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Saminadane T, Geddam S, Krishnaswamy P, Jothiganapathy K, Tamilselvan A, Ramadoss BR, Sri Hari Reddy P, Singh US, Singh RK, Platten JD, Gregorio GB, Singh NK, Bisht DS, Kota S, Ponnuvel S, Guntupalli P. Development of early maturing salt-tolerant rice variety KKL(R) 3 using a combination of conventional and molecular breeding approaches. Front Genet 2024; 14:1332691. [PMID: 38371308 PMCID: PMC10869446 DOI: 10.3389/fgene.2023.1332691] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Accepted: 12/27/2023] [Indexed: 02/20/2024] Open
Abstract
Introduction: Soil salinity poses a severe threat to rice production, resulting in stunted growth, leaf damage, and substantial yield losses. This study focuses on developing an early maturing seedling stage salinity tolerant rice variety by integrating conventional breeding methods with marker assisted breeding (MAB) approaches. Methods: Seedling-stage salinity tolerance Quantitative Trait Locus (QTL) "Saltol" from the salt-tolerant parent FL478 was introduced into the high-yielding but salt-sensitive rice variety ADT 45. This was achieved through a combination of conventional breeding and MAB. The breeding process involved rigorous selection, screening, and physiological parameter assessments. Results: KKL(R) 3 (KR 15066) identified as the top performing Recombinant Inbred Line (RIL), consistently demonstrating maximum mean grain yields under both salinity (3435.6 kg/ha) and normal (6421.8 kg/ha) conditions. In comparison to the early maturing, salt-tolerant national check variety CSR 10, KKL(R) 3 exhibited a substantial yield increase over 50%. Discussion: The notable improvement observed in KKL(R) 3 positions it as a promising variety for release, offering a reliable solution to maximize yields, ensure food security, and promote agricultural sustainability in both saline and non-saline environments. The study highlights the effectiveness of MAB in developing salt-tolerant rice varieties and emphasizes the significance of the Saltol QTL in enhancing seedling stage salinity tolerance. The potential release of KKL(R) 3 has the capacity to revolutionize rice production in salt affected regions, providing farmers with a reliable solution to maximize yields and contribute to food security while ensuring agricultural sustainability.
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Affiliation(s)
- Thirumeni Saminadane
- Department of Plant Breeding and Genetics, Pandit Jawaharlal Nehru College of Agriculture and Research Institute, Karaikal, Puducherry, India
| | - Sathyadevi Geddam
- Department of Plant Breeding and Genetics, Pandit Jawaharlal Nehru College of Agriculture and Research Institute, Karaikal, Puducherry, India
| | - Paramasivam Krishnaswamy
- Department of Plant Breeding and Genetics, Pandit Jawaharlal Nehru College of Agriculture and Research Institute, Karaikal, Puducherry, India
| | - Karthick Jothiganapathy
- Department of Plant Breeding and Genetics, Pandit Jawaharlal Nehru College of Agriculture and Research Institute, Karaikal, Puducherry, India
| | - Anandhan Tamilselvan
- Department of Plant Breeding and Genetics, Pandit Jawaharlal Nehru College of Agriculture and Research Institute, Karaikal, Puducherry, India
- Centre for Plant Breeding and Genetics, Tamil Nadu Agricultural University, Coimbatore, Tamilnadu, India
| | - Bharathi Raja Ramadoss
- Centre for Plant Breeding and Genetics, Tamil Nadu Agricultural University, Coimbatore, Tamilnadu, India
| | - Patil Sri Hari Reddy
- Department of Plant Breeding and Genetics, Pandit Jawaharlal Nehru College of Agriculture and Research Institute, Karaikal, Puducherry, India
| | - Uma Shankar Singh
- International Rice Research Institute, Manila, Metro Manila, Philippines
| | - Rakesh Kumar Singh
- International Rice Research Institute, Manila, Metro Manila, Philippines
| | | | - Glenn B. Gregorio
- College of Agriculture and Food Science, University of the Philippines Los Banos (UPLB), Los Baños, Laguna, Philippines
| | - Nagendra Kumar Singh
- Genomics Laboratory, Indian Council of Agricultural Research (ICAR) - National Institute for Plant Biotechnology, New Delhi, India
| | - Deepak Singh Bisht
- Genomics Laboratory, Indian Council of Agricultural Research (ICAR) - National Institute for Plant Biotechnology, New Delhi, India
| | - Suneetha Kota
- ICAR - Indian Institute of Rice Research, Hyderabad, Telangana, India
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Yeon J, Porwal C, McGrath PT, Sengupta P. Identification of a spontaneously arising variant affecting thermotaxis behavior in a recombinant inbred Caenorhabditis elegans line. G3 (Bethesda) 2023; 13:jkad186. [PMID: 37572357 PMCID: PMC10542565 DOI: 10.1093/g3journal/jkad186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 06/26/2023] [Accepted: 08/02/2023] [Indexed: 08/14/2023]
Abstract
Analyses of the contributions of genetic variants in wild strains to phenotypic differences have led to a more complete description of the pathways underlying cellular functions. Causal loci are typically identified via interbreeding of strains with distinct phenotypes in order to establish recombinant inbred lines (RILs). Since the generation of RILs requires growth for multiple generations, their genomes may contain not only different combinations of parental alleles but also genetic changes that arose de novo during the establishment of these lines. Here, we report that in the course of generating RILs between Caenorhabditis elegans strains that exhibit distinct thermotaxis behavioral phenotypes, we identified spontaneously arising variants in the ttx-1 locus. ttx-1 encodes the terminal selector factor for the AFD thermosensory neurons, and loss-of-function mutations in ttx-1 abolish thermotaxis behaviors. The identified genetic changes in ttx-1 in the RIL are predicted to decrease ttx-1 function in part via specifically affecting a subset of AFD-expressed ttx-1 isoforms. Introduction of the relevant missense mutation in the laboratory C. elegans strain via gene editing recapitulates the thermotaxis behavioral defects of the RIL. Our results suggest that spontaneously occurring genomic changes in RILs may complicate identification of loci contributing to phenotypic variation, but that these mutations may nevertheless lead to the identification of important causal molecules and mechanisms.
