (for QYrCW357-3DL), and AX-109995005 (for QYrCW357-6BS) were evaluated in a diversity panel including 225 wheat cultivars and breeding lines. These results suggested that these high-throughput markers could be used to introduce QYrCW357-1BL, QYrCW357-2AL, QYrCW357-3DL, and QYrCW357-6BS into commercial wheat cultivars. Combinations of these genes with other APR QTL should lead to higher levels of stripe rust resistance along with the beneficial effects of multi-disease resistance gene Yr29 on improving resistance to other diseases.
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Affiliation(s)
- Shuo Huang
- State Key Laboratory of Crop Stress Biology for Arid Areas, Plant Protection, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China
| | - Yibo Zhang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China
| | - Hui Ren
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China
| | - Xiang Li
- State Key Laboratory of Crop Stress Biology for Arid Areas, Plant Protection, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China
| | - Xin Zhang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China
| | - Zeyuan Zhang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China
| | - Chuanliang Zhang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China
| | - Shengjie Liu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China
| | - Xiaoting Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China
| | - Qingdong Zeng
- State Key Laboratory of Crop Stress Biology for Arid Areas, Plant Protection, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China
| | - Qilin Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China
| | - Ravi P Singh
- International Maize and Wheat Improvement Center (CIMMYT), 56237, El Batan, Texcoco, Estado de Mexico, Mexico
| | - Sridhar Bhavani
- International Maize and Wheat Improvement Center (CIMMYT), 56237, El Batan, Texcoco, Estado de Mexico, Mexico
| | - Jianhui Wu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China.
| | - Dejun Han
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China.
| | - Zhensheng Kang
- State Key Laboratory of Crop Stress Biology for Arid Areas, Plant Protection, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China.
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5
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Tan Q, Bu S, Chen G, Yan Z, Chang Z, Zhu H, Yang W, Zhan P, Lin S, Xiong L, Chen S, Liu G, Liu Z, Wang S, Zhang G. Reconstruction of the High Stigma Exsertion Rate Trait in Rice by Pyramiding Multiple QTLs. FRONTIERS IN PLANT SCIENCE 2022; 13:921700. [PMID: 35747883 PMCID: PMC9209754 DOI: 10.3389/fpls.2022.921700] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2022] [Accepted: 05/05/2022] [Indexed: 05/25/2023]
Abstract
Asian cultivated rice is a self-pollinating crop, which has already lost some traits of natural outcrossing in the process of domestication. However, male sterility lines (MSLs) need to have a strong outcrossing ability to produce hybrid seeds by outcrossing with restorer lines of male parents in hybrid rice seed production. Stigma exsertion rate (SER) is a trait related to outcrossing ability. Reconstruction of the high-SER trait is essential in the MSL breeding of rice. In previous studies, we detected eighteen quantitative trait loci (QTLs) for SER from Oryza sativa, Oryza glaberrima, and Oryza glumaepatula using single-segment substitution lines (SSSLs) in the genetic background of Huajingxian 74 (HJX74). In this study, eleven of the QTLs were used to develop pyramiding lines. A total of 29 pyramiding lines with 2-6 QTLs were developed from 10 SSSLs carrying QTLs for SER in the HJX74 genetic background. The results showed that the SER increased with increasing QTLs in the pyramiding lines. The SER in the lines with 5-6 QTLs was as high as wild rice with strong outcrossing ability. The epistasis of additive by additive interaction between QTLs in the pyramiding lines was less-than-additive or negative effect. One QTL, qSER3a-sat, showed minor-effect epistasis and increased higher SER than other QTLs in pyramiding lines. The detection of epistasis of QTLs on SER uncovered the genetic architecture of SER, which provides a basis for using these QTLs to improve SER levels in MSL breeding. The reconstruction of the high-SER trait will help to develop the MSLs with strong outcrossing ability in rice.
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Affiliation(s)
- Quanya Tan
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, China
| | - Suhong Bu
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, China
| | - Guodong Chen
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, China
| | - Zhenguang Yan
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, China
| | - Zengyuan Chang
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, China
| | - Haitao Zhu
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, China
| | - Weifeng Yang
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, China
| | - Penglin Zhan
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, China
| | - Shaojun Lin
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, China
| | - Liang Xiong
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, China
| | - Songliang Chen
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, China
| | - Guifu Liu
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, China
| | - Zupei Liu
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, China
| | - Shaokui Wang
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, China
| | - Guiquan Zhang
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, China
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Boinot M, Karakas E, Koehl K, Pagter M, Zuther E. Cold stress and freezing tolerance negatively affect the fitness of Arabidopsis thaliana accessions under field and controlled conditions. PLANTA 2022; 255:39. [PMID: 35032192 PMCID: PMC8761124 DOI: 10.1007/s00425-021-03809-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Accepted: 12/08/2021] [Indexed: 05/15/2023]
Abstract
Higher acclimated freezing tolerance improved winter survival, but reduced reproductive fitness of Arabidopsis thaliana accessions under field and controlled conditions. Low temperature is one of the most important abiotic factors influencing plant fitness and geographical distribution. In addition, cold stress is known to influence crop yield and is therefore of great economic importance. Increased freezing tolerance can be acquired by the process of cold acclimation, but this may be associated with a fitness cost. To assess the influence of cold stress on the fitness of plants, long-term field trials over 5 years were performed with six natural accessions of Arabidopsis thaliana ranging from very tolerant to very sensitive to freezing. Fitness parameters, as seed yield and 1000 seed mass, were measured and correlation analyses with temperature and freezing tolerance data performed. The results were compared with fitness parameters from controlled chamber experiments over 3 years with application of cold priming and triggering conditions. Winter survival and seed yield per plant were positively correlated with temperature in field experiments. In addition, winter survival and 1000 seed mass were correlated with the cold-acclimated freezing tolerance of the selected Arabidopsis accessions. The results provide strong evidence for a trade-off between higher freezing tolerance and reproductive fitness in A. thaliana, which might have ecological impacts in the context of global warming.
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Affiliation(s)
- Maximilian Boinot
- Max Planck Institute of Molecular Plant Physiology, Am Muehlenberg 1, 14476, Potsdam, Germany
| | - Esra Karakas
- Max Planck Institute of Molecular Plant Physiology, Am Muehlenberg 1, 14476, Potsdam, Germany
| | - Karin Koehl
- Max Planck Institute of Molecular Plant Physiology, Am Muehlenberg 1, 14476, Potsdam, Germany
| | - Majken Pagter
- Max Planck Institute of Molecular Plant Physiology, Am Muehlenberg 1, 14476, Potsdam, Germany
- Department of Chemistry and Bioscience, Aalborg University, 9220, Aalborg East, Denmark
| | - Ellen Zuther
- Max Planck Institute of Molecular Plant Physiology, Am Muehlenberg 1, 14476, Potsdam, Germany.
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7
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Flannery SE, Pastorelli F, Wood WHJ, Hunter CN, Dickman MJ, Jackson PJ, Johnson MP. Comparative proteomics of thylakoids from Arabidopsis grown in laboratory and field conditions. PLANT DIRECT 2021; 5:e355. [PMID: 34712896 PMCID: PMC8528093 DOI: 10.1002/pld3.355] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 09/21/2021] [Accepted: 09/28/2021] [Indexed: 06/13/2023]
Abstract
Compared to controlled laboratory conditions, plant growth in the field is rarely optimal since it is frequently challenged by large fluctuations in light and temperature which lower the efficiency of photosynthesis and lead to photo-oxidative stress. Plants grown under natural conditions therefore place an increased onus on the regulatory mechanisms that protect and repair the delicate photosynthetic machinery. Yet, the exact changes in thylakoid proteome composition which allow plants to acclimate to the natural environment remain largely unexplored. Here, we use quantitative label-free proteomics to demonstrate that field-grown Arabidopsis plants incorporate aspects of both the low and high light acclimation strategies previously observed in laboratory-grown plants. Field plants showed increases in the relative abundance of ATP synthase, cytochrome b 6 f, ferredoxin-NADP+ reductases (FNR1 and FNR2) and their membrane tethers TIC62 and TROL, thylakoid architecture proteins CURT1A, CURT1B, RIQ1, and RIQ2, the minor monomeric antenna complex CP29.3, rapidly-relaxing non-photochemical quenching (qE)-related proteins PSBS and VDE, the photosystem II (PSII) repair machinery and the cyclic electron transfer complexes NDH, PGRL1B, and PGR5, in addition to decreases in the amounts of LHCII trimers composed of LHCB1.1, LHCB1.2, LHCB1.4, and LHCB2 proteins and CP29.2, all features typical of a laboratory high light acclimation response. Conversely, field plants also showed increases in the abundance of light harvesting proteins LHCB1.3 and CP29.1, zeaxanthin epoxidase (ZEP) and the slowly-relaxing non-photochemical quenching (qI)-related protein LCNP, changes previously associated with a laboratory low light acclimation response. Field plants also showed distinct changes to the proteome including the appearance of stress-related proteins ELIP1 and ELIP2 and changes to proteins that are largely invariant under laboratory conditions such as state transition related proteins STN7 and TAP38. We discuss the significance of these alterations in the thylakoid proteome considering the unique set of challenges faced by plants growing under natural conditions.
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Affiliation(s)
- Sarah E. Flannery
- Department of Molecular Biology and BiotechnologyUniversity of SheffieldSheffieldUK
| | - Federica Pastorelli
- Department of Molecular Biology and BiotechnologyUniversity of SheffieldSheffieldUK
| | - William H. J. Wood
- Department of Molecular Biology and BiotechnologyUniversity of SheffieldSheffieldUK
| | - C. Neil Hunter
- Department of Molecular Biology and BiotechnologyUniversity of SheffieldSheffieldUK
| | - Mark J. Dickman
- Department of Chemical and Biological EngineeringUniversity of SheffieldSheffieldUK
| | - Philip J. Jackson
- Department of Molecular Biology and BiotechnologyUniversity of SheffieldSheffieldUK
- Department of Chemical and Biological EngineeringUniversity of SheffieldSheffieldUK
| | - Matthew P. Johnson
- Department of Molecular Biology and BiotechnologyUniversity of SheffieldSheffieldUK
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8
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Mapping QTLs for yield component traits using overwintering cultivated rice. J Genet 2021. [DOI: 10.1007/s12041-021-01279-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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9
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Zhou X, Chan KCC, Huang Z, Wang J. Determining dependency and redundancy for identifying gene-gene interaction associated with complex disease. J Bioinform Comput Biol 2020; 18:2050035. [PMID: 33064052 DOI: 10.1142/s0219720020500353] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
As interactions among genetic variants in different genes can be an important factor for predicting complex diseases, many computational methods have been proposed to detect if a particular set of genes has interaction with a particular complex disease. However, even though many such methods have been shown to be useful, they can be made more effective if the properties of gene-gene interactions can be better understood. Towards this goal, we have attempted to uncover patterns in gene-gene interactions and the patterns reveal an interesting property that can be reflected in an inequality that describes the relationship between two genotype variables and a disease-status variable. We show, in this paper, that this inequality can be generalized to [Formula: see text] genotype variables. Based on this inequality, we establish a conditional independence and redundancy (CIR)-based definition of gene-gene interaction and the concept of an interaction group. From these new definitions, a novel measure of gene-gene interaction is then derived. We discuss the properties of these concepts and explain how they can be used in a novel algorithm to detect high-order gene-gene interactions. Experimental results using both simulated and real datasets show that the proposed method can be very promising.
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Affiliation(s)
- Xiangdong Zhou
- College of Mathematics and Computer Science, Fuzhou University Fuzhou, Fujian 350108, P. R. China
| | - Keith C C Chan
- Department of Computing, The Hong Kong Polytechnic University, Kowloon, Hong Kong, P. R. China
| | - Zhihua Huang
- College of Mathematics and Computer Science, Fuzhou University Fuzhou, Fujian 350108, P. R. China
| | - Jingbin Wang
- College of Mathematics and Computer Science, Fuzhou University Fuzhou, Fujian 350108, P. R. China
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Brock MT, Rubin MJ, DellaPenna D, Weinig C. A Nested Association Mapping Panel in Arabidopsis thaliana for Mapping and Characterizing Genetic Architecture. G3 (BETHESDA, MD.) 2020; 10:3701-3708. [PMID: 32788287 PMCID: PMC7534452 DOI: 10.1534/g3.120.401239] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Accepted: 08/08/2020] [Indexed: 12/20/2022]
Abstract
Linkage and association mapping populations are crucial public resources that facilitate the characterization of trait genetic architecture in natural and agricultural systems. We define a large nested association mapping panel (NAM) from 14 publicly available recombinant inbred line populations (RILs) of Arabidopsis thaliana, which share a common recurrent parent (Col-0). Using a genotype-by-sequencing approach (GBS), we identified single nucleotide polymorphisms (SNPs; range 563-1525 per population) and subsequently built updated linkage maps in each of the 14 RIL sets. Simulations in individual RIL populations indicate that our GBS markers have improved power to detect small effect QTL and enhanced resolution of QTL support intervals in comparison to original linkage maps. Using these robust linkage maps, we imputed a common set of publicly available parental SNPs into each RIL linkage map, generating overlapping markers across all populations. Though ultimately depending on allele frequencies at causal loci, simulations of the NAM panel suggest that surveying between 4 to 7 of the 14 RIL populations provides high resolution of the genetic architecture of complex traits, relative to a single mapping population.