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Affiliation(s)
- Jihye Yeon
- Department of Biology, Brandeis University, Waltham, MA 02454, USA
| | - Charmi Porwal
- Department of Biology, Brandeis University, Waltham, MA 02454, USA
| | - Patrick T McGrath
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Piali Sengupta
- Department of Biology, Brandeis University, Waltham, MA 02454, USA
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Wu J, Chang X, Li C, Zhang Z, Zhang J, Yin C, Ma W, Chen H, Zhou F, Lin Y. QTLs Related to Rice Callus Regeneration Ability: Localization and Effect Verification of qPRR3. Cells 2022; 11. [PMID: 36552888 DOI: 10.3390/cells11244125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Accepted: 12/13/2022] [Indexed: 12/24/2022] Open
Abstract
Mature and efficient tissue culture systems are already available for most japonica rice varieties (Oryza sativa ssp. geng). However, it remains challenging to regenerate the majority of indica rice varieties (Oryza sativa ssp. xian). In this study, quantitative trait loci (QTLs) associated with rice callus regeneration ability were identified based on the plant regeneration rate (PRR) and total green plant rate (TGPR) of the 93-11 × Nip recombinant inbred line population. Significant positive correlations were found between PRR and TGPR. A total of three QTLs (one for PRR and two for TGPR) were identified. qPRR3 (located on chromosome 3) was detected for both traits, which could explain 13.40% and 17.07% of the phenotypic variations of PRR and TGPR, respectively. Subsequently, the effect of qPRR3 on callus regeneration ability was validated by cryptographically tagged near-isogenic lines (NILs), and the QTL was narrowed to an interval of approximately 160 kb. The anatomical structure observation of the regenerated callus of the NILs revealed that qPRR3 can improve the callus regeneration ability by promoting the regeneration of shoots.
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Wu J, Mao L, Tao J, Wang X, Zhang H, Xin M, Shang Y, Zhang Y, Zhang G, Zhao Z, Wang Y, Cui M, Wei L, Song X, Sun X. Dynamic Quantitative Trait Loci Mapping for Plant Height in Recombinant Inbred Line Population of Upland Cotton. Front Plant Sci 2022; 13:914140. [PMID: 35769288 PMCID: PMC9235862 DOI: 10.3389/fpls.2022.914140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Accepted: 05/06/2022] [Indexed: 06/15/2023]
Abstract
Plant height (PH) is a key plant architecture trait for improving the biological productivity of cotton. Ideal PH of cotton is conducive to lodging resistance and mechanized harvesting. To detect quantitative trait loci (QTL) and candidate genes of PH in cotton, a genetic map was constructed with a recombinant inbred line (RIL) population of upland cotton. PH phenotype data under nine environments and three best linear unbiased predictions (BLUPs) were used for QTL analyses. Based on restriction-site-associated DNA sequence (RAD-seq), the genetic map contained 5,850 single-nucleotide polymorphism (SNP) markers, covering 2,747.12 cM with an average genetic distance of 0.47 cM. Thirty-seven unconditional QTL explaining 1.03-12.50% of phenotypic variance, including four major QTL and seven stable QTL, were identified. Twenty-eight conditional QTL explaining 3.27-28.87% of phenotypic variance, including 1 major QTL, were identified. Importantly, five QTL, including 4 stable QTL, were both unconditional and conditional QTL. Among the 60 PH QTL (including 39 newly identified), none of them were involved in the whole period of PH growth, indicating that QTL related to cotton PH development have dynamic expression characteristics. Based on the functional annotation of Arabidopsis homologous genes and transcriptome data of upland cotton TM-1, 14 candidate genes were predicted within 10 QTL. Our research provides valuable information for understanding the genetic mechanism of PH development, which also increases the economic production of cotton.
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Affiliation(s)
- Jing Wu
- State Key Laboratory of Crop Biology, Agronomy College, Shandong Agricultural University, Taian, China
| | - Lili Mao
- State Key Laboratory of Crop Biology, Agronomy College, Shandong Agricultural University, Taian, China
| | - Jincai Tao
- State Key Laboratory of Crop Biology, Agronomy College, Shandong Agricultural University, Taian, China
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest Agriculture and Forestry University, Xianyang, China
| | - Xiuxiu Wang
- State Key Laboratory of Crop Biology, Agronomy College, Shandong Agricultural University, Taian, China
| | - Haijun Zhang
- State Key Laboratory of Crop Biology, Agronomy College, Shandong Agricultural University, Taian, China
| | - Ming Xin
- State Key Laboratory of Crop Biology, Agronomy College, Shandong Agricultural University, Taian, China
| | - Yongqi Shang
- State Key Laboratory of Crop Biology, Agronomy College, Shandong Agricultural University, Taian, China
| | - Yanan Zhang
- State Key Laboratory of Crop Biology, Agronomy College, Shandong Agricultural University, Taian, China
| | - Guihua Zhang
- Heze Academy of Agricultural Sciences, Heze, China
| | | | - Yiming Wang
- State Key Laboratory of Crop Biology, Agronomy College, Shandong Agricultural University, Taian, China
| | - Mingshuo Cui
- State Key Laboratory of Crop Biology, Agronomy College, Shandong Agricultural University, Taian, China
| | - Liming Wei
- State Key Laboratory of Crop Biology, Agronomy College, Shandong Agricultural University, Taian, China
| | - Xianliang Song
- State Key Laboratory of Crop Biology, Agronomy College, Shandong Agricultural University, Taian, China
| | - Xuezhen Sun
- State Key Laboratory of Crop Biology, Agronomy College, Shandong Agricultural University, Taian, China
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Xu Z, Wang F, Zhou Z, Meng Q, Chen Y, Han X, Tie S, Liu C, Hao Z, Li M, Zhang D, Han J, Wang Z, Li X, Weng J. Identification and Fine-Mapping of a Novel QTL, qMrdd2, That Confers Resistance to Maize Rough Dwarf Disease. Plant Dis 2022; 106:65-72. [PMID: 34132596 DOI: 10.1094/pdis-03-20-0495-re] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Maize rough dwarf disease (MRDD) is caused by a virus and seriously affects maize quality and yield worldwide. MRDD can be most effectively controlled with disease-resistant hybrids of corn. Here, MRDD-resistant (Qi319) and -susceptible (Ye478) parental inbred maize lines and their 314 recombinant inbred lines (RILs) that were derived from a cross between them were evaluated across three environments. A stable resistance QTL, qMrdd2, was identified and mapped using best linear unbiased prediction (BLUP) values to a 0.55-Mb region between the markers MK807 and MK811 on chromosome 2 (B73 RefGen_v3) and was found to explain 8.6 to 11.0% of the total phenotypic variance in MRDD resistance. We validated the effect of qMrdd2 using a chromosome segment substitution line (CSSL) that was derived from a cross between maize inbred Qi319 as the MRDD resistance donor and Ye478 as the recipient. Disease severity index of the CSSL haplotype II harboring qMrdd2 was significantly lower than that of the susceptible parent Ye478. Subsequently, we fine-mapped qMrdd2 to a 315-kb region flanked by the markers RD81 and RD87, thus testing recombinant-derived progeny using selfed backcrossed families. In this study, we identified a novel QTL for MRDD resistance by combining the RIL and CSSL populations, thus providing important genetic information that can be used for breeding MRDD-resistant varieties of maize.
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Affiliation(s)
- Zhennan Xu
- Institute of Crop Science, Chinese Academy of Agricultural Science, Haidian District, Beijing 100081, China
- Northeast Agricultural University, XiangFang District, Harbin, Heilongjiang 150030, China
| | - Feifei Wang
- Northeast Agricultural University, XiangFang District, Harbin, Heilongjiang 150030, China
| | - Zhiqiang Zhou
- Northeast Agricultural University, XiangFang District, Harbin, Heilongjiang 150030, China
| | - Qingchang Meng
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Xuanwu District, Nanjing 210014, China
| | - Yanping Chen
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Xuanwu District, Nanjing 210014, China
| | - Xiaohua Han
- The Cereal Crops Institute, Henan Academy of Agricultural Sciences, Jinshui District, Zhengzhou 450002, China
| | - Shuanggui Tie
- The Cereal Crops Institute, Henan Academy of Agricultural Sciences, Jinshui District, Zhengzhou 450002, China
| | - Changlin Liu
- Northeast Agricultural University, XiangFang District, Harbin, Heilongjiang 150030, China
| | - Zhuanfang Hao
- Northeast Agricultural University, XiangFang District, Harbin, Heilongjiang 150030, China
| | - Mingshun Li
- Northeast Agricultural University, XiangFang District, Harbin, Heilongjiang 150030, China
| | - Degui Zhang
- Northeast Agricultural University, XiangFang District, Harbin, Heilongjiang 150030, China
| | - Jienan Han
- Northeast Agricultural University, XiangFang District, Harbin, Heilongjiang 150030, China
| | - Zhenhua Wang
- Northeast Agricultural University, XiangFang District, Harbin, Heilongjiang 150030, China
| | - Xinhai Li
- Institute of Crop Science, Chinese Academy of Agricultural Science, Haidian District, Beijing 100081, China
| | - Jianfeng Weng
- Institute of Crop Science, Chinese Academy of Agricultural Science, Haidian District, Beijing 100081, China
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6
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Zhao X, Yu K, Pang C, Wu X, Shi R, Sun C, Zhang W, Chen F, Zhang J, Wang X. QTL Analysis of Five Silique-Related Traits in Brassica napus L. Across Multiple Environments. Front Plant Sci 2021; 12:766271. [PMID: 34887891 PMCID: PMC8650614 DOI: 10.3389/fpls.2021.766271] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2021] [Accepted: 10/06/2021] [Indexed: 06/12/2023]
Abstract
As an important physiological and reproductive organ, the silique is a determining factor of seed yield and a breeding target trait in rapeseed (Brassica napus L.). Genetic studies of silique-related traits are helpful for rapeseed marker-assisted high-yield breeding. In this study, a recombinant inbred population containing 189 lines was used to perform a quantitative trait loci (QTLs) analysis for five silique-related traits in seven different environments. As a result, 120 consensus QTLs related to five silique-related traits were identified, including 23 for silique length, 25 for silique breadth, 29 for silique thickness, 22 for seed number per silique and 21 for silique volume, which covered all the chromosomes, except C5. Among them, 13 consensus QTLs, one, five, two, four and one for silique length, silique breadth, silique thickness, seed number per silique and silique volume, respectively, were repeatedly detected in multiple environments and explained 4.38-13.0% of the phenotypic variation. On the basis of the functional annotations of Arabidopsis homologous genes and previously reported silique-related genes, 12 potential candidate genes underlying these 13 QTLs were screened and found to be stable in multiple environments by analyzing the re-sequencing results of the two parental lines. These findings provide new insights into the gene networks affecting silique-related traits at the QTL level in rapeseed.