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Affiliation(s)
- Marcus T Brock
- Department of Botany, University of Wyoming, Laramie, WY 82071
| | - Matthew J Rubin
- Department of Botany, University of Wyoming, Laramie, WY 82071
- Program in Ecology, University of Wyoming, Laramie, WY 82071
- Donald Danforth Plant Science Center, St. Louis, MO 63132
| | - Dean DellaPenna
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824
| | - Cynthia Weinig
- Department of Botany, University of Wyoming, Laramie, WY 82071
- Program in Ecology, University of Wyoming, Laramie, WY 82071
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824
- Department of Molecular Biology, University of Wyoming, Laramie, WY 82071
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11
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Yi G, Shin H, Park HR, Park JE, Ahn JH, Lim S, Lee JG, Lee EJ, Huh JH. Revealing biomass heterosis in the allodiploid xBrassicoraphanus, a hybrid between Brassica rapa and Raphanus sativus, through integrated transcriptome and metabolites analysis. BMC PLANT BIOLOGY 2020; 20:252. [PMID: 32493222 PMCID: PMC7268423 DOI: 10.1186/s12870-020-02470-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2019] [Accepted: 05/26/2020] [Indexed: 05/15/2023]
Abstract
BACKGROUND Heterosis is biologically important but the molecular basis of the phenomenon is poorly understood. We characterized intergeneric hybrids between B. rapa cv. Chiifu and R. sativus cv. WK10039 as an extreme example of heterosis. Taking advantage of clear heterosis phenotypes and the genetic distance between parents, we performed transcriptome and metabolite analysis to decipher the molecular basis of heterosis. RESULTS The heterosis was expressed as fresh weight in the field and as inflorescence stem length in the glass house. Flowering time, distributed as a normal segregating population, ranged from the early flowering of one parent to the late flowering of the other, in contrast to the homogeneous flowering time in a typical F1 population, indicating unstable allelic interactions. The transcriptome and metabolome both indicated that sugar metabolism was altered, suggesting that the change in metabolism was linked to the heterosis. Because alleles were not shared between the hybridized genomes, classic models only partly explain this heterosis, indicating that other mechanisms are involved. CONCLUSION The differential expression of genes for primary and secondary metabolism, along with the altered metabolite profiles, suggests that heterosis could involve a change in balance between primary and secondary metabolism.
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Affiliation(s)
- Gibum Yi
- Department of Plant Science, Seoul National University, Gwanak-gu, Seoul, 08826 South Korea
- Plant Genomics and Breeding Institute, Seoul National University, Seoul, 08826 South Korea
- Department of Central Area Crop Science, National Institute of Crop Science, RDA, Suwon, 16429 Republic of Korea
| | - Hosub Shin
- Department of Plant Science, Seoul National University, Gwanak-gu, Seoul, 08826 South Korea
| | - Hye Rang Park
- Department of Plant Science, Seoul National University, Gwanak-gu, Seoul, 08826 South Korea
| | - Jeong Eun Park
- Department of Plant Science, Seoul National University, Gwanak-gu, Seoul, 08826 South Korea
| | - Jong Hwa Ahn
- Department of Plant Science, Seoul National University, Gwanak-gu, Seoul, 08826 South Korea
- Illumina Korea, Yeongdeungpo-gu, Seoul, 07325 South Korea
| | - Sooyeon Lim
- Department of Plant Science, Seoul National University, Gwanak-gu, Seoul, 08826 South Korea
- Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, 08826 South Korea
- National Institute of Horticultural and Herbal Science, RDA, Wanju-gun, Jeollabuk-do 55365 South Korea
| | - Jeong Gu Lee
- Department of Plant Science, Seoul National University, Gwanak-gu, Seoul, 08826 South Korea
| | - Eun Jin Lee
- Department of Plant Science, Seoul National University, Gwanak-gu, Seoul, 08826 South Korea
- Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, 08826 South Korea
| | - Jin Hoe Huh
- Department of Plant Science, Seoul National University, Gwanak-gu, Seoul, 08826 South Korea
- Plant Genomics and Breeding Institute, Seoul National University, Seoul, 08826 South Korea
- Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, 08826 South Korea
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12
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Rahman MA, Thomson MJ, De Ocampo M, Egdane JA, Salam MA, Shah-E-Alam M, Ismail AM. Assessing trait contribution and mapping novel QTL for salinity tolerance using the Bangladeshi rice landrace Capsule. RICE (NEW YORK, N.Y.) 2019; 12:63. [PMID: 31410650 PMCID: PMC6692794 DOI: 10.1186/s12284-019-0319-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Accepted: 07/25/2019] [Indexed: 05/15/2023]
Abstract
BACKGROUND Salinity is one of the most widespread abiotic stresses affecting rice productivity worldwide. The purpose of this study was to establish the relative importance of different traits associated with salinity tolerance in rice and to identify new quantitative trait loci (QTL) conferring tolerance to salinity at seedling stage. A total of 231 F2:3 plants derived from a cross between a sensitive variety BRRI dhan29 (BR29 hereafter) and Capsule, a salt tolerant Bangladeshi indica landrace, were evaluated under salt stress in a phytotron. RESULTS Out of the 231 F2 plants, 47 highly tolerant and 47 most sensitive lines were selected, representing the two extreme tails of the phenotypic distribution. These 94 plants were genotyped for 105 simple sequence repeat (SSR) and insertion/deletion (InDel) markers. A genetic linkage map spanning approximately 1442.9 cM of the 12 linkage groups with an average marker distance of 13.7 cM was constructed. QTL were identified on the long arm of chromosome 1 for Na+ concentration, K+ concentration, Na+-K+ ratio and survival; chromosome 3 for Na+ concentration, survival and overall phenotypic evaluation using the Standard Evaluation system (SES); and chromosome 5 for SES. A total of 6 pairwise epistatic interactions were also detected between QTL-linked and QTL-unlinked regions. Graphical genotyping indicated an association between the phenotypes of the extreme families and their QTL genotypes. Path coefficient analysis revealed that Na+ concentration, survival, Na+-K+ ratio and the overall phenotypic performance (SES score) are the major traits associated with salinity tolerance of Capsule. CONCLUSIONS Capsule provides an alternative source of salinity tolerance aside from Pokkali and Nona Bokra, the two Indian salt tolerant landraces traditionally used for breeding salt tolerant rice varieties. Pyramiding the new QTL identified in this study with previously discovered loci, such as Saltol, will facilitate breeding varieties that are highly tolerant of salt stress.
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Affiliation(s)
- M Akhlasur Rahman
- International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines
- Bangladesh Rice Research Institute, Gazipur, 1701, Bangladesh
| | - Michael J Thomson
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX, 77843, USA
| | - Marjorie De Ocampo
- International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines
| | - James A Egdane
- International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines
| | - M A Salam
- Bangladesh Rice Research Institute, Gazipur, 1701, Bangladesh
| | - M Shah-E-Alam
- Bangladesh Agricultural University, Mymensingh, 2202, Bangladesh
| | - Abdelbagi M Ismail
- International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines.
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Samis KE, Stinchcombe JR, Murren CJ. Population climatic history predicts phenotypic responses in novel environments for Arabidopsis thaliana in North America. AMERICAN JOURNAL OF BOTANY 2019; 106:1068-1080. [PMID: 31364776 DOI: 10.1002/ajb2.1334] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Accepted: 05/28/2019] [Indexed: 05/28/2023]
Abstract
PREMISE Determining how species perform in novel climatic environments is essential for understanding (1) responses to climate change and (2) evolutionary consequences of biological invasions. For the vast majority of species, the number of population characteristics that will predict performance and patterns of natural selection in novel locations in the wild remains limited. METHODS We evaluated phenological, vegetative, architectural, and fitness-related traits in experimental gardens in contrasting climates (Ontario, Canada, and South Carolina, USA) in the North American non-native distribution of Arabidopsis thaliana. We assessed the effects of climatic distance, geographic distance, and genetic features of history on performance and patterns of natural selection in the novel garden settings. RESULTS We found that plants had greater survivorship, flowered earlier, were larger, and produced more fruit in the south, and that genotype-by-environment interactions were significant between gardens. However, our analyses revealed similar patterns of natural selection between gardens in distinct climate zones. After accounting for genetic ancestry, we also detected that population climatic distance best predicted performance within gardens. CONCLUSIONS These data suggest that colonization success in novel, non-native environments is determined by a combination of climate and genetic history. When performance at novel sites was assessed with seed sources from geographically and genetically disparate, established non-native populations, proximity to the garden alone was insufficient to predict performance. Our study highlights the need to evaluate seed sources from diverse origins to describe comprehensively phenotypic responses to novel environments, particularly for taxa in which many source populations may contribute to colonization.
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Affiliation(s)
- Karen E Samis
- Department of Biology, University of Prince Edward Island, Charlottetown, Prince Edward Island, Canada
| | - John R Stinchcombe
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada
- Koffler Scientific Reserve at Joker's Hill, University of Toronto, Toronto, Ontario, Canada
| | - Courtney J Murren
- Department of Biology, College of Charleston, Charleston, South Carolina, 29424, USA
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A Low Resolution Epistasis Mapping Approach To Identify Chromosome Arm Interactions in Allohexaploid Wheat. G3-GENES GENOMES GENETICS 2019; 9:675-684. [PMID: 30455184 PMCID: PMC6404624 DOI: 10.1534/g3.118.200646] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Epistasis is an important contributor to genetic variance. In inbred populations, pairwise epistasis is present as additive by additive interactions. Testing for epistasis presents a multiple testing problem as the pairwise search space for modest numbers of markers is large. Single markers do not necessarily track functional units of interacting chromatin as well as haplotype based methods do. To harness the power of multiple markers while minimizing the number of tests conducted, we present a low resolution test for epistatic interactions across whole chromosome arms. Epistasis covariance matrices were constructed from the additive covariances of individual chromosome arms. These covariances were subsequently used to estimate an epistatic variance parameter while correcting for background additive and epistatic effects. We find significant epistasis for 2% of the interactions tested for four agronomic traits in a winter wheat breeding population. Interactions across homeologous chromosome arms were identified, but were less abundant than other chromosome arm pair interactions. The homeologous chromosome arm pair 4BL/4DL showed a strong negative relationship between additive and interaction effects that may be indicative of functional redundancy. Several chromosome arms appeared to act as hubs in an interaction network, suggesting that they may contain important regulatory factors. The differential patterns of epistasis across different traits demonstrate that detection of epistatic interactions is robust when correcting for background additive and epistatic effects in the population. The low resolution epistasis mapping method presented here identifies important epistatic interactions with a limited number of statistical tests at the cost of low precision.
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15
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Bernacki MJ, Czarnocka W, Rusaczonek A, Witoń D, Kęska S, Czyż J, Szechyńska-Hebda M, Karpiński S. LSD1-, EDS1- and PAD4-dependent conditional correlation among salicylic acid, hydrogen peroxide, water use efficiency and seed yield in Arabidopsis thaliana. PHYSIOLOGIA PLANTARUM 2019; 165:369-382. [PMID: 30461017 DOI: 10.1111/ppl.12863] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Revised: 09/23/2018] [Accepted: 10/26/2018] [Indexed: 06/09/2023]
Abstract
In Arabidopsis thaliana, LESION SIMULATING DISEASE 1 (LSD1), ENHANCED DISEASE SUSCEPTIBILITY 1 (EDS1) and PHYTOALEXIN DEFICIENT 4 (PAD4) proteins are regulators of cell death (CD) in response to abiotic and biotic stresses. Hormones, such as salicylic acid (SA), and reactive oxygen species, such as hydrogen peroxide (H2 O2 ), are key signaling molecules involved in plant CD. The proposed mathematical models presented in this study suggest that LSD1, EDS1 and PAD4 together with SA and H2 O2 are involved in the control of plant water use efficiency (WUE), vegetative growth and generative development. The analysis of Arabidopsis wild-type and single mutants lsd1, eds1, and pad4, as well as double mutants eds1/lsd1 and pad4/lsd1, demonstrated the strong conditional correlation between SA/H2 O2 and WUE that is dependent on LSD1, EDS1 and PAD4 proteins. Moreover, we found a strong correlation between the SA/H2 O2 homeostasis of 4-week-old Arabidopsis leaves and a total seed yield of 9-week-old plants. Altogether, our results prove that SA and H2 O2 are conditionally regulated by LSD1/EDS/PAD4 to govern WUE, biomass accumulation and seed yield. Conditional correlation and the proposed models presented in this study can be used as the starting points in the creation of a plant breeding algorithm that would allow to estimate the seed yield at the initial stage of plant growth, based on WUE, SA and H2 O2 content.
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Affiliation(s)
- Maciej J Bernacki
- Department of Plant Genetics, Breeding, and Biotechnology, Faculty of Horticulture, Biotechnology and Landscape Architecture, Warsaw University of Life Sciences, Warsaw, Poland
| | - Weronika Czarnocka
- Department of Plant Genetics, Breeding, and Biotechnology, Faculty of Horticulture, Biotechnology and Landscape Architecture, Warsaw University of Life Sciences, Warsaw, Poland
- Department of Botany, Faculty of Agriculture and Biology, Warsaw University of Life Sciences, Warsaw, Poland
| | - Anna Rusaczonek
- Department of Plant Genetics, Breeding, and Biotechnology, Faculty of Horticulture, Biotechnology and Landscape Architecture, Warsaw University of Life Sciences, Warsaw, Poland
| | - Damian Witoń
- Department of Plant Genetics, Breeding, and Biotechnology, Faculty of Horticulture, Biotechnology and Landscape Architecture, Warsaw University of Life Sciences, Warsaw, Poland
| | - Sergiusz Kęska
- Faculty of Sciences, Siedlce University of Natural Sciences and Humanities, Siedlce, Poland
| | - Janusz Czyż
- Department of Plant Genetics, Breeding, and Biotechnology, Faculty of Horticulture, Biotechnology and Landscape Architecture, Warsaw University of Life Sciences, Warsaw, Poland
| | - Magdalena Szechyńska-Hebda
- The Plant Breeding and Acclimatization Institute-National Research Institute, 05-870 Błonie, Poland
- Department of Stress Biology, The Franciszek Górski Institute of Plant Physiology, Polish Academy of Sciences, 30-239 Cracow, Poland
| | - Stanisław Karpiński
- Department of Plant Genetics, Breeding, and Biotechnology, Faculty of Horticulture, Biotechnology and Landscape Architecture, Warsaw University of Life Sciences, Warsaw, Poland
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Zaidem ML, Groen SC, Purugganan MD. Evolutionary and ecological functional genomics, from lab to the wild. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 97:40-55. [PMID: 30444573 DOI: 10.1111/tpj.14167] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Revised: 11/10/2018] [Accepted: 11/13/2018] [Indexed: 05/12/2023]
Abstract
Plant phenotypes are the result of both genetic and environmental forces that act to modulate trait expression. Over the last few years, numerous approaches in functional genomics and systems biology have led to a greater understanding of plant phenotypic variation and plant responses to the environment. These approaches, and the questions that they can address, have been loosely termed evolutionary and ecological functional genomics (EEFG), and have been providing key insights on how plants adapt and evolve. In particular, by bringing these studies from the laboratory to the field, EEFG studies allow us to gain greater knowledge of how plants function in their natural contexts.