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Affiliation(s)
- Xiaozhen Zhao
- Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Cotton and Rapeseed, Ministry of Agriculture and Rural Affairs, Nanjing, China
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
| | - Kunjiang Yu
- College of Agriculture, Guizhou University, Guiyang, China
| | - Chengke Pang
- Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Cotton and Rapeseed, Ministry of Agriculture and Rural Affairs, Nanjing, China
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
| | - Xu Wu
- Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Cotton and Rapeseed, Ministry of Agriculture and Rural Affairs, Nanjing, China
| | - Rui Shi
- Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Cotton and Rapeseed, Ministry of Agriculture and Rural Affairs, Nanjing, China
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
| | - Chengming Sun
- Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Cotton and Rapeseed, Ministry of Agriculture and Rural Affairs, Nanjing, China
| | - Wei Zhang
- Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Cotton and Rapeseed, Ministry of Agriculture and Rural Affairs, Nanjing, China
| | - Feng Chen
- Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Cotton and Rapeseed, Ministry of Agriculture and Rural Affairs, Nanjing, China
| | - Jiefu Zhang
- Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Cotton and Rapeseed, Ministry of Agriculture and Rural Affairs, Nanjing, China
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
| | - Xiaodong Wang
- Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Cotton and Rapeseed, Ministry of Agriculture and Rural Affairs, Nanjing, China
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Dhungana SK, Park JH, Oh JH, Kang BK, Seo JH, Sung JS, Kim HS, Shin SO, Baek IY, Jung CS. Quantitative Trait Locus Mapping for Drought Tolerance in Soybean Recombinant Inbred Line Population. Plants (Basel) 2021; 10:1816. [PMID: 34579348 DOI: 10.3390/plants10091816] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Revised: 08/25/2021] [Accepted: 08/30/2021] [Indexed: 11/30/2022]
Abstract
Improving drought stress tolerance of soybean could be an effective way to minimize the yield reduction in the drought prevailing regions. Identification of drought tolerance-related quantitative trait loci (QTLs) is useful to facilitate the development of stress-tolerant varieties. This study aimed to identify the QTLs for drought tolerance in soybean using a recombinant inbred line (RIL) population developed from the cross between a drought-tolerant ‘PI416937’ and a susceptible ‘Cheonsang’ cultivar. Phenotyping was done with a weighted drought coefficient derived from the vegetative and reproductive traits. The genetic map was constructed using 2648 polymorphic SNP markers that distributed on 20 chromosomes with a mean genetic distance of 1.36 cM between markers. A total of 10 QTLs with 3.52–4.7 logarithm of odds value accounting for up to 12.9% phenotypic variance were identified on seven chromosomes. Five chromosomes—2, 7, 10, 14, and 20—contained one QTL each, and chromosomes 1 and 19 harbored two and three QTLs, respectively. The chromosomal locations of seven QTLs overlapped or located close to the related QTLs and/or potential candidate genes reported earlier. The QTLs and closely linked markers could be utilized in maker-assisted selection to accelerate the breeding for drought tolerance in soybean.
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Rabbi SMHA, Kumar A, Mohajeri Naraghi S, Sapkota S, Alamri MS, Elias EM, Kianian S, Seetan R, Missaoui A, Solanki S, Mergoum M. Identification of Main-Effect and Environmental Interaction QTL and Their Candidate Genes for Drought Tolerance in a Wheat RIL Population Between Two Elite Spring Cultivars. Front Genet 2021; 12:656037. [PMID: 34220939 PMCID: PMC8249774 DOI: 10.3389/fgene.2021.656037] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Accepted: 05/13/2021] [Indexed: 01/22/2023] Open
Abstract
Understanding the genetics of drought tolerance can expedite the development of drought-tolerant cultivars in wheat. In this study, we dissected the genetics of drought tolerance in spring wheat using a recombinant inbred line (RIL) population derived from a cross between a drought-tolerant cultivar, ‘Reeder’ (PI613586), and a high-yielding but drought-susceptible cultivar, ‘Albany.’ The RIL population was evaluated for grain yield (YLD), grain volume weight (GVW), thousand kernel weight (TKW), plant height (PH), and days to heading (DH) at nine different environments. The Infinium 90 k-based high-density genetic map was generated using 10,657 polymorphic SNP markers representing 2,057 unique loci. Quantitative trait loci (QTL) analysis detected a total of 11 consistent QTL for drought tolerance-related traits. Of these, six QTL were exclusively identified in drought-prone environments, and five were constitutive QTL (identified under both drought and normal conditions). One major QTL on chromosome 7B was identified exclusively under drought environments and explained 13.6% of the phenotypic variation (PV) for YLD. Two other major QTL were detected, one each on chromosomes 7B and 2B under drought-prone environments, and explained 14.86 and 13.94% of phenotypic variation for GVW and YLD, respectively. One novel QTL for drought tolerance was identified on chromosome 2D. In silico expression analysis of candidate genes underlaying the exclusive QTLs associated with drought stress identified the enrichment of ribosomal and chloroplast photosynthesis-associated proteins showing the most expression variability, thus possibly contributing to stress response by modulating the glycosyltransferase (TraesCS6A01G116400) and hexosyltransferase (TraesCS7B01G013300) unique genes present in QTL 21 and 24, respectively. While both parents contributed favorable alleles to these QTL, unexpectedly, the high-yielding and less drought-tolerant parent contributed desirable alleles for drought tolerance at four out of six loci. Regardless of the origin, all QTL with significant drought tolerance could assist significantly in the development of drought-tolerant wheat cultivars, using genomics-assisted breeding approaches.
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Affiliation(s)
- S M Hisam Al Rabbi
- Department of Plant Sciences, North Dakota State University, Fargo, ND, United States
| | - Ajay Kumar
- Department of Plant Sciences, North Dakota State University, Fargo, ND, United States
| | | | - Suraj Sapkota
- Institute of Plant Breeding, Genetics, and Genomics, University of Georgia, Griffin, GA, United States
| | - Mohammed S Alamri
- Department of Food Science and Nutrition, King Saud University, Riyadh, Saudi Arabia
| | - Elias M Elias
- Department of Plant Sciences, North Dakota State University, Fargo, ND, United States
| | - Shahryar Kianian
- USDA-ARS Cereal Disease Laboratory, University of Minnesota, St. Paul, MN, United States
| | - Raed Seetan
- Department of Computer Science, Slippery Rock University, Slippery Rock, PA, United States
| | - Ali Missaoui
- Institute of Plant Breeding, Genetics, and Genomics, University of Georgia, Griffin, GA, United States.,Department of Crop and Soil Sciences, University of Georgia, Griffin, GA, United States
| | - Shyam Solanki
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA, United States
| | - Mohamed Mergoum
- Institute of Plant Breeding, Genetics, and Genomics, University of Georgia, Griffin, GA, United States.,Department of Crop and Soil Sciences, University of Georgia, Griffin, GA, United States
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Sterken MG, Bevers RPJ, Volkers RJM, Riksen JAG, Kammenga JE, Snoek BL. Dissecting the eQTL Micro-Architecture in Caenorhabditis elegans. Front Genet 2020; 11:501376. [PMID: 33240309 PMCID: PMC7670075 DOI: 10.3389/fgene.2020.501376] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2019] [Accepted: 10/13/2020] [Indexed: 01/11/2023] Open
Abstract
The study of expression quantitative trait loci (eQTL) using natural variation in inbred populations has yielded detailed information about the transcriptional regulation of complex traits. Studies on eQTL using recombinant inbred lines (RILs) led to insights on cis and trans regulatory loci of transcript abundance. However, determining the underlying causal polymorphic genes or variants is difficult, but ultimately essential for the understanding of regulatory networks of complex traits. This requires insight into whether associated loci are single eQTL or a combination of closely linked eQTL, and how this QTL micro-architecture depends on the environment. We addressed these questions by testing for independent replication of previously mapped eQTL in Caenorhabditis elegans using new data from introgression lines (ILs). Both populations indicate that the overall heritability of gene expression, number, and position of eQTL differed among environments. Across environments we were able to replicate 70% of the cis- and 40% of the trans-eQTL using the ILs. Testing eight different simulation models, we suggest that additive effects explain up to 60–93% of RIL/IL heritability for all three environments. Closely linked eQTL explained up to 40% of RIL/IL heritability in the control environment whereas only 7% in the heat-stress and recovery environments. In conclusion, we show that reproducibility of eQTL was higher for cis vs. trans eQTL and that the environment affects the eQTL micro-architecture.
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Affiliation(s)
- Mark G Sterken
- Laboratory of Nematology, Wageningen University & Research, Wageningen, Netherlands
| | - Roel P J Bevers
- Laboratory of Nematology, Wageningen University & Research, Wageningen, Netherlands
| | - Rita J M Volkers
- Laboratory of Nematology, Wageningen University & Research, Wageningen, Netherlands
| | - Joost A G Riksen
- Laboratory of Nematology, Wageningen University & Research, Wageningen, Netherlands
| | - Jan E Kammenga
- Laboratory of Nematology, Wageningen University & Research, Wageningen, Netherlands
| | - Basten L Snoek
- Laboratory of Nematology, Wageningen University & Research, Wageningen, Netherlands.,Theoretical Biology & Bioinformatics, Utrecht University, Utrecht, Netherlands
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10
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Jin J, Liu D, Qi Y, Ma J, Zhen W. Major QTL for Seven Yield-Related Traits in Common Wheat (Triticum aestivum L.). Front Genet 2020; 11:1012. [PMID: 33005181 PMCID: PMC7485215 DOI: 10.3389/fgene.2020.01012] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2020] [Accepted: 08/10/2020] [Indexed: 11/13/2022] Open
Abstract
Flag leaves, plant height (PH), and spike-related traits are key determinants contributing to yield potential in wheat. In this study, we developed a recombinant inbred line (RIL) population with 94 lines derived from the cross between 'AS985472' and 'Sumai 3.' A genetic map spanned 3553.69 cM in length were constructed using 1978 DArT markers. Severn traits including flag leaf width (FLW), flag leaf length (FLL), PH, anthesis date (AD), spike length (SL), spikelet number spike (SNS), and spike density (SD) were evaluated against this RIL population under three different environments. Combined phenotypic data and genetic map, we identified quantitative trait loci (QTL) for each trait. A total of four major and stably expressed QTLs for FLW, PH, and SD were detected on chromosomes 2D and 4B. Of them, the major QTLs individually explained 10.10 - 30.68% of the phenotypic variation. QTLs with pleiotropic effects were identified on chromosomes 4A and 6D as well. Furthermore, the genetic relationships between seven yield-related traits were detected and discussed. A few genes related to leaf growth and development at the interval of a major locus for FLW on chromosome 2D were predicated. Overall, the present study provided useful information for understanding the genetic basis of yield-related traits and will be useful for marker-assisted selection in wheat breeding.