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Affiliation(s)
- Maricris L Zaidem
- Department of Biology, Center for Genomics and Systems Biology, New York University, 12 Waverly Place, New York, NY, 10003, USA
| | - Simon C Groen
- Department of Biology, Center for Genomics and Systems Biology, New York University, 12 Waverly Place, New York, NY, 10003, USA
| | - Michael D Purugganan
- 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
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17
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Study of QTLs linked to awn length and their relationships with chloroplasts under control and saline environments in bread wheat. Genes Genomics 2018; 41:223-231. [PMID: 30378005 DOI: 10.1007/s13258-018-0757-2] [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: 07/04/2018] [Accepted: 10/24/2018] [Indexed: 10/28/2022]
Abstract
INTRODUCTION Some studies in wheat showed that awns may have a useful effect on yield, especially under drought stress. Up to this time few researches has identified the awn length QTLs with different effect in salinity stress. OBJECTIVE The primary objective of this study was to examine the additive (a) and the epistatic (aa) QTLs involve in wheat awns length in control and saline environments. METHODS A F7 RIL population consisting of 319 sister lines, derived from a cross between wheat cultivars Roshan and Falat (seri82), and the two parents were grown in two environments (control and Saline) based on an alpha lattice design with two replications in each environment. At flowering, awn length was measured for each line. For QTL analysis, the linkage map of the ''Roshan × Falat'' population was used, which included 748 markers including 719 DArT, 29 simple sequenced repeats (SSRs). Additive and pleiotropic QTLs were identified. In order to reveal the relationship between the identified QTL for awns length and the role of the gene or genes that it expresses, the awns length locus location and characteristics of its related CDS, gene, UTRs, ORF, exons and Introns were studied using ensemble plant ( http://plants.ensembl.org/Triticum_aestivum ). Furthermore, the promoter analysis has been done using NSITE-PL. RESULTS We identified 6 additive QTLs for awn length by QTL Cartographer program using single-environment phenotypical values. Also, we detected three additive and two epistatic QTLs for awn length by the QTLNetwork program using multi-environment phenotypical values. Our results showed that none of the additive and epistatic QTLs had interactions with environment. One of the additive QTLs located on chromosome 4A was co-located with QTLs for number of sterile spikelet per spike in both environment and number of seed per spike in control environment. COCLUSION Studies of the locus linked to the awns length QTL revealed the role of awn and its chloroplasts in grain filing during abiotic stress could be enhanced by over expression of some genes like GTP-Binding proteins which are enriched in chloroplasts encoded by genes included wPt-5730 locus.
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Shared Genomic Regions Underlie Natural Variation in Diverse Toxin Responses. Genetics 2018; 210:1509-1525. [PMID: 30341085 PMCID: PMC6283156 DOI: 10.1534/genetics.118.301311] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Accepted: 10/16/2018] [Indexed: 01/25/2023] Open
Abstract
Phenotypic complexity is caused by the contributions of environmental factors and multiple genetic loci, interacting or acting independently. Studies of yeast and Arabidopsis often find that the majority of natural variation across phenotypes is attributable to independent additive quantitative trait loci (QTL). Detected loci in these organisms explain most of the estimated heritable variation. By contrast, many heritable components underlying phenotypic variation in metazoan models remain undetected. Before the relative impacts of additive and interactive variance components on metazoan phenotypic variation can be dissected, high replication and precise phenotypic measurements are required to obtain sufficient statistical power to detect loci contributing to this missing heritability. Here, we used a panel of 296 recombinant inbred advanced intercross lines of Caenorhabditis elegans and a high-throughput fitness assay to detect loci underlying responses to 16 different toxins, including heavy metals, chemotherapeutic drugs, pesticides, and neuropharmaceuticals. Using linkage mapping, we identified 82 QTL that underlie variation in responses to these toxins, and predicted the relative contributions of additive loci and genetic interactions across various growth parameters. Additionally, we identified three genomic regions that impact responses to multiple classes of toxins. These QTL hotspots could represent common factors impacting toxin responses. We went further to generate near-isogenic lines and chromosome substitution strains, and then experimentally validated these QTL hotspots, implicating additive and interactive loci that underlie toxin-response variation.
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19
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Zhu W, Zaidem M, Van de Weyer AL, Gutaker RM, Chae E, Kim ST, Bemm F, Li L, Todesco M, Schwab R, Unger F, Beha MJ, Demar M, Weigel D. Modulation of ACD6 dependent hyperimmunity by natural alleles of an Arabidopsis thaliana NLR resistance gene. PLoS Genet 2018; 14:e1007628. [PMID: 30235212 PMCID: PMC6168153 DOI: 10.1371/journal.pgen.1007628] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Revised: 10/02/2018] [Accepted: 08/14/2018] [Indexed: 01/09/2023] Open
Abstract
Plants defend themselves against pathogens by activating an array of immune responses. Unfortunately, immunity programs may also cause unintended collateral damage to the plant itself. The quantitative disease resistance gene ACCELERATED CELL DEATH 6 (ACD6) serves to balance growth and pathogen resistance in natural populations of Arabidopsis thaliana. An autoimmune allele, ACD6-Est, which strongly reduces growth under specific laboratory conditions, is found in over 10% of wild strains. There is, however, extensive variation in the strength of the autoimmune phenotype expressed by strains with an ACD6-Est allele, indicative of genetic modifiers. Quantitative genetic analysis suggests that ACD6 activity can be modulated in diverse ways, with different strains often carrying different large-effect modifiers. One modifier is SUPPRESSOR OF NPR1-1, CONSTITUTIVE 1 (SNC1), located in a highly polymorphic cluster of nucleotide-binding domain and leucine-rich repeat (NLR) immune receptor genes, which are prototypes for qualitative disease resistance genes. Allelic variation at SNC1 correlates with ACD6-Est activity in multiple accessions, and a common structural variant affecting the NL linker sequence can explain differences in SNC1 activity. Taken together, we find that an NLR gene can mask the activity of an ACD6 autoimmune allele in natural A. thaliana populations, thereby linking different arms of the plant immune system. Plants defend themselves against pathogens by activating immune responses. Unfortunately, these can cause unintended collateral damage to the plant itself. Nevertheless, some wild plants have genetic variants that confer a low threshold for the activation of immunity. While these enable a plant to respond particularly quickly to pathogen attack, such variants might be potentially dangerous. We are investigating one such variant of the immune gene ACCELERATED CELL DEATH 6 (ACD6) in the plant Arabidopsis thaliana. We discovered that there are variants at other genetic loci that can mask the effects of an overly active ACD6 gene. One of these genes, SUPPRESSOR OF NPR1-1, CONSTITUTIVE 1 (SNC1), codes for a known immune receptor. The SNC1 variant that attenuates ACD6 activity is rather common in A. thaliana populations, suggesting that new combinations of the hyperactive ACD6 variant and this antagonistic SNC1 variant will often arise by natural crosses. Similarly, because the two genes are unlinked, outcrossing will often lead to the hyperactive ACD6 variants being unmasked again. We propose that allelic diversity at SNC1 contributes to the maintenance of the hyperactive ACD6 variant in natural A. thaliana populations.
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Affiliation(s)
- Wangsheng Zhu
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Maricris Zaidem
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Anna-Lena Van de Weyer
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Rafal M. Gutaker
- Research Group for Ancient Genomics and Evolution, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Eunyoung Chae
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Sang-Tae Kim
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Felix Bemm
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Lei Li
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Marco Todesco
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Rebecca Schwab
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Frederik Unger
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Marcel Janis Beha
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Monika Demar
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Detlef Weigel
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany
- * E-mail:
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Bernacki MJ, Czarnocka W, Witoń D, Rusaczonek A, Szechyńska-Hebda M, Ślesak I, Dąbrowska-Bronk J, Karpiński S. ENHANCED DISEASE SUSCEPTIBILITY 1 (EDS1) affects development, photosynthesis, and hormonal homeostasis in hybrid aspen (Populus tremula L. × P. tremuloides). JOURNAL OF PLANT PHYSIOLOGY 2018; 226:91-102. [PMID: 29730441 DOI: 10.1016/j.jplph.2018.04.014] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2018] [Revised: 04/08/2018] [Accepted: 04/23/2018] [Indexed: 05/23/2023]
Abstract
ENHANCED DISEASE SUSCEPTIBILITY 1 (EDS1) was first described as a protein involved in salicylic acid (SA)-, ethylene-, and reactive oxygen species (ROS)-dependent defense and acclimation responses. It is a molecular regulator of biotic and abiotic stress-induced programmed cell death. Its role is relatively well known in annual plants, such as Arabidopsis thaliana or Nicotiana benthamiana. However, little is known about its functions in woody plants. Therefore, in this study, we aimed to characterize the function of EDS1 in the Populus tremula L. × P. tremuloides hybrid grown for several seasons in the natural environment. We used two transgenic lines, eds1-7 and eds1-12, with decreased EDS1 expression levels in this study. The observed changes in physiological and biochemical parameters corresponded with the EDS1 silencing level. Both transgenic lines produced more lateral shoots in comparison to the wild-type (WT) plants, which resulted in the modification of tree morphology. Photosynthetic parameters, such as quantum yield of photosystem II (ϕPSII), photochemical and non-photochemical quenching (qP and NPQ, respectively), as well as chlorophyll content were found to be increased in both transgenic lines, which resulted in changes in photosynthetic efficiency. Our data also revealed lower foliar concentrations of SA and ROS, the latter resulting most probably from more efficient antioxidant system in both transgenic lines. In addition, our data indicated significantly decreased rate of leaf senescence during several autumn seasons. Transcriptomic analysis revealed deregulation of 2215 and 376 genes in eds1-12 and eds1-7, respectively, and also revealed 207 genes that were commonly deregulated in both transgenic lines. The deregulation was primarily observed in the genes involved in photosynthesis, signaling, hormonal metabolism, and development, which was found to agree with the results of biochemical and physiological tests. In general, our data proved that poplar EDS1 affects tree morphology, photosynthetic efficiency, ROS and SA metabolism, as well as leaf senescence.
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Affiliation(s)
- Maciej Jerzy Bernacki
- Department of Plant Genetics, Breeding and Biotechnology, Faculty of Horticulture, Biotechnology and Landscape Architecture, Warsaw University of Life Sciences, Nowoursynowska Street 159, 02-776 Warszawa, Poland
| | - Weronika Czarnocka
- Department of Plant Genetics, Breeding and Biotechnology, Faculty of Horticulture, Biotechnology and Landscape Architecture, Warsaw University of Life Sciences, Nowoursynowska Street 159, 02-776 Warszawa, Poland; Department of Botany, Faculty of Agriculture and Biology, Warsaw University of Life Sciences, Nowoursynowska Street 159, 02-776 Warszawa, Poland
| | - Damian Witoń
- Department of Plant Genetics, Breeding and Biotechnology, Faculty of Horticulture, Biotechnology and Landscape Architecture, Warsaw University of Life Sciences, Nowoursynowska Street 159, 02-776 Warszawa, Poland
| | - Anna Rusaczonek
- Department of Plant Genetics, Breeding and Biotechnology, Faculty of Horticulture, Biotechnology and Landscape Architecture, Warsaw University of Life Sciences, Nowoursynowska Street 159, 02-776 Warszawa, Poland
| | - Magdalena Szechyńska-Hebda
- The Franciszek Górski Institute of Plant Physiology, Polish Academy of Sciences, Niezapominajek Street 21, 30-001 Cracow, Poland; Plant Breeding and Acclimatization Institute, 05-870 Błonie, Radzików, Poland
| | - Ireneusz Ślesak
- Department of Plant Genetics, Breeding and Biotechnology, Faculty of Horticulture, Biotechnology and Landscape Architecture, Warsaw University of Life Sciences, Nowoursynowska Street 159, 02-776 Warszawa, Poland; The Franciszek Górski Institute of Plant Physiology, Polish Academy of Sciences, Niezapominajek Street 21, 30-001 Cracow, Poland
| | - Joanna Dąbrowska-Bronk
- Department of Plant Genetics, Breeding and Biotechnology, Faculty of Horticulture, Biotechnology and Landscape Architecture, Warsaw University of Life Sciences, Nowoursynowska Street 159, 02-776 Warszawa, Poland
| | - Stanisław Karpiński
- Department of Plant Genetics, Breeding and Biotechnology, Faculty of Horticulture, Biotechnology and Landscape Architecture, Warsaw University of Life Sciences, Nowoursynowska Street 159, 02-776 Warszawa, Poland.
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21
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Sardi M, Gasch AP. Genetic background effects in quantitative genetics: gene-by-system interactions. Curr Genet 2018; 64:1173-1176. [PMID: 29644456 DOI: 10.1007/s00294-018-0835-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2018] [Revised: 04/04/2018] [Accepted: 04/06/2018] [Indexed: 01/18/2023]
Abstract
Proper cell function depends on networks of proteins that interact physically and functionally to carry out physiological processes. Thus, it seems logical that the impact of sequence variation in one protein could be significantly influenced by genetic variants at other loci in a genome. Nonetheless, the importance of such genetic interactions, known as epistasis, in explaining phenotypic variation remains a matter of debate in genetics. Recent work from our lab revealed that genes implicated from an association study of toxin tolerance in Saccharomyces cerevisiae show extensive interactions with the genetic background: most implicated genes, regardless of allele, are important for toxin tolerance in only one of two tested strains. The prevalence of background effects in our study adds to other reports of widespread genetic-background interactions in model organisms. We suggest that these effects represent many-way interactions with myriad features of the cellular system that vary across classes of individuals. Such gene-by-system interactions may influence diverse traits and require new modeling approaches to accurately represent genotype-phenotype relationships across individuals.
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Affiliation(s)
- Maria Sardi
- Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, 53706, USA
- Cargill, Incorporated, Minneapolis, MN, 55440, USA
| | - Audrey P Gasch
- Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, 53706, USA.
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, WI, 53706, USA.
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22
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Iwayama K, Aisaka Y, Kutsuna N, Nagano AJ. FIT: statistical modeling tool for transcriptome dynamics under fluctuating field conditions. Bioinformatics 2018; 33:1672-1680. [PMID: 28158396 PMCID: PMC5447243 DOI: 10.1093/bioinformatics/btx049] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2016] [Accepted: 01/28/2017] [Indexed: 12/31/2022] Open
Abstract
Motivation Considerable attention has been given to the quantification of environmental effects on organisms. In natural conditions, environmental factors are continuously changing in a complex manner. To reveal the effects of such environmental variations on organisms, transcriptome data in field environments have been collected and analyzed. Nagano et al. proposed a model that describes the relationship between transcriptomic variation and environmental conditions and demonstrated the capability to predict transcriptome variation in rice plants. However, the computational cost of parameter optimization has prevented its wide application. Results We propose a new statistical model and efficient parameter optimization based on the previous study. We developed and released FIT, an R package that offers functions for parameter optimization and transcriptome prediction. The proposed method achieves comparable or better prediction performance within a shorter computational time than the previous method. The package will facilitate the study of the environmental effects on transcriptomic variation in field conditions. Availability and Implementation Freely available from CRAN (https://cran.r-project.org/web/packages/FIT/). Supplementary information Supplementary data are available at Bioinformatics online
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Affiliation(s)
- Koji Iwayama
- Research Institute for Food and Agriculture, Ryukoku University, Otsu, Shiga, Japan
| | | | - Natsumaro Kutsuna
- LPixel Inc, Hongo, Bunkyo-ku, Tokyo, Japan.,Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa-shi, Chiba, Japan
| | - Atsushi J Nagano
- Department of Plant Life Science, Faculty of Agriculture, Ryukoku University, Otsu, Shiga, Japan.,Center for Ecological Research, Kyoto University, Otsu, Shiga, Japan.,JST PRESTO, Kawaguchi, Saitama, Japan
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23
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Xu Y, Wu Y, Wu J. Capturing pair-wise epistatic effects associated with three agronomic traits in barley. Genetica 2018; 146:161-170. [PMID: 29349538 DOI: 10.1007/s10709-018-0008-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2017] [Accepted: 01/11/2018] [Indexed: 11/25/2022]
Abstract
Genetic association mapping has been widely applied to determine genetic markers favorably associated with a trait of interest and provide information for marker-assisted selection. Many association mapping studies commonly focus on main effects due to intolerable computing intensity. This study aims to select several sets of DNA markers with potential epistasis to maximize genetic variations of some key agronomic traits in barley. By doing so, we integrated a MDR (multifactor dimensionality reduction) method with a forward variable selection approach. This integrated approach was used to determine single nucleotide polymorphism pairs with epistasis effects associated with three agronomic traits: heading date, plant height, and grain yield in barley from the barley Coordinated Agricultural Project. Our results showed that four, seven, and five SNP pairs accounted for 51.06, 45.66 and 40.42% for heading date, plant height, and grain yield, respectively with epistasis being considered, while corresponding contributions to these three traits were 45.32, 31.39, 31.31%, respectively without epistasis being included. The results suggested that epistasis model was more effective than non-epistasis model in this study and can be more preferred for other applications.
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Affiliation(s)
- Yi Xu
- Department of Agronomy, Horticulture, and Plant Science, South Dakota State University, Box 2140C, Brookings, SD, 57007, USA
| | - Yajun Wu
- Department of Biology and Microbiology, South Dakota State University, Brookings, SD, 57007, USA
| | - Jixiang Wu
- Department of Agronomy, Horticulture, and Plant Science, South Dakota State University, Box 2140C, Brookings, SD, 57007, USA.
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24
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Singh A, Roy S. High altitude population of Arabidopsis thaliana is more plastic and adaptive under common garden than controlled condition. BMC Ecol 2017; 17:39. [PMID: 29237449 PMCID: PMC5729231 DOI: 10.1186/s12898-017-0149-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2017] [Accepted: 12/06/2017] [Indexed: 11/30/2022] Open
Abstract
BACKGROUND Population differentiation and their adaptation to a particular environment depend on their ability to respond to a new environment. This, in turn is governed to an extent, by the degree of phenotypic plasticity exhibited by the populations. The populations of same species inhabiting different climatic conditions may differ in their phenotypic plasticity. Himalayan populations of Arabidopsis thaliana originating from a steep altitude are exposed to different climatic conditions ranging from sub-tropical to temperate. Thus they might have experienced different selection pressures during evolution and may respond differently under common environmental condition. RESULTS Phenotypic plasticity and differentiation of natural populations of A. thaliana grown under common garden and controlled conditions were determined. A total of seventeen morphological traits, their plasticity, association between traits and environment were performed using 45 accessions from three populations. Plants from different altitudes differed in phenotypes, their selection and fitness under two conditions. Under both the conditions lower altitude population was characterized by higher leaf count and larger silique than higher and middle altitude population. Flowering time of high altitude population increased while that of low and medium altitude decreased under controlled condition compared to open field. An increase in seed weight and germination was observed for all the population under open field than controlled. Rosette area was under divergent selection in both the condition. The heritability of lower altitude population was the highest under both the conditions, where as it was the least for higher altitude population further indicating that the high altitude populations are more responsive towards phenotypic changes under new environmental conditions. Ninety-nine percent of variability in traits and their plasticity co-varied with the altitude of their origin. The population of high altitude was more plastic and differentiated as compared to the lower altitude one. CONCLUSIONS Arabidopsis thaliana population native to different altitudes of the west Himalaya responds differently when grown under common environments. The success of high altitude population is more in common garden than the controlled conditions. The significant variability in phenotype and its association with altitude of origin predicts for non-random genetic differentiation among the populations.
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Affiliation(s)
- Akanksha Singh
- Genetics and Molecular Biology Division, CSIR-National Botanical Research Institute, Lucknow, Uttar Pradesh 226001 India
- Academy of Scientific and Innovative Research (AcSIR), Anusandhan Bhawan, 2 Rafi Marg, New Delhi, 110 001 India
| | - Sribash Roy
- Genetics and Molecular Biology Division, CSIR-National Botanical Research Institute, Lucknow, Uttar Pradesh 226001 India
- Academy of Scientific and Innovative Research (AcSIR), Anusandhan Bhawan, 2 Rafi Marg, New Delhi, 110 001 India
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25
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Noble LM, Chelo I, Guzella T, Afonso B, Riccardi DD, Ammerman P, Dayarian A, Carvalho S, Crist A, Pino-Querido A, Shraiman B, Rockman MV, Teotónio H. Polygenicity and Epistasis Underlie Fitness-Proximal Traits in the Caenorhabditis elegans Multiparental Experimental Evolution (CeMEE) Panel. Genetics 2017; 207:1663-1685. [PMID: 29066469 PMCID: PMC5714472 DOI: 10.1534/genetics.117.300406] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Accepted: 10/10/2017] [Indexed: 01/27/2023] Open
Abstract
Understanding the genetic basis of complex traits remains a major challenge in biology. Polygenicity, phenotypic plasticity, and epistasis contribute to phenotypic variance in ways that are rarely clear. This uncertainty can be problematic for estimating heritability, for predicting individual phenotypes from genomic data, and for parameterizing models of phenotypic evolution. Here, we report an advanced recombinant inbred line (RIL) quantitative trait locus mapping panel for the hermaphroditic nematode Caenorhabditis elegans, the C. elegans multiparental experimental evolution (CeMEE) panel. The CeMEE panel, comprising 507 RILs at present, was created by hybridization of 16 wild isolates, experimental evolution for 140-190 generations, and inbreeding by selfing for 13-16 generations. The panel contains 22% of single-nucleotide polymorphisms known to segregate in natural populations, and complements existing C. elegans mapping resources by providing fine resolution and high nucleotide diversity across > 95% of the genome. We apply it to study the genetic basis of two fitness components, fertility and hermaphrodite body size at time of reproduction, with high broad-sense heritability in the CeMEE. While simulations show that we should detect common alleles with additive effects as small as 5%, at gene-level resolution, the genetic architectures of these traits do not feature such alleles. We instead find that a significant fraction of trait variance, approaching 40% for fertility, can be explained by sign epistasis with main effects below the detection limit. In congruence, phenotype prediction from genomic similarity, while generally poor ([Formula: see text]), requires modeling epistasis for optimal accuracy, with most variance attributed to the rapidly evolving chromosome arms.
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Affiliation(s)
- Luke M Noble
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York 10003
| | - Ivo Chelo
- Instituto Gulbenkian de Ciência, P-2781-901 Oeiras, Portugal
| | - Thiago Guzella
- Institut de Biologie, École Normale Supérieure, Centre National de la Recherche Scientifique (CNRS) UMR 8197, Institut National de la Santé et de la Recherche Médicale (INSERM) U1024, F-75005 Paris, France
| | - Bruno Afonso
- Instituto Gulbenkian de Ciência, P-2781-901 Oeiras, Portugal
- Institut de Biologie, École Normale Supérieure, Centre National de la Recherche Scientifique (CNRS) UMR 8197, Institut National de la Santé et de la Recherche Médicale (INSERM) U1024, F-75005 Paris, France
| | - David D Riccardi
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York 10003
| | - Patrick Ammerman
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York 10003
| | - Adel Dayarian
- Kavli Institute for Theoretical Physics, University of California, Santa Barbara, California 93106
| | - Sara Carvalho
- Instituto Gulbenkian de Ciência, P-2781-901 Oeiras, Portugal
| | - Anna Crist
- Institut de Biologie, École Normale Supérieure, Centre National de la Recherche Scientifique (CNRS) UMR 8197, Institut National de la Santé et de la Recherche Médicale (INSERM) U1024, F-75005 Paris, France
| | | | - Boris Shraiman
- Kavli Institute for Theoretical Physics, University of California, Santa Barbara, California 93106
- Department of Physics, University of California, Santa Barbara, California 93106
| | - Matthew V Rockman
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York 10003
| | - Henrique Teotónio
- Institut de Biologie, École Normale Supérieure, Centre National de la Recherche Scientifique (CNRS) UMR 8197, Institut National de la Santé et de la Recherche Médicale (INSERM) U1024, F-75005 Paris, France
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26
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Rahman MA, Bimpong IK, Bizimana JB, Pascual ED, Arceta M, Swamy BPM, Diaw F, Rahman MS, Singh RK. Mapping QTLs using a novel source of salinity tolerance from Hasawi and their interaction with environments in rice. RICE (NEW YORK, N.Y.) 2017; 10:47. [PMID: 29098463 PMCID: PMC5668218 DOI: 10.1186/s12284-017-0186-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2017] [Accepted: 10/23/2017] [Indexed: 05/21/2023]
Abstract
BACKGROUND Salinity is one of the most severe and widespread abiotic stresses that affect rice production. The identification of major-effect quantitative trait loci (QTLs) for traits related to salinity tolerance and understanding of QTL × environment interactions (QEIs) can help in more precise and faster development of salinity-tolerant rice varieties through marker-assisted breeding. Recombinant inbred lines (RILs) derived from IR29/Hasawi (a novel source of salinity) were screened for salinity tolerance in the IRRI phytotron in the Philippines (E1) and in two other diverse environments in Senegal (E2) and Tanzania (E3). QTLs were mapped for traits related to salinity tolerance at the seedling stage. RESULTS The RILs were genotyped using 194 polymorphic SNPs (single nucleotide polymorphisms). After removing segregation distortion markers (SDM), a total of 145 and 135 SNPs were used to construct a genetic linkage map with a length of 1655 and 1662 cM, with an average marker density of 11.4 cM in E1 and 12.3 cM in E2 and E3, respectively. A total of 34 QTLs were identified on 10 chromosomes for five traits using ICIM-ADD and segregation distortion locus (SDL) mapping (IM-ADD) under salinity stress across environments. Eight major genomic regions on chromosome 1 between 170 and 175 cM (qSES1.3, qSES1.4, qSL1.2, qSL1.3, qRL1.1, qRL1.2, qFWsht1.2, qDWsht1.2), chromosome 4 at 32 cM (qSES4.1, qFWsht4.2, qDWsht4.2), chromosome 6 at 115 cM (qFWsht6.1, qDWsht6.1), chromosome 8 at 105 cM (qFWsht8.1, qDWsht8.1), and chromosome 12 at 78 cM (qFWsht12.1, qDWsht12.1) have co-localized QTLs for the multiple traits that might be governing seedling stage salinity tolerance through multiple traits in different phenotyping environments, thus suggesting these as hot spots for tolerance of salinity. Forty-nine and 30 significant pair-wise epistatic interactions were detected between QTL-linked and QTL-unlinked regions using single-environment and multi-environment analyses. CONCLUSIONS The identification of genomic regions for salinity tolerance in the RILs showed that Hasawi possesses alleles that are novel for salinity tolerance. The common regions for the multiple QTLs across environments as co-localized regions on chromosomes 1, 4, 6, 8, and 12 could be due to linkage or pleiotropic effect, which might be helpful for multiple QTL introgression for marker-assisted breeding programs to improve the salinity tolerance of adaptive and popular but otherwise salinity-sensitive rice varieties.
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Affiliation(s)
- M Akhlasur Rahman
- International Rice Research Institute (IRRI), DAPO Box 7777, Metro Manila, Philippines
- Bangladesh Rice Research Institute, Gazipur, 1701, Bangladesh
| | | | | | - Evangeline D Pascual
- Institute of Biological Sciences, University of the Philippines at Los Baños, Laguna, Philippines
| | - Marydee Arceta
- International Rice Research Institute (IRRI), DAPO Box 7777, Metro Manila, Philippines
| | | | - Faty Diaw
- Africa Rice Center, Sahel Regional Station, BP 96, St Louis, Senegal
| | | | - R K Singh
- International Rice Research Institute (IRRI), DAPO Box 7777, Metro Manila, Philippines.
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Kerwin RE, Feusier J, Muok A, Lin C, Larson B, Copeland D, Corwin JA, Rubin MJ, Francisco M, Li B, Joseph B, Weinig C, Kliebenstein DJ. Epistasis × environment interactions among Arabidopsis thaliana glucosinolate genes impact complex traits and fitness in the field. THE NEW PHYTOLOGIST 2017; 215:1249-1263. [PMID: 28608555 DOI: 10.1111/nph.14646] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Accepted: 04/26/2017] [Indexed: 06/07/2023]
Abstract
Despite the growing number of studies showing that genotype × environment and epistatic interactions control fitness, the influences of epistasis × environment interactions on adaptive trait evolution remain largely uncharacterized. Across three field trials, we quantified aliphatic glucosinolate (GSL) defense chemistry, leaf damage, and relative fitness using mutant lines of Arabidopsis thaliana varying at pairs of causal aliphatic GSL defense genes to test the impact of epistatic and epistasis × environment interactions on adaptive trait variation. We found that aliphatic GSL accumulation was primarily influenced by additive and epistatic genetic variation, leaf damage was primarily influenced by environmental variation and relative fitness was primarily influenced by epistasis and epistasis × environment interactions. Epistasis × environment interactions accounted for up to 48% of the relative fitness variation in the field. At a single field site, the impact of epistasis on relative fitness varied significantly over 2 yr, showing that epistasis × environment interactions within a location can be temporally dynamic. These results suggest that the environmental dependency of epistasis can profoundly influence the response to selection, shaping the adaptive trajectories of natural populations in complex ways, and deserves further consideration in future evolutionary studies.