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Affiliation(s)
- Jingjing Jin
- College of Plant Protection, Hebei Agricultural University, Baoding, China.,State Key Laboratory of North China Crop Improvement and Regulation, Baoding, China
| | - Dan Liu
- Neijiang Academy of Agricultural Sciences, Neijiang, China.,School of Life Sciences and Engineering, Southwest University of Science and Technology, Mianyang, China
| | - Yongzhi Qi
- College of Plant Protection, Hebei Agricultural University, Baoding, China.,State Key Laboratory of North China Crop Improvement and Regulation, Baoding, China
| | - Jun Ma
- College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
| | - Wenchao Zhen
- State Key Laboratory of North China Crop Improvement and Regulation, Baoding, China.,College of Agronomy, Hebei Agricultural University, Baoding, China
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11
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Chen QC, Guo Y, Warner RM. Identification of Quantitative Trait Loci for Component Traits of Flowering Capacity Across Temperature in Petunia. G3 (Bethesda) 2019; 9:3601-10. [PMID: 31527047 DOI: 10.1534/g3.119.400653] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
For ornamental annual bedding plants, flowering performance is critical. Flowering performance includes the length of the flowering period, the longevity of individual flowers, and the number of flowers produced during the flowering period, or flowering capacity. Flowering capacity is a function of several component traits, including the number of branches producing flowers, the number of inflorescences per flowering branch, and the number of flower buds per inflorescence. We employed an F7Petunia axillaris × P. exserta recombinant inbred line population to identify QTL for flowering capacity component traits. The population was phenotyped at 14, 17, and 20° over two years. Fifteen robust QTL (rQTL; QTL detected in two or more temperatures/years) were identified across six of the seven Petunia chromosomes (Chr) for total flower bud number (FlBud), branch number (Branch), flowering branch number (FlBranch), and primary shoot flower bud number (FlBudPS). The largest effect QTL explained up to 28.8, 34.9, 36, and 23.1% of the phenotypic variation for FlBub, FlBudPS, Branch, and FlBranch, respectively. rQTL for FlBud and FlBranch co-localized on Chr 1, and rQTL for FlBud, FlBudPS, and FlBranch co-localized on Chr 4. These regions in particular should be useful for identifying genes controlling flowering capacity of this important ornamental plant.
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12
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Onda Y, Inoue K, Sawada Y, Shimizu M, Takahagi K, Uehara-Yamaguchi Y, Hirai MY, Garvin DF, Mochida K. Genetic Variation for Seed Metabolite Levels in Brachypodium distachyon. Int J Mol Sci 2019; 20:ijms20092348. [PMID: 31083584 PMCID: PMC6540107 DOI: 10.3390/ijms20092348] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Revised: 04/26/2019] [Accepted: 04/27/2019] [Indexed: 12/27/2022] Open
Abstract
Metabolite composition and concentrations in seed grains are important traits of cereals. To identify the variation in the seed metabolotypes of a model grass, namely Brachypodium distachyon, we applied a widely targeted metabolome analysis to forty inbred lines of B. distachyon and examined the accumulation patterns of 183 compounds in the seeds. By comparing the metabolotypes with the population structure of these lines, we found signature metabolites that represent different accumulation patterns for each of the three B. distachyon subpopulations. Moreover, we found that thirty-seven metabolites exhibited significant differences in their accumulation between the lines Bd21 and Bd3-1. Using a recombinant inbred line (RIL) population from a cross between Bd3-1 and Bd21, we identified the quantitative trait loci (QTLs) linked with this variation in the accumulation of thirteen metabolites. Our metabolite QTL analysis illustrated that different genetic factors may presumably regulate the accumulation of 4-pyridoxate and pyridoxamine in vitamin B6 metabolism. Moreover, we found two QTLs on chromosomes 1 and 4 that affect the accumulation of an anthocyanin, chrysanthemin. These QTLs genetically interacted to regulate the accumulation of this compound. This study demonstrates the potential for metabolite QTL mapping in B. distachyon and provides new insights into the genetic dissection of metabolomic traits in temperate grasses.
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Affiliation(s)
- Yoshihiko Onda
- Bioproductivity Informatics Research Team, RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan.
- Kihara Institute for Biological Research, Yokohama City University, 641-12 Maioka-cho, Totsuka-ku, Yokohama, Kanagawa 244-0813, Japan.
| | - Komaki Inoue
- Bioproductivity Informatics Research Team, RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan.
| | - Yuji Sawada
- Metabolic Systems Research Team, RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan.
| | - Minami Shimizu
- Bioproductivity Informatics Research Team, RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan.
| | - Kotaro Takahagi
- Bioproductivity Informatics Research Team, RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan.
- Kihara Institute for Biological Research, Yokohama City University, 641-12 Maioka-cho, Totsuka-ku, Yokohama, Kanagawa 244-0813, Japan.
- Graduate School of Nanobioscience, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan.
| | - Yukiko Uehara-Yamaguchi
- Bioproductivity Informatics Research Team, RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan.
| | - Masami Y Hirai
- Metabolic Systems Research Team, RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan.
| | - David F Garvin
- Plant Science Research Unit, United States Department of Agriculture, Agricultural Research Service, 1991 Upper Buford Circle, St. Paul, MN 55108, USA.
| | - Keiichi Mochida
- Bioproductivity Informatics Research Team, RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan.
- Kihara Institute for Biological Research, Yokohama City University, 641-12 Maioka-cho, Totsuka-ku, Yokohama, Kanagawa 244-0813, Japan.
- Graduate School of Nanobioscience, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan.
- Institute of Plant Science and Resource, Okayama University, 2-20-1 Chuo, Kurashiki, Okayama 710-0046, Japan.
- Microalgae Production Control Technology Laboratory, RIKEN Baton Zone Program, RIKEN Cluster for Science, Technology and Innovation Hub, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan.