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Affiliation(s)
- Rachel E Kerwin
- Department of Plant Sciences, University of California Davis, Davis, CA, 95616, USA
- Department of Genetics, University of Georgia, Athens, GA, 30602, USA
| | - Julie Feusier
- Department of Plant Sciences, University of California Davis, Davis, CA, 95616, USA
| | - Alise Muok
- Department of Plant Sciences, University of California Davis, Davis, CA, 95616, USA
| | - Catherine Lin
- Department of Plant Sciences, University of California Davis, Davis, CA, 95616, USA
| | - Brandon Larson
- Department of Plant Sciences, University of California Davis, Davis, CA, 95616, USA
| | - Daniel Copeland
- Department of Plant Sciences, University of California Davis, Davis, CA, 95616, USA
| | - Jason A Corwin
- Department of Plant Sciences, University of California Davis, Davis, CA, 95616, USA
| | - Matthew J Rubin
- Department of Botany, University of Wyoming, Laramie, WY, 82071, USA
| | - Marta Francisco
- Misión Biológica de Galicia, Spanish Council for Scientific Research (MBG-CSIC), Pontevedra, 36143, Spain
| | - Baohua Li
- Department of Plant Sciences, University of California Davis, Davis, CA, 95616, USA
| | - Bindu Joseph
- Department of Plant Sciences, University of California Davis, Davis, CA, 95616, USA
| | - Cynthia Weinig
- Department of Botany, University of Wyoming, Laramie, WY, 82071, USA
| | - Daniel J Kliebenstein
- Department of Plant Sciences, University of California Davis, Davis, CA, 95616, USA
- DynaMo Centre of Excellence, Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Thorvaldsensvej 40, 1871, Frederiksberg C, Denmark
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28
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Moellers TC, Singh A, Zhang J, Brungardt J, Kabbage M, Mueller DS, Grau CR, Ranjan A, Smith DL, Chowda-Reddy RV, Singh AK. Main and epistatic loci studies in soybean for Sclerotinia sclerotiorum resistance reveal multiple modes of resistance in multi-environments. Sci Rep 2017; 7:3554. [PMID: 28620159 PMCID: PMC5472596 DOI: 10.1038/s41598-017-03695-9] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2017] [Accepted: 05/10/2017] [Indexed: 11/09/2022] Open
Abstract
Genome-wide association (GWAS) and epistatic (GWES) studies along with expression studies in soybean [Glycine max (L.) Merr.] were leveraged to dissect the genetics of Sclerotinia stem rot (SSR) [caused by Sclerotinia sclerotiorum (Lib.) de Bary], a significant fungal disease causing yield and quality losses. A large association panel of 466 diverse plant introduction accessions were phenotyped in multiple field and controlled environments to: (1) discover sources of resistance, (2) identify SNPs associated with resistance, and (3) determine putative candidate genes to elucidate the mode of resistance. We report 58 significant main effect loci and 24 significant epistatic interactions associated with SSR resistance, with candidate genes involved in a wide range of processes including cell wall structure, hormone signaling, and sugar allocation related to plant immunity, revealing the complex nature of SSR resistance. Putative candidate genes [for example, PHYTOALEXIN DEFFICIENT 4 (PAD4), ETHYLENE-INSENSITIVE 3-LIKE 1 (EIL3), and ETHYLENE RESPONSE FACTOR 1 (ERF1)] clustered into salicylic acid (SA), jasmonic acid (JA), and ethylene (ET) pathways suggest the involvement of a complex hormonal network typically activated by both necrotrophic (ET/JA) and biotrophic (SA) pathogens supporting that S. sclerotiorum is a hemibiotrophic plant pathogen.
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Affiliation(s)
- Tara C Moellers
- Department of Agronomy, Iowa State University, Ames, Iowa, 50011, United States of America
| | - Arti Singh
- Department of Agronomy, Iowa State University, Ames, Iowa, 50011, United States of America
| | - Jiaoping Zhang
- Department of Agronomy, Iowa State University, Ames, Iowa, 50011, United States of America
| | - Jae Brungardt
- Department of Agronomy, Iowa State University, Ames, Iowa, 50011, United States of America
| | - Mehdi Kabbage
- Department of Plant Pathology, University of Wisconsin-Madison, Madison, Wisconsin, 53706, United States of America
| | - Daren S Mueller
- Department of Plant Pathology, Iowa State University, Ames, Iowa, 50011, United States of America
| | - Craig R Grau
- Department of Plant Pathology, University of Wisconsin-Madison, Madison, Wisconsin, 53706, United States of America
| | - Ashish Ranjan
- Department of Plant Pathology, University of Wisconsin-Madison, Madison, Wisconsin, 53706, United States of America
| | - Damon L Smith
- Department of Plant Pathology, University of Wisconsin-Madison, Madison, Wisconsin, 53706, United States of America
| | - R V Chowda-Reddy
- Department of Agronomy, Iowa State University, Ames, Iowa, 50011, United States of America
| | - Asheesh K Singh
- Department of Agronomy, Iowa State University, Ames, Iowa, 50011, United States of America.
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Rutter MT, Wieckowski YM, Murren CJ, Strand AE. Fitness effects of mutation: testing genetic redundancy in Arabidopsis thaliana. J Evol Biol 2017; 30:1124-1135. [PMID: 28387971 DOI: 10.1111/jeb.13081] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2015] [Accepted: 03/09/2017] [Indexed: 01/05/2023]
Abstract
Screens of organisms with disruptive mutations in a single gene often fail to detect phenotypic consequences for the majority of mutants. One explanation for this phenomenon is that the presence of paralogous loci provides genetic redundancy. However, it is also possible that the assayed traits are affected by few loci, that effects could be subtle or that phenotypic effects are restricted to certain environments. We assayed a set of T-DNA insertion mutant lines of Arabidopsis thaliana to determine the frequency with which mutation affected fitness-related phenotypes. We found that between 8% and 42% of the assayed lines had altered fitness from the wild type. Furthermore, many of these lines exhibited fitness greater than the wild type. In a second experiment, we grew a subset of the lines in multiple environments and found whether a T-DNA insert increased or decreased fitness traits depended on the assay environment. Overall, our evidence contradicts the hypothesis that genetic redundancy is a common phenomenon in A. thaliana for fitness traits. Evidence for redundancy from prior screens of knockout mutants may often be an artefact of the design of the phenotypic assays which have focused on less complex phenotypes than fitness and have used single environments. Finally, our study adds to evidence that beneficial mutations may represent a significant component of the mutational spectrum of A. thaliana.
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Affiliation(s)
- M T Rutter
- Department of Biology, College of Charleston, Charleston, SC, USA
| | - Y M Wieckowski
- Department of Biology, College of Charleston, Charleston, SC, USA
| | - C J Murren
- Department of Biology, College of Charleston, Charleston, SC, USA
| | - A E Strand
- Department of Biology, College of Charleston, Charleston, SC, USA
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30
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The Effect of Photoperiod on Flowering Time, Plant Architecture, and Biomass in Setaria. GENETICS AND GENOMICS OF SETARIA 2017. [DOI: 10.1007/978-3-319-45105-3_12] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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Lovell JT, Shakirov EV, Schwartz S, Lowry DB, Aspinwall MJ, Taylor SH, Bonnette J, Palacio-Mejia JD, Hawkes CV, Fay PA, Juenger TE. Promises and Challenges of Eco-Physiological Genomics in the Field: Tests of Drought Responses in Switchgrass. PLANT PHYSIOLOGY 2016; 172:734-748. [PMID: 27246097 PMCID: PMC5047078 DOI: 10.1104/pp.16.00545] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2016] [Accepted: 05/26/2016] [Indexed: 05/21/2023]
Abstract
Identifying the physiological and genetic basis of stress tolerance in plants has proven to be critical to understanding adaptation in both agricultural and natural systems. However, many discoveries were initially made in the controlled conditions of greenhouses or laboratories, not in the field. To test the comparability of drought responses across field and greenhouse environments, we undertook three independent experiments using the switchgrass reference genotype Alamo AP13. We analyzed physiological and gene expression variation across four locations, two sampling times, and three years. Relatively similar physiological responses and expression coefficients of variation across experiments masked highly dissimilar gene expression responses to drought. Critically, a drought experiment utilizing small pots in the greenhouse elicited nearly identical physiological changes as an experiment conducted in the field, but an order of magnitude more differentially expressed genes. However, we were able to define a suite of several hundred genes that were differentially expressed across all experiments. This list was strongly enriched in photosynthesis, water status, and reactive oxygen species responsive genes. The strong across-experiment correlations between physiological plasticity-but not differential gene expression-highlight the complex and diverse genetic mechanisms that can produce phenotypically similar responses to various soil water deficits.
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Affiliation(s)
- John T Lovell
- Department of Integrative Biology, University of Texas at Austin, Austin, Texas (J.T.L., E.V.S., S.S., J.B., J.D.P.-M., C.V.H., T.E.J.); Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan, Republic of Tatarstan, Russia (E.V.S.); Department of Plant Biology, Michigan State University, East Lansing, Michigan (D.B.L.);Hawkesbury Institute for the Environment, Western Sydney University, Richmond, Australia (M.J.A.); Departments of Environmental Studies and Biology, Keene State College, Keene, New Hampshire USA (S.H.T.); andUSDA-ARS Grassland Soil and Water Research Laboratory, Temple, Texas 76502 (P.A.F.)
| | - Eugene V Shakirov
- Department of Integrative Biology, University of Texas at Austin, Austin, Texas (J.T.L., E.V.S., S.S., J.B., J.D.P.-M., C.V.H., T.E.J.); Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan, Republic of Tatarstan, Russia (E.V.S.); Department of Plant Biology, Michigan State University, East Lansing, Michigan (D.B.L.);Hawkesbury Institute for the Environment, Western Sydney University, Richmond, Australia (M.J.A.); Departments of Environmental Studies and Biology, Keene State College, Keene, New Hampshire USA (S.H.T.); andUSDA-ARS Grassland Soil and Water Research Laboratory, Temple, Texas 76502 (P.A.F.)
| | - Scott Schwartz
- Department of Integrative Biology, University of Texas at Austin, Austin, Texas (J.T.L., E.V.S., S.S., J.B., J.D.P.-M., C.V.H., T.E.J.); Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan, Republic of Tatarstan, Russia (E.V.S.); Department of Plant Biology, Michigan State University, East Lansing, Michigan (D.B.L.);Hawkesbury Institute for the Environment, Western Sydney University, Richmond, Australia (M.J.A.); Departments of Environmental Studies and Biology, Keene State College, Keene, New Hampshire USA (S.H.T.); andUSDA-ARS Grassland Soil and Water Research Laboratory, Temple, Texas 76502 (P.A.F.)
| | - David B Lowry
- Department of Integrative Biology, University of Texas at Austin, Austin, Texas (J.T.L., E.V.S., S.S., J.B., J.D.P.-M., C.V.H., T.E.J.); Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan, Republic of Tatarstan, Russia (E.V.S.); Department of Plant Biology, Michigan State University, East Lansing, Michigan (D.B.L.);Hawkesbury Institute for the Environment, Western Sydney University, Richmond, Australia (M.J.A.); Departments of Environmental Studies and Biology, Keene State College, Keene, New Hampshire USA (S.H.T.); andUSDA-ARS Grassland Soil and Water Research Laboratory, Temple, Texas 76502 (P.A.F.)
| | - Michael J Aspinwall
- Department of Integrative Biology, University of Texas at Austin, Austin, Texas (J.T.L., E.V.S., S.S., J.B., J.D.P.-M., C.V.H., T.E.J.); Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan, Republic of Tatarstan, Russia (E.V.S.); Department of Plant Biology, Michigan State University, East Lansing, Michigan (D.B.L.);Hawkesbury Institute for the Environment, Western Sydney University, Richmond, Australia (M.J.A.); Departments of Environmental Studies and Biology, Keene State College, Keene, New Hampshire USA (S.H.T.); andUSDA-ARS Grassland Soil and Water Research Laboratory, Temple, Texas 76502 (P.A.F.)
| | - Samuel H Taylor
- Department of Integrative Biology, University of Texas at Austin, Austin, Texas (J.T.L., E.V.S., S.S., J.B., J.D.P.-M., C.V.H., T.E.J.); Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan, Republic of Tatarstan, Russia (E.V.S.); Department of Plant Biology, Michigan State University, East Lansing, Michigan (D.B.L.);Hawkesbury Institute for the Environment, Western Sydney University, Richmond, Australia (M.J.A.); Departments of Environmental Studies and Biology, Keene State College, Keene, New Hampshire USA (S.H.T.); andUSDA-ARS Grassland Soil and Water Research Laboratory, Temple, Texas 76502 (P.A.F.)
| | - Jason Bonnette
- Department of Integrative Biology, University of Texas at Austin, Austin, Texas (J.T.L., E.V.S., S.S., J.B., J.D.P.-M., C.V.H., T.E.J.); Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan, Republic of Tatarstan, Russia (E.V.S.); Department of Plant Biology, Michigan State University, East Lansing, Michigan (D.B.L.);Hawkesbury Institute for the Environment, Western Sydney University, Richmond, Australia (M.J.A.); Departments of Environmental Studies and Biology, Keene State College, Keene, New Hampshire USA (S.H.T.); andUSDA-ARS Grassland Soil and Water Research Laboratory, Temple, Texas 76502 (P.A.F.)
| | - Juan Diego Palacio-Mejia
- Department of Integrative Biology, University of Texas at Austin, Austin, Texas (J.T.L., E.V.S., S.S., J.B., J.D.P.-M., C.V.H., T.E.J.); Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan, Republic of Tatarstan, Russia (E.V.S.); Department of Plant Biology, Michigan State University, East Lansing, Michigan (D.B.L.);Hawkesbury Institute for the Environment, Western Sydney University, Richmond, Australia (M.J.A.); Departments of Environmental Studies and Biology, Keene State College, Keene, New Hampshire USA (S.H.T.); andUSDA-ARS Grassland Soil and Water Research Laboratory, Temple, Texas 76502 (P.A.F.)
| | - Christine V Hawkes
- Department of Integrative Biology, University of Texas at Austin, Austin, Texas (J.T.L., E.V.S., S.S., J.B., J.D.P.-M., C.V.H., T.E.J.); Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan, Republic of Tatarstan, Russia (E.V.S.); Department of Plant Biology, Michigan State University, East Lansing, Michigan (D.B.L.);Hawkesbury Institute for the Environment, Western Sydney University, Richmond, Australia (M.J.A.); Departments of Environmental Studies and Biology, Keene State College, Keene, New Hampshire USA (S.H.T.); andUSDA-ARS Grassland Soil and Water Research Laboratory, Temple, Texas 76502 (P.A.F.)
| | - Philip A Fay
- Department of Integrative Biology, University of Texas at Austin, Austin, Texas (J.T.L., E.V.S., S.S., J.B., J.D.P.-M., C.V.H., T.E.J.); Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan, Republic of Tatarstan, Russia (E.V.S.); Department of Plant Biology, Michigan State University, East Lansing, Michigan (D.B.L.);Hawkesbury Institute for the Environment, Western Sydney University, Richmond, Australia (M.J.A.); Departments of Environmental Studies and Biology, Keene State College, Keene, New Hampshire USA (S.H.T.); andUSDA-ARS Grassland Soil and Water Research Laboratory, Temple, Texas 76502 (P.A.F.)
| | - Thomas E Juenger
- Department of Integrative Biology, University of Texas at Austin, Austin, Texas (J.T.L., E.V.S., S.S., J.B., J.D.P.-M., C.V.H., T.E.J.); Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan, Republic of Tatarstan, Russia (E.V.S.); Department of Plant Biology, Michigan State University, East Lansing, Michigan (D.B.L.);Hawkesbury Institute for the Environment, Western Sydney University, Richmond, Australia (M.J.A.); Departments of Environmental Studies and Biology, Keene State College, Keene, New Hampshire USA (S.H.T.); andUSDA-ARS Grassland Soil and Water Research Laboratory, Temple, Texas 76502 (P.A.F.)
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Li C, Li Y, Shi Y, Song Y, Zhang D, Buckler ES, Zhang Z, Li Y, Wang T. Analysis of recombination QTLs, segregation distortion, and epistasis for fitness in maize multiple populations using ultra-high-density markers. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2016; 129:1775-1784. [PMID: 27379519 DOI: 10.1007/s00122-016-2739-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2016] [Accepted: 06/04/2016] [Indexed: 06/06/2023]
Abstract
Using two nested association mapping populations and high-density markers, some important genomic regions controlling recombination frequency and segregation distortion were detected. Understanding the maize genomic features would be useful for the study of genetic diversity and evolution and for maize breeding. Here, we used two maize nested association mapping (NAM) populations separately derived in China (CN-NAM) and the US (US-NAM) to explore the maize genomic features. The two populations containing 36 families and about 7000 recombinant inbred lines were evaluated with genotyping-by-sequencing. Through the comparison between the two NAMs, we revealed that segregation distortion is little, whereas epistasis for fitness is present in the two maize NAM populations. When conducting quantitative trait loci (QTL) mapping for the total number of recombination events, we detected 14 QTLs controlling recombination. Using high-density markers to identify segregation distortion regions (SDRs), a total of 445 SDRs were detected within the 36 families, among which 15 common SDRs were found in at least ten families. About 80 % of the known maize gametophytic factors (ga) genes controlling segregation distortion were overlapped with highly significant SDRs. In addition, we also found that the regions with high recombination rate and high gene density usually tended to have little segregation distortion. This study will facilitate population genetic studies and gene cloning affecting recombination variation and segregation distortion in maize, which can improve plant breeding progress.
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Affiliation(s)
- Chunhui Li
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Yongxiang Li
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Yunsu Shi
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Yanchun Song
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Dengfeng Zhang
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Edward S Buckler
- Institute for Genomic Diversity, Cornell University, Ithaca, NY, USA
| | - Zhiwu Zhang
- Institute for Genomic Diversity, Cornell University, Ithaca, NY, USA
| | - Yu Li
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
| | - Tianyu Wang
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
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Edwards CE, Ewers BE, Weinig C. Genotypic variation in biomass allocation in response to field drought has a greater affect on yield than gas exchange or phenology. BMC PLANT BIOLOGY 2016; 16:185. [PMID: 27558796 PMCID: PMC4997677 DOI: 10.1186/s12870-016-0876-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2016] [Accepted: 08/16/2016] [Indexed: 05/05/2023]
Abstract
BACKGROUND Plant performance in agricultural and natural settings varies with moisture availability, and understanding the range of potential drought responses and the underlying genetic architecture is important for understanding how plants will respond to both natural and artificial selection in various water regimes. Here, we raised genotypes of Brassica rapa under well-watered and drought treatments in the field. Our primary goal was to understand the genetic architecture and yield effects of different drought-escape and dehydration-avoidance strategies. RESULTS Drought treatments reduced soil moisture by 62 % of field capacity. Drought decreased biomass accumulation and fruit production by as much as 48 %, whereas instantaneous water-use efficiency and root:shoot ratio increased. Genotypes differed in the mean value of all traits and in the sensitivity of biomass accumulation, root:shoot ratio, and fruit production to drought. Bivariate correlations involving gas-exchange and phenology were largely constant across environments, whereas those involving root:shoot varied across treatments. Although root:shoot was typically unrelated to gas-exchange or yield under well-watered conditions, genotypes with low to moderate increases in root:shoot allocation in response to drought survived the growing season, maintained maximum photosynthesis levels, and produced more fruit than genotypes with the greatest root allocation under drought. QTL for gas-exchange and yield components (total biomass or fruit production) had common effects across environments while those for root:shoot were often environment-specific. CONCLUSIONS Increases in root allocation beyond those needed to survive and maintain favorable water relations came at the cost of fruit production. The environment-specific effects of root:shoot ratio on yield and the differential expression of QTL for this trait across water regimes have important implications for efforts to improve crops for drought resistance.
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Affiliation(s)
- Christine E Edwards
- Department of Botany, University of Wyoming, Laramie, WY, 82071, USA.
- Current Address: Center for Conservation and Sustainable Development, Missouri Botanical Garden, PO Box 299, St. Louis, MO, 63166, USA.
| | - Brent E Ewers
- Department of Botany, University of Wyoming, Laramie, WY, 82071, USA
- Program in Ecology, University of Wyoming, Laramie, WY, 82071, USA
| | - Cynthia Weinig
- Department of Botany, University of Wyoming, Laramie, WY, 82071, USA
- Program in Ecology, University of Wyoming, Laramie, WY, 82071, USA
- Department of Molecular Biology, University of Wyoming, Laramie, WY, 82071, USA
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Abstract
The extent to which gene interaction or epistasis contributes to fitness variation within populations remains poorly understood, despite its importance to a myriad of evolutionary questions. Here, we report a multi-year field study estimating fitness of Mimulus guttatus genetic lines in which pairs of naturally segregating loci exist in an otherwise uniform background. An allele at QTL x5b-a locus originally mapped for its effect on flower size-positively affects survival if combined with one genotype at quantitative trait locus x10a (aa) but has negative effects when combined with the other genotypes (Aa and AA). The viability differences between genotypes parallel phenotypic differences for the time and node at which a plant flowers. Viability is negatively correlated with fecundity across genotypes, indicating antagonistic pleiotropy for fitness components. This trade-off reduces the genetic variance for total fitness relative to the individual fitness components and thus may serve to maintain variation. Additionally, we find that the effects of each locus and their interaction often vary with the environment.
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Affiliation(s)
- Patrick J Monnahan
- Department of Ecology and Evolutionary Biology, University of Kansas, 1200 Sunnyside Avenue, Lawrence, KS 66045, USA
| | - John K Kelly
- Department of Ecology and Evolutionary Biology, University of Kansas, 1200 Sunnyside Avenue, Lawrence, KS 66045, USA
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35
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Yang D, Li M, Liu Y, Chang L, Cheng H, Chen J, Chai S. Identification of Quantitative Trait Loci and Water Environmental Interactions for Developmental Behaviors of Leaf Greenness in Wheat. FRONTIERS IN PLANT SCIENCE 2016; 7:273. [PMID: 27014298 PMCID: PMC4782216 DOI: 10.3389/fpls.2016.00273] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2015] [Accepted: 02/21/2016] [Indexed: 05/30/2023]
Abstract
The maintenance of leaf greenness in wheat, highly responsible for yield potential and resistance to drought stress, has been proved to be quantitatively inherited and susceptible to interact with environments by traditional genetic analysis. In order to further dissect the developmental genetic behaviors of flag leaf greenness under terminal drought, unconditional and conditional QTL mapping strategies were performed with a mixed linear model in 120 F8-derived recombinant inbred lines (RILs) from two Chinese common wheat cultivars (Longjian 19 × Q9086) in different water environments. A total of 65 additive QTLs (A-QTLs) and 42 pairs of epistatic QTLs (AA-QTLs) were identified as distribution on almost all 21 chromosomes except 5A, explaining from 0.24 to 3.29 % of the phenotypic variation. Of these, 22 A-QTLs and 25 pairs of AA-QTLs were common in two sets of mapping methods but the others differed. These putative QTLs were essentially characteristic of time- and environmentally-dependent expression patterns. Indeed some loci were expressed at two or more stages, while no single QTL was continually active through whole measuring duration. More loci were detected in early growth periods but most of QTL × water environment interactions (QEIs) happened in mid-anaphase, where drought stress was more conducted with negative regulation on QTL expressions. Compared to other genetic components, epistatic effects and additive QEIs effects could be predominant in regulating phenotypic variations during the ontogeny of leaf greenness. Several QTL cluster regions were suggestive of tight linkage or expression pleiotropy in the inheritance of these traits. Some reproducibly-expressed QTLs or common loci consistent with previously detected would be useful to the genetic improvement of staygreen types in wheat through MAS, especially in water-deficit environments.
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Affiliation(s)
- Delong Yang
- Gansu Provincial Key Lab of Aridland Crop Science/School of Life Science and Technology, Gansu Agricultural UniversityLanzhou, China
| | - Mengfei Li
- Gansu Provincial Key Lab of Aridland Crop Science/School of Life Science and Technology, Gansu Agricultural UniversityLanzhou, China
| | - Yuan Liu
- Gansu Provincial Key Lab of Aridland Crop Science/School of Life Science and Technology, Gansu Agricultural UniversityLanzhou, China
| | - Lei Chang
- School of Agronomy, Gansu Agricultural UniversityLanzhou, China
| | - Hongbo Cheng
- Gansu Provincial Key Lab of Aridland Crop Science/School of Life Science and Technology, Gansu Agricultural UniversityLanzhou, China
| | - Jingjing Chen
- Gansu Provincial Key Lab of Aridland Crop Science/School of Life Science and Technology, Gansu Agricultural UniversityLanzhou, China
| | - Shouxi Chai
- School of Agronomy, Gansu Agricultural UniversityLanzhou, China
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36
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Voorend W, Nelissen H, Vanholme R, De Vliegher A, Van Breusegem F, Boerjan W, Roldán-Ruiz I, Muylle H, Inzé D. Overexpression of GA20-OXIDASE1 impacts plant height, biomass allocation and saccharification efficiency in maize. PLANT BIOTECHNOLOGY JOURNAL 2016; 14:997-1007. [PMID: 26903034 PMCID: PMC5019232 DOI: 10.1111/pbi.12458] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2015] [Revised: 07/17/2015] [Accepted: 07/28/2015] [Indexed: 05/07/2023]
Abstract
Increased biomass yield and quality are of great importance for the improvement of feedstock for the biorefinery. For the production of bioethanol, both stem biomass yield and the conversion efficiency of the polysaccharides in the cell wall to fermentable sugars are of relevance. Increasing the endogenous levels of gibberellic acid (GA) by ectopic expression of GA20-OXIDASE1 (GA20-OX1), the rate-limiting step in GA biosynthesis, is known to affect cell division and cell expansion, resulting in larger plants and organs in several plant species. In this study, we examined biomass yield and quality traits of maize plants overexpressing GA20-OX1 (GA20-OX1). GA20-OX1 plants accumulated more vegetative biomass than control plants in greenhouse experiments, but not consistently over two years of field trials. The stems of these plants were longer but also more slender. Investigation of GA20-OX1 biomass quality using biochemical analyses showed the presence of more cellulose, lignin and cell wall residue. Cell wall analysis as well as expression analysis of lignin biosynthetic genes in developing stems revealed that cellulose and lignin were deposited earlier in development. Pretreatment of GA20-OX1 biomass with NaOH resulted in a higher saccharification efficiency per unit of dry weight, in agreement with the higher cellulose content. On the other hand, the cellulose-to-glucose conversion was slower upon HCl or hot-water pretreatment, presumably due to the higher lignin content. This study showed that biomass yield and quality traits can be interconnected, which is important for the development of future breeding strategies to improve lignocellulosic feedstock for bioethanol production.