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13
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Khasanova A, Lovell JT, Bonnette J, Weng X, Jenkins J, Yoshinaga Y, Schmutz J, Juenger TE. The Genetic Architecture of Shoot and Root Trait Divergence Between Mesic and Xeric Ecotypes of a Perennial Grass. Front Plant Sci 2019; 10:366. [PMID: 31019518 PMCID: PMC6458277 DOI: 10.3389/fpls.2019.00366] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Accepted: 03/08/2019] [Indexed: 05/16/2023]
Abstract
Environmental heterogeneity can drive patterns of functional trait variation and lead to the formation of locally adapted ecotypes. Plant ecotypes are often differentiated by suites of correlated root and shoot traits that share common genetic, developmental, and physiological relationships. For instance, although plant water loss is largely governed by shoot systems, root systems determine water access and constrain shoot water status. To evaluate the genetic basis of root and shoot trait divergence, we developed a recombinant inbred population derived from mesic and xeric ecotypes of the perennial grass Panicum hallii. Our study sheds light on the genetic architecture underlying the relationships between root and shoot traits. We identified several genomic "hotspots" which control suites of correlated root and shoot traits, thus indicating genetic coordination between plant organ systems in the process of ecotypic divergence. Genomic regions of colocalized quantitative trait locus (QTL) for the majority of shoot and root growth related traits were independent of colocalized QTL for shoot and root resource acquisition traits. The allelic effects of individual QTL underscore ecological specialization for drought adaptation between ecotypes and reveal possible hybrid breakdown through epistatic interactions. These results have implications for understanding the factors constraining or facilitating local adaptation in plants.
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Affiliation(s)
- Albina Khasanova
- Department of Integrative Biology, The University of Texas at Austin, Austin, TX, United States
| | - John T. Lovell
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, United States
| | - Jason Bonnette
- Department of Integrative Biology, The University of Texas at Austin, Austin, TX, United States
| | - Xiaoyu Weng
- Department of Integrative Biology, The University of Texas at Austin, Austin, TX, United States
| | - Jerry Jenkins
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, United States
| | - Yuko Yoshinaga
- United States Department of Energy, Joint Genome Institute, Walnut Creek, CA, United States
| | - Jeremy Schmutz
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, United States
| | - Thomas E. Juenger
- Department of Integrative Biology, The University of Texas at Austin, Austin, TX, United States
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14
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Zhang Y, Sun Y, Sun J, Feng H, Wang Y. Identification and validation of major and minor QTLs controlling seed coat color in Brassica rapa L. Breed Sci 2019; 69:47-54. [PMID: 31086483 PMCID: PMC6507729 DOI: 10.1270/jsbbs.18108] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Accepted: 10/11/2018] [Indexed: 05/30/2023]
Abstract
Seed coat color is an important agronomic trait in Brassica rapa. Yellow seeds are a desirable trait for breeding oilseed Brassica crops. To identify quantitative trait loci (QTLs) that condition seed coat color in B. rapa, we used a population of recombinant inbred lines (RILs) derived from crossing 09A001, a standard rapid-cycling (RcBr) inbred line of B. rapa L. ssp. dichotoma with yellow seeds, with 08A061, an inbred line of heading Chinese cabbage with dark brown seeds. Using two phenotypic scoring methods, we detected a total of nine QTLs distributed on four chromosomes (Chrs.), A03, A06, A08, and A09, that explained 3.17 to 55.73% of the phenotypic variation for seed color. To validate the effects of the identified QTLs in the RIL population, chromosome segment substitution lines (CSSLs) harboring the chromosomal segment carrying the candidate QTL region from 08A061 were selected, and two co-localized major QTLs, qSC9.1 and qSCb9.1, and one minor QTL, qSC3.1, were successfully validated. The validated QTL located on Chr. A03 appears to be a new locus underlying seed coat color in B. rapa. These findings provide additional insight that will help explain the complex genetic mechanisms underlying the seed coat color trait in B. rapa.
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Affiliation(s)
- Yinghuan Zhang
- College of Horticulture, Shenyang Agricultural University,
Shenyang 110866,
China
| | - Yunxia Sun
- College of Horticulture, Shenyang Agricultural University,
Shenyang 110866,
China
| | - Junpeng Sun
- Liaoing Dongya Seed Limited Company,
Shenyang 110164,
China
| | - Hui Feng
- College of Horticulture, Shenyang Agricultural University,
Shenyang 110866,
China
| | - Yugang Wang
- College of Horticulture, Shenyang Agricultural University,
Shenyang 110866,
China
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15
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Fujii K, Sayama T, Takagi K, Kosuge K, Okano K, Kaga A, Ishimoto M. Identification and dissection of single seed weight QTLs by analysis of seed yield components in soybean. Breed Sci 2018; 68:177-187. [PMID: 29875601 PMCID: PMC5982185 DOI: 10.1270/jsbbs.17098] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2017] [Accepted: 10/23/2017] [Indexed: 05/20/2023]
Abstract
Single seed weight (SSW), or seed size, is a seed yield components (SYC) in soybean, and it is suggested that the genetic factors regulating SSW are involved in the control of other SYCs. The quantitative trait loci (QTLs) for SSW and their effects on the other SYCs were investigated using a recombinant inbred line population derived from typical small- and large-seeded cultivars that were cultivated in two different environments. QTL analysis detected four environmentally stable QTLs for SSW, two of which coincided with the defined loci, qSw17-1 and Ln. The effects of the other loci, qSw12-1 and qSw13-1, were confirmed by analyzing residual heterozygous line progenies derived from the recombinant population. These four QTL regions were also involved in the control of an additional SYC, namely the large-seeded allele at each locus that reduced either the number of pods per plant or the number of ovules per pod. These results suggest the presence of at least two different regulatory mechanisms for SSW. Isolation of genes responsible for these QTLs provides an important tool in the understanding and utilization of SSW diversity for soybean breeding.