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Affiliation(s)
- Wannes Voorend
- Department of Plant Systems Biology, VIB, Gent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Gent, Belgium
- Plant Sciences Unit - Growth and Development, Institute for Agricultural and Fisheries Research (ILVO), Melle, Belgium
| | - Hilde Nelissen
- Department of Plant Systems Biology, VIB, Gent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Gent, Belgium
| | - Ruben Vanholme
- Department of Plant Systems Biology, VIB, Gent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Gent, Belgium
| | - Alex De Vliegher
- Plant Sciences Unit - Crop Husbandry and Environment, Institute for Agricultural and Fisheries Research (ILVO), Merelbeke, Belgium
| | - Frank Van Breusegem
- Department of Plant Systems Biology, VIB, Gent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Gent, Belgium
| | - Wout Boerjan
- Department of Plant Systems Biology, VIB, Gent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Gent, Belgium
| | - Isabel Roldán-Ruiz
- Plant Sciences Unit - Growth and Development, Institute for Agricultural and Fisheries Research (ILVO), Melle, Belgium
| | - Hilde Muylle
- Plant Sciences Unit - Growth and Development, Institute for Agricultural and Fisheries Research (ILVO), Melle, Belgium
| | - Dirk Inzé
- Department of Plant Systems Biology, VIB, Gent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Gent, Belgium
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Plessis A, Hafemeister C, Wilkins O, Gonzaga ZJ, Meyer RS, Pires I, Müller C, Septiningsih EM, Bonneau R, Purugganan M. Multiple abiotic stimuli are integrated in the regulation of rice gene expression under field conditions. eLife 2015; 4. [PMID: 26609814 PMCID: PMC4718725 DOI: 10.7554/elife.08411] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2015] [Accepted: 11/25/2015] [Indexed: 02/06/2023] Open
Abstract
Plants rely on transcriptional dynamics to respond to multiple climatic fluctuations and contexts in nature. We analyzed the genome-wide gene expression patterns of rice (Oryza sativa) growing in rainfed and irrigated fields during two distinct tropical seasons and determined simple linear models that relate transcriptomic variation to climatic fluctuations. These models combine multiple environmental parameters to account for patterns of expression in the field of co-expressed gene clusters. We examined the similarities of our environmental models between tropical and temperate field conditions, using previously published data. We found that field type and macroclimate had broad impacts on transcriptional responses to environmental fluctuations, especially for genes involved in photosynthesis and development. Nevertheless, variation in solar radiation and temperature at the timescale of hours had reproducible effects across environmental contexts. These results provide a basis for broad-based predictive modeling of plant gene expression in the field. DOI:http://dx.doi.org/10.7554/eLife.08411.001 Plants need to be able to sense and respond to changes in temperature, light levels and other aspects of their environment. One way in which plants can rapidly respond to these changes is to modify how genes involved in growth and other processes are expressed. Therefore, understanding how this happens may help us to improve the ability of crops to grow when exposed to drought or other extreme environmental conditions. Most previous studies into the effect of the environment on plant gene expression have been carried out under controlled conditions in a laboratory. These findings cannot reflect the full range of gene expression patterns that occur in the natural environment, where multiple factors (e.g. sunlight, water, nutrients) may vary at the same time. Therefore, it is important to also analyze the effect of fluctuations in multiple environmental factors in more complex field experiments. Plessis et al. developed mathematical models to analyze the gene expression patterns of rice plants grown in the tropical environment of the Philippines using two different farming practices. One field of rice was flooded and constantly supplied with fresh water (referred to as the irrigated field), while the other field was dry and only received water from rainfall (the rainfed field). The experiments show that temperature and levels of sunlight (including UV radiation) have a strong impact on gene expression in the rice plants. Short-term variations in temperature and sunlight levels also have the most consistent effect across the different fields and seasons tested. However, for many genes, the plants grown in the irrigated field responded to the changes in environmental conditions in a different way to the plants grown in the rainfed field. Further analysis identified groups of genes whose expression combined responses to several environmental factors at the same time. For example, certain genes that responded to increases in sunlight in the absence of drought responded to both sunlight levels and the shortage of water when a drought occurred. The next step is to test more types of environments and climates to be able to predict gene expression responses under future climatic conditions. DOI:http://dx.doi.org/10.7554/eLife.08411.002
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Affiliation(s)
- Anne Plessis
- Department of Biology, New York University, New York, United States.,Center for Genomics and Systems Biology, New York University, New York, United States
| | - Christoph Hafemeister
- Department of Biology, New York University, New York, United States.,Center for Genomics and Systems Biology, New York University, New York, United States
| | - Olivia Wilkins
- Department of Biology, New York University, New York, United States.,Center for Genomics and Systems Biology, New York University, New York, United States
| | | | - Rachel Sarah Meyer
- Department of Biology, New York University, New York, United States.,Center for Genomics and Systems Biology, New York University, New York, United States
| | - Inês Pires
- Department of Biology, New York University, New York, United States.,Center for Genomics and Systems Biology, New York University, New York, United States
| | - Christian Müller
- Simons Center for Data Analysis, Simons Foundation, New York, United States
| | | | - Richard Bonneau
- Department of Biology, New York University, New York, United States.,Center for Genomics and Systems Biology, New York University, New York, United States.,Simons Center for Data Analysis, Simons Foundation, New York, United States
| | - Michael Purugganan
- Department of Biology, New York University, New York, United States.,Center for Genomics and Systems Biology, New York University, New York, United States
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Kerwin R, Feusier J, Corwin J, Rubin M, Lin C, Muok A, Larson B, Li B, Joseph B, Francisco M, Copeland D, Weinig C, Kliebenstein DJ. Natural genetic variation in Arabidopsis thaliana defense metabolism genes modulates field fitness. eLife 2015; 4. [PMID: 25867014 PMCID: PMC4396512 DOI: 10.7554/elife.05604] [Citation(s) in RCA: 76] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2014] [Accepted: 03/18/2015] [Indexed: 01/06/2023] Open
Abstract
Natural populations persist in complex environments, where biotic stressors, such as pathogen and insect communities, fluctuate temporally and spatially. These shifting biotic pressures generate heterogeneous selective forces that can maintain standing natural variation within a species. To directly test if genes containing causal variation for the Arabidopsis thaliana defensive compounds, glucosinolates (GSL) control field fitness and are therefore subject to natural selection, we conducted a multi-year field trial using lines that vary in only specific causal genes. Interestingly, we found that variation in these naturally polymorphic GSL genes affected fitness in each of our environments but the pattern fluctuated such that highly fit genotypes in one trial displayed lower fitness in another and that no GSL genotype or genotypes consistently out-performed the others. This was true both across locations and within the same location across years. These results indicate that environmental heterogeneity may contribute to the maintenance of GSL variation observed within Arabidopsis thaliana. DOI:http://dx.doi.org/10.7554/eLife.05604.001 ‘Genetic variation’ describes the naturally occurring differences in DNA sequences that are found among individuals of the same species. These genetic differences arise from random mutations and may be passed on to their offspring. Some of these mutations may improve the ability of an individual to survive and reproduce—known as fitness—and are likely to become more common in the population. Other mutations may reduce an individual's fitness and are likely to be lost. However, it is believed that most of the mutations will have no effect on the fitness of individuals. It is not known why many of these ‘neutral’ genetic differences are maintained in populations. Some researchers have proposed that they are kept by chance and that there is no direct advantage to the population of keeping them unless these neutral mutations later become beneficial. However, other researchers think that the genetic variation itself may improve the fitness of the population by allowing it to quickly adapt to changes in the environment. Arabidopsis thaliana is a small plant that lives in many different environments and has high levels of genetic variation in many of its physical traits. One of these traits is the production of molecules called glucosinolates, which help the plants to defend against herbivores and infection by microbes. Previous studies have suggested that variation in the genes that make glucosinolates may improve the fitness of A. thaliana populations. To test this idea, Kerwin et al. carried out a field trial using A. thaliana plants that were genetically identical except for some of the genes involved in the production of glucosinolates. Kerwin et al. grew the plants in several different environments over several years. The field trial shows that variation in these genes affected the fitness of the plants in each of the different environments. However, the fitness benefit depended on the environment, and no single gene variant provided the best fitness across all environments, or over all the years of the trial. Kerwin et al.'s findings suggest that changes in the environment may contribute to the maintenance of genetic variation in the genes that make glucosinolates. This raises the questions of how many other genes in plants (or other species such as humans) have genetic variation that contributes to fitness across varied environments; and how can this link be tested in natural settings. DOI:http://dx.doi.org/10.7554/eLife.05604.002
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Affiliation(s)
- Rachel Kerwin
- Department of Plant Sciences, University of California, Davis, Davis, United States
| | - Julie Feusier
- Department of Plant Sciences, University of California, Davis, Davis, United States
| | - Jason Corwin
- Department of Plant Sciences, University of California, Davis, Davis, United States
| | - Matthew Rubin
- Department of Botany, University of Wyoming, Laramie, United States
| | - Catherine Lin
- Department of Plant Sciences, University of California, Davis, Davis, United States
| | - Alise Muok
- Department of Plant Sciences, University of California, Davis, Davis, United States
| | - Brandon Larson
- Department of Plant Sciences, University of California, Davis, Davis, United States
| | - Baohua Li
- Department of Plant Sciences, University of California, Davis, Davis, United States
| | - Bindu Joseph
- Department of Plant Sciences, University of California, Davis, Davis, United States
| | - Marta Francisco
- Department of Plant Sciences, University of California, Davis, Davis, United States
| | - Daniel Copeland
- Department of Plant Sciences, University of California, Davis, Davis, United States
| | - Cynthia Weinig
- Department of Genetics, University of Utah, Salt Lake City, United States
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Postma FM, Ågren J. Maternal environment affects the genetic basis of seed dormancy inArabidopsis thaliana. Mol Ecol 2015; 24:785-97. [DOI: 10.1111/mec.13061] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2014] [Revised: 12/16/2014] [Accepted: 12/30/2014] [Indexed: 02/01/2023]
Affiliation(s)
- Froukje M. Postma
- Department of Plant Ecology and Evolution; Evolutionary Biology Centre; Uppsala University; Norbyvägen 18 D SE-752 36 Uppsala Sweden
| | - Jon Ågren
- Department of Plant Ecology and Evolution; Evolutionary Biology Centre; Uppsala University; Norbyvägen 18 D SE-752 36 Uppsala Sweden
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40
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Association between nucleotide oligomerisation domain two (Nod2) gene polymorphisms and canine inflammatory bowel disease. Vet Immunol Immunopathol 2014; 161:32-41. [DOI: 10.1016/j.vetimm.2014.06.003] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2014] [Revised: 06/06/2014] [Accepted: 06/19/2014] [Indexed: 02/07/2023]
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41
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Fu D, Xiao M, Hayward A, Jiang G, Zhu L, Zhou Q, Li J, Zhang M. What is crop heterosis: new insights into an old topic. J Appl Genet 2014; 56:1-13. [PMID: 25027629 DOI: 10.1007/s13353-014-0231-z] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2014] [Revised: 06/28/2014] [Accepted: 07/01/2014] [Indexed: 01/09/2023]
Abstract
Heterosis (or hybrid vigor) refers to a natural phenomenon whereby hybrid offspring of genetically diverse individuals out-perform their parents in multiple traits including yield, adaptability and resistances to biotic and abiotic stressors. Innovations in technology and research continue to clarify the mechanisms underlying crop heterosis, however the intrinsic relationship between the biological basis of heterosis remain unclear. In this review, we aim to provide insight into the molecular genetic basis of heterosis by presenting recent advances in the 'omics' of heterosis and the role of non-coding regions, particularly in relation to energy-use efficiency. We propose that future research should focus on integrating the expanding datasets from different species and hybrid combinations, to mine key heterotic genes and unravel interactive 'omics' networks associated with heterosis. Improved understanding of heterosis and the biological basis for its manipulation in agriculture should help to streamline its use in enhancing crop productivity.
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Affiliation(s)
- Donghui Fu
- The Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Agronomy College, Jiangxi Agricultural University, Nanchang, 330045, China,
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42
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Gegas VC, Wargent JJ, Pesquet E, Granqvist E, Paul ND, Doonan JH. Endopolyploidy as a potential alternative adaptive strategy for Arabidopsis leaf size variation in response to UV-B. JOURNAL OF EXPERIMENTAL BOTANY 2014; 65:2757-66. [PMID: 24470468 PMCID: PMC4047990 DOI: 10.1093/jxb/ert473] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
The extent of endoreduplication in leaf growth is group- or even species-specific, and its adaptive role is still unclear. A survey of Arabidopsis accessions for variation at the level of endopolyploidy, cell number, and cell size in leaves revealed extensive genetic variation in endopolyploidy level. High endopolyploidy is associated with increased leaf size, both in natural and in genetically unstructured (mapping) populations. The underlying genes were identified as quantitative trait loci that control endopolyploidy in nature by modulating the progression of successive endocycles during organ development. This complex genetic architecture indicates an adaptive mechanism that allows differential organ growth over a broad geographic range and under stressful environmental conditions. UV-B radiation was identified as a significant positive climatic predictor for high endopolyploidy. Arabidopsis accessions carrying the increasing alleles for endopolyploidy also have enhanced tolerance to UV-B radiation. UV-absorbing secondary metabolites provide an additional protective strategy in accessions that display low endopolyploidy. Taken together, these results demonstrate that high constitutive endopolyploidy is a significant predictor for organ size in natural populations and is likely to contribute to sustaining plant growth under high incident UV radiation. Endopolyploidy may therefore form part of the range of UV-B tolerance mechanisms that exist in natural populations.
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Affiliation(s)
- Vasilis C Gegas
- John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Jason J Wargent
- Lancaster Environment Centre, Lancaster University, Lancaster LA1 4YQ, UK
| | - Edouard Pesquet
- John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Emma Granqvist
- John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Nigel D Paul
- Lancaster Environment Centre, Lancaster University, Lancaster LA1 4YQ, UK
| | - John H Doonan
- IBERS, Aberystwyth University, Aberystwyth SY23 2AX, UK
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Bloomer RH, Lloyd AM, Symonds VV. The genetic architecture of constitutive and induced trichome density in two new recombinant inbred line populations of Arabidopsis thaliana: phenotypic plasticity, epistasis, and bidirectional leaf damage response. BMC PLANT BIOLOGY 2014; 14:119. [PMID: 24885520 PMCID: PMC4108038 DOI: 10.1186/1471-2229-14-119] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2013] [Accepted: 04/25/2014] [Indexed: 05/23/2023]
Abstract
BACKGROUND Herbivory imposes an important selective pressure on plants. In Arabidopsis thaliana leaf trichomes provide a key defense against insect herbivory; however, trichome production incurs a fitness cost in the absence of herbivory. Previous work on A. thaliana has shown an increase in trichome density in response to leaf damage, suggesting a mechanism by which the cost associated with constitutively high trichome density might be mitigated; however, the genetic basis of trichome density induction has not been studied. RESULTS Here, we describe the mapping of quantitative trait loci (QTL) for constitutive and damage induced trichome density in two new recombinant inbred line populations of A. thaliana; mapping for constitutive and induced trichome density also allowed for the investigation of damage response (plasticity) QTL. Both novel and previously identified QTL for constitutive trichome density and the first QTL for induced trichome density and response are identified. Interestingly, two of the four parental accessions and multiple RILs in each population exhibited lower trichome density following leaf damage, a response not previously described in A. thaliana. Importantly, a single QTL was mapped for the response phenotype and allelic variation at this locus appears to determine response trajectory in RILs. The data also show that epistatic interactions are a significant component of the genetic architecture of trichome density. CONCLUSIONS Together, our results provide further insights into the genetic architecture of constitutive trichome density and new insights into induced trichome density in A. thaliana specifically and to our understanding of the genetic underpinnings of natural variation generally.
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Affiliation(s)
- Rebecca H Bloomer
- Institute of Fundamental Sciences, Massey University, Private Bag 11222, Palmerston North 4442, New Zealand
| | - Alan M Lloyd
- Institute for Cellular and Molecular Biology, University of Texas, Austin, TX, USA
| | - V Vaughan Symonds
- Institute of Fundamental Sciences, Massey University, Private Bag 11222, Palmerston North 4442, New Zealand
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Vanhaeren H, Gonzalez N, Coppens F, De Milde L, Van Daele T, Vermeersch M, Eloy NB, Storme V, Inzé D. Combining growth-promoting genes leads to positive epistasis in Arabidopsis thaliana. eLife 2014; 3:e02252. [PMID: 24843021 PMCID: PMC4014012 DOI: 10.7554/elife.02252] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Several genes positively influence final leaf size in Arabidopsis when mutated or overexpressed. The connections between these growth regulators are still poorly understood although such knowledge would further contribute to understand the processes driving leaf growth. In this study, we performed a combinatorial screen with 13 transgenic Arabidopsis lines with an increased leaf size. We found that from 61 analyzed combinations, 39% showed an additional increase in leaf size and most resulted from a positive epistasis on growth. Similar to what is found in other organisms in which such an epistasis assay was performed, only few genes were highly connected in synergistic combinations as we observed a positive epistasis in the majority of the combinations with samba, BRI1(OE) or SAUR19(OE). Furthermore, positive epistasis was found with combinations of genes with a similar mode of action, but also with genes which affect distinct processes, such as cell proliferation and cell expansion.DOI: http://dx.doi.org/10.7554/eLife.02252.001.
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Affiliation(s)
- Hannes Vanhaeren
- Department of Plant Systems Biology, Vlaams Instituut voor Biotechnologie, Ghent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
| | - Nathalie Gonzalez
- Department of Plant Systems Biology, Vlaams Instituut voor Biotechnologie, Ghent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
| | - Frederik Coppens
- Department of Plant Systems Biology, Vlaams Instituut voor Biotechnologie, Ghent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
| | - Liesbeth De Milde
- Department of Plant Systems Biology, Vlaams Instituut voor Biotechnologie, Ghent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
| | - Twiggy Van Daele
- Department of Plant Systems Biology, Vlaams Instituut voor Biotechnologie, Ghent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
| | - Mattias Vermeersch
- Department of Plant Systems Biology, Vlaams Instituut voor Biotechnologie, Ghent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
| | - Nubia B Eloy
- Department of Plant Systems Biology, Vlaams Instituut voor Biotechnologie, Ghent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
| | - Veronique Storme
- Department of Plant Systems Biology, Vlaams Instituut voor Biotechnologie, Ghent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
| | - Dirk Inzé
- Department of Plant Systems Biology, Vlaams Instituut voor Biotechnologie, Ghent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
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45
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Dechaine JM, Brock MT, Weinig C. QTL architecture of reproductive fitness characters in Brassica rapa. BMC PLANT BIOLOGY 2014; 14:66. [PMID: 24641198 PMCID: PMC4004417 DOI: 10.1186/1471-2229-14-66] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2013] [Accepted: 03/03/2014] [Indexed: 05/19/2023]
Abstract
BACKGROUND Reproductive output is critical to both agronomists seeking to increase seed yield and to evolutionary biologists interested in understanding natural selection. We examine the genetic architecture of diverse reproductive fitness traits in recombinant inbred lines (RILs) developed from a crop (seed oil) × wild-like (rapid cycling) genotype of Brassica rapa in field and greenhouse environments. RESULTS Several fitness traits showed strong correlations and QTL-colocalization across environments (days to bolting, fruit length and seed color). Total fruit number was uncorrelated across environments and most QTL affecting this trait were correspondingly environment-specific. Most fitness components were positively correlated, consistent with life-history theory that genotypic variation in resource acquisition masks tradeoffs. Finally, we detected evidence of transgenerational pleiotropy, that is, maternal days to bolting was negatively correlated with days to offspring germination. A QTL for this transgenerational correlation was mapped to a genomic region harboring one copy of FLOWERING LOCUS C, a genetic locus known to affect both days to flowering as well as germination phenotypes. CONCLUSIONS This study characterizes the genetic structure of important fitness/yield traits within and between generations in B. rapa. Several identified QTL are suitable candidates for fine-mapping for the improvement of yield in crop Brassicas. Specifically, brFLC1, warrants further investigation as a potential regulator of phenology between generations.
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Affiliation(s)
- Jennifer M Dechaine
- Department of Biological Sciences, Central Washington University, Ellensburg, WA 98926, USA
| | - Marcus T Brock
- Department of Botany, University of Wyoming, Laramie, WY 82071, USA
| | - Cynthia Weinig
- Department of Botany, University of Wyoming, Laramie, WY 82071, USA
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46
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Yang Z, Xin D, Liu C, Jiang H, Han X, Sun Y, Qi Z, Hu G, Chen Q. Identification of QTLs for seed and pod traits in soybean and analysis for additive effects and epistatic effects of QTLs among multiple environments. Mol Genet Genomics 2013; 288:651-67. [PMID: 24022198 DOI: 10.1007/s00438-013-0779-z] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2013] [Accepted: 08/27/2013] [Indexed: 01/10/2023]
Abstract
Soybean seed and pod traits are important yield components. Selection for high yield style in seed and pod along with agronomic traits is a goal of many soybean breeders. The intention of this study was to identify quantitative trait loci (QTL) underlying seed and pod traits in soybean among eleven environments in China. 147 recombinant inbred lines were advanced through single-seed-descent method. The population was derived from a cross between Charleston (an American high yield soybean cultivar) and DongNong594 (a Chinese high yield soybean cultivar). A total of 157 polymorphic simple sequence repeat markers were used to construct a genetic linkage map. The phenotypic data of seed and pod traits [number of one-seed pod, number of two-seed pod, number of three-seed pod, number of four-seed pod, number of (two plus three)-seed pod, number of (three plus four)-seed pod, seed weight per plant, number of pod per plant] were recorded in eleven environments. In the analysis of single environment, fourteen main effect QTLs were identified. In the conjoint analysis of multiple environments, twenty-four additive QTLs were identified, and additive QTLs by environments interactions (AE) were evaluated and analyzed at the same time among eleven environments; twenty-three pairs of epistatic QTLs were identified, and epistasis (additive by additive) by environments interactions (AAE) were also analyzed and evaluated among eleven environments. Comparing the results of identification between single environment mapping and multiple environments conjoint mapping, three main effect QTLs with positive additive values and another three main effect QTLs with negative additive values, had no interactions with all environments, supported that these QTLs could be used in molecular assistant breeding in the future. These different effect QTLs could supply a good foundation to the gene clone and molecular asisstant breeding of soybean seed and pod traits.
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47
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Jun TH, Rouf Mian MA, Michel AP. Genetic mapping of three quantitative trait loci for soybean aphid resistance in PI 567324. Heredity (Edinb) 2013; 111:16-22. [PMID: 23486080 PMCID: PMC3692319 DOI: 10.1038/hdy.2013.10] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2012] [Revised: 01/28/2013] [Accepted: 01/30/2013] [Indexed: 11/09/2022] Open
Abstract
Host-plant resistance is an effective method for controlling soybean aphid (Aphis glycines Matsumura), the most damaging insect pest of soybean (Glycine max (L.) Merr.) in North America. Recently, resistant soybean lines have been discovered and at least four aphid resistance genes (Rag1, Rag2, Rag3 and rag4) have been mapped on different soybean chromosomes. However, the evolution of new soybean aphid biotypes capable of defeating host-plant resistance conferred by most single genes demonstrates the need for finding germplasm with multigenic resistance to the aphid. This study was conducted to map quantitative trait loci (QTL) for aphid resistance in PI 567324. We identified two major QTL (QTL_13_1 and QTL_13_2) for aphid resistance on soybean chromosome 13 using 184 recombinant inbred lines from a 'Wyandot' × PI 567324 cross. QTL_13_1 was located close to the previously reported Rag2 gene locus, and QTL_13_2 was close to the rag4 locus. A minor QTL (QTL_6_1) was also detected on chromosome 6, where no gene for soybean aphid resistance has been reported so far. These results indicate that PI 567324 possesses oligogenic resistance to the soybean aphid. The molecular markers closely linked to the QTL reported here will be useful for development of cultivars with oligogenic resistance that are expected to provide broader and more durable resistance against soybean aphids compared with cultivars with monogenic resistance.
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Affiliation(s)
- T-H Jun
- Department of Entomology, The Ohio State
University/OARDC, Wooster, OH, USA
| | - M A Rouf Mian
- USDA-ARS, Department of Horticulture and Crop
Science, The Ohio State University, Wooster, OH,
USA
| | - A P Michel
- Department of Entomology, The Ohio State
University/OARDC, Wooster, OH, USA
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48
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Wituszyńska W, Gałązka K, Rusaczonek A, Vanderauwera S, Van Breusegem F, Karpiński S. Multivariable environmental conditions promote photosynthetic adaptation potential in Arabidopsis thaliana. JOURNAL OF PLANT PHYSIOLOGY 2013; 170:548-59. [PMID: 23287000 DOI: 10.1016/j.jplph.2012.11.016] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2012] [Revised: 11/17/2012] [Accepted: 11/21/2012] [Indexed: 05/20/2023]
Abstract
Most of our knowledge on the regulation of photosynthesis originates from studies performed in highly controlled laboratory conditions. However, in their natural habitats plants are simultaneously subjected to a broad range of abiotic and biotic stimuli which influence photosynthetic efficiency; hence there is an emerging need to examine the process of photosynthesis under multivariable field conditions in order to elucidate the mechanisms that underlie its regulation. Such knowledge has potential for providing novel targets that would improve both crop yield and performance. In the present study we compared laboratory- and field-grown Arabidopsis thaliana plants in terms of photosynthetic efficiency in modulated light intensities and CO2 concentrations. We show here that the field-acclimated plants display highly efficient photosynthesis and are more tolerant to variable light intensities and CO2 concentrations than their laboratory-grown counterparts. We also demonstrate that some structural rearrangements of LHCII and PSII, together with altered pigments composition and stomatal density, are responsible for the differences in assimilation and photochemistry. Furthermore, we employ a transcript profiling approach to explain the genetic mechanisms underlying these adaptations and suggest that they are mainly induced by the high and fluctuating light intensities which occur in the natural environment.
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Affiliation(s)
- Weronika Wituszyńska
- Department of Plant Genetics, Breeding and Biotechnology, Faculty of Horticulture and Landscape Architecture, Warsaw University of Life Sciences, Nowoursynowska Street 159, 02-776 Warszawa, Poland
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49
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Sheng Z, Pettersson ME, Hu X, Luo C, Qu H, Shu D, Shen X, Carlborg O, Li N. Genetic dissection of growth traits in a Chinese indigenous × commercial broiler chicken cross. BMC Genomics 2013; 14:151. [PMID: 23497136 PMCID: PMC3679733 DOI: 10.1186/1471-2164-14-151] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2012] [Accepted: 02/28/2013] [Indexed: 11/18/2022] Open
Abstract
Background In China, consumers often prefer indigenous broiler chickens over commercial breeds, as they have characteristic meat qualities requested within traditional culinary customs. However, the growth-rate of these indigenous breeds is slower than that of the commercial broilers, which means they have not yet reached their full economic value. Therefore, combining the valuable meat quality of the native chickens with the efficiency of the commercial broilers is of interest. In this study, we generated an F2 intercross between the slow growing native broiler breed, Huiyang Beard chicken, and the fast growing commercial broiler breed, High Quality chicken Line A, and used it to map loci explaining the difference in growth rate between these breeds. Results A genome scan to identify main-effect loci affecting 24 growth-related traits revealed nine distinct QTL on six chromosomes. Many QTL were pleiotropic and conformed to the correlation patterns observed between phenotypes. Most of the mapped QTL were found in locations where growth QTL have been reported in other populations, although the effects were greater in this population. A genome scan for pairs of interacting loci identified a number of additional QTL in 10 other genomic regions. The epistatic pairs explained 6–8% of the residual phenotypic variance. Seven of the 10 epistatic QTL mapped in regions containing candidate genes in the ubiquitin mediated proteolysis pathway, suggesting the importance of this pathway in the regulation of growth in this chicken population. Conclusions The main-effect QTL detected using a standard one-dimensional genome scan accounted for a significant fraction of the observed phenotypic variance in this population. Furthermore, genes in known pathways present interesting candidates for further exploration. This study has thus located several QTL regions as promising candidates for further study, which will increase our understanding of the genetic mechanisms underlying growth-related traits in chickens.
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Affiliation(s)
- Zheya Sheng
- State Key Laboratory for Agro-Biotechnology, China Agricultural University, Beijing, People's Republic of China
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50
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Méndez-Vigo B, Gomaa NH, Alonso-Blanco C, Xavier Picó F. Among- and within-population variation in flowering time of Iberian Arabidopsis thaliana estimated in field and glasshouse conditions. THE NEW PHYTOLOGIST 2013; 197:1332-1343. [PMID: 23252608 DOI: 10.1111/nph.12082] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2012] [Accepted: 11/05/2012] [Indexed: 05/08/2023]
Abstract
The study of the evolutionary and population genetics of quantitative traits requires the assessment of within- and among-population patterns of variation. We carried out experiments including eight Iberian Arabidopsis thaliana populations (10 individuals per population) in glasshouse and field conditions. We quantified among- and within-population variation for flowering time and for several field life-history traits. Individuals were genotyped with microsatellites, single nucleotide polymorphisms and four well-known flowering genes (FRI, FLC, CRY2 and PHYC). Phenotypic and genotypic data were used to conduct Q(ST)-F(ST) comparisons. Life-history traits varied significantly among- and within-populations. Flowering time also showed substantial within- and among-population variation as well as significant genotype × environment interactions among the various conditions. Individuals bearing FRI truncations exhibited reduced recruitment in field conditions and differential flowering time behavior across experimental conditions, suggesting that FRI contributes to the observed significant genotype × environment interactions. Flowering time estimated in field conditions was the only trait showing significantly higher quantitative genetic differentiation than neutral genetic differentiation values. Overall, our results show that these A. thaliana populations are genetically more differentiated for flowering time than for neutral markers, suggesting that flowering time is likely to be under divergent selection.
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Affiliation(s)
- Belén Méndez-Vigo
- Departamento de Genética Molecular de Plantas, Centro Nacional de Biotecnología (CNB), Consejo Superior de Investigaciones Científicas (CSIC), 28049, Madrid, Spain
| | - Nasr H Gomaa
- Department of Botany, Faculty of Science, Beni-Suef University, Beni-Suef, Egypt
| | - Carlos Alonso-Blanco
- Departamento de Genética Molecular de Plantas, Centro Nacional de Biotecnología (CNB), Consejo Superior de Investigaciones Científicas (CSIC), 28049, Madrid, Spain
| | - F Xavier Picó
- Departamento de Ecología Integrativa, Estación Biológica de Doñana (EBD), Consejo Superior de Investigaciones Científicas (CSIC), 41092, Sevilla, Spain
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