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Affiliation(s)
- Kenichiro Fujii
- Institute of Crop Science, National Agriculture and Food Research Organization (NARO),
2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518,
Japan
- National Institute of Agrobiological Sciences,
2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602,
Japan
| | - Takashi Sayama
- Institute of Crop Science, National Agriculture and Food Research Organization (NARO),
2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518,
Japan
- National Institute of Agrobiological Sciences,
2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602,
Japan
| | - Kyoko Takagi
- National Institute of Agrobiological Sciences,
2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602,
Japan
| | - Kazumasa Kosuge
- Plant Biotechnology Institute, Ibaraki Agriculture Center,
3165-1 Ago, Kasama, Ibaraki 319-0206,
Japan
| | - Katsunori Okano
- Plant Biotechnology Institute, Ibaraki Agriculture Center,
3165-1 Ago, Kasama, Ibaraki 319-0206,
Japan
| | - Akito Kaga
- Institute of Crop Science, National Agriculture and Food Research Organization (NARO),
2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518,
Japan
- National Institute of Agrobiological Sciences,
2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602,
Japan
| | - Masao Ishimoto
- Institute of Crop Science, National Agriculture and Food Research Organization (NARO),
2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518,
Japan
- National Institute of Agrobiological Sciences,
2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602,
Japan
- Corresponding author (e-mail: )
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16
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Ulloa M, Hulse-Kemp AM, De Santiago LM, Stelly DM, Burke JJ. Insights Into Upland Cotton ( Gossypium hirsutum L.) Genetic Recombination Based on 3 High-Density Single-Nucleotide Polymorphism and a Consensus Map Developed Independently With Common Parents. Genomics Insights 2017; 10:1178631017735104. [PMID: 29308012 PMCID: PMC5751910 DOI: 10.1177/1178631017735104] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/16/2017] [Accepted: 09/10/2017] [Indexed: 11/17/2022]
Abstract
High-density linkage maps are vital to supporting the correct placement of scaffolds and gene sequences on chromosomes and fundamental to contemporary organismal research and scientific approaches to genetic improvement, especially in paleopolyploids with exceptionally complex genomes, eg, upland cotton (Gossypium hirsutum L., "2n = 52"). Three independently developed intraspecific upland mapping populations were analyzed to generate 3 high-density genetic linkage single-nucleotide polymorphism (SNP) maps and a consensus map using the CottonSNP63K array. The populations consisted of a previously reported F2, a recombinant inbred line (RIL), and reciprocal RIL population, from "Phytogen 72" and "Stoneville 474" cultivars. The cluster file provided 7417 genotyped SNP markers, resulting in 26 linkage groups corresponding to the 26 chromosomes (c) of the allotetraploid upland cotton (AD)1 arisen from the merging of 2 genomes ("A" Old World and "D" New World). Patterns of chromosome-specific recombination were largely consistent across mapping populations. The high-density genetic consensus map included 7244 SNP markers that spanned 3538 cM and comprised 3824 SNP bins, of which 1783 and 2041 were in the At and Dt subgenomes with 1825 and 1713 cM map lengths, respectively. Subgenome average distances were nearly identical, indicating that subgenomic differences in bin number arose due to the high numbers of SNPs on the Dt subgenome. Examination of expected recombination frequency or crossovers (COs) on the chromosomes within each population of the 2 subgenomes revealed that COs were also not affected by the SNPs or SNP bin number in these subgenomes. Comparative alignment analyses identified historical ancestral At-subgenomic translocations of c02 and c03, as well as of c04 and c05. The consensus map SNP sequences aligned with high congruency to the NBI assembly of Gossypium hirsutum. However, the genomic comparisons revealed evidence of additional unconfirmed possible duplications, inversions and translocations, and unbalance SNP sequence homology or SNP sequence/loci genomic dominance, or homeolog loci bias of the upland tetraploid At and Dt subgenomes. The alignments indicated that 364 SNP-associated previously unintegrated scaffolds can be placed in pseudochromosomes of the NBI G hirsutum assembly. This is the first intraspecific SNP genetic linkage consensus map assembled in G hirsutum with a core of reproducible mendelian SNP markers assayed on different populations and it provides further knowledge of chromosome arrangement of genic and nongenic SNPs. Together, the consensus map and RIL populations provide a synergistically useful platform for localizing and identifying agronomically important loci for improvement of the cotton crop.
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Affiliation(s)
- Mauricio Ulloa
- USDA-ARS, PA, Plant Stress and Germplasm Development Research Unit, Lubbock, TX, USA
| | - Amanda M Hulse-Kemp
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX, USA
| | - Luis M De Santiago
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX, USA
- Interdisciplinary Program in Genetics, Texas A&M University, College Station, TX, USA
| | - David M Stelly
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX, USA
| | - John J Burke
- USDA-ARS, PA, Plant Stress and Germplasm Development Research Unit, Lubbock, TX, USA
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17
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Ma J, Luo W, Zhang H, Zhou XH, Qin NN, Wei YM, Liu YX, Jiang QT, Chen GY, Zheng YL, Lan XJ. Identification of quantitative trait loci for seedling root traits from Tibetan semi-wild wheat (Triticum aestivum subsp. tibetanum). Genome 2017; 60:1068-1075. [PMID: 28841403 DOI: 10.1139/gen-2017-0097] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
As a primitive hexaploid wheat resource distributed only in Tibet, Tibetan semi-wild wheat (Triticum aestivum subsp. tibetanum Shao) possesses unique characteristics that could be exploited in wheat breeding programs. Its good root system could offer a stable platform for above-ground components. To detect possible excellent locus for root traits from Tibetan semi-wild wheat, we identified QTLs for root traits using a recombinant inbred line population derived from a cross between Tibetan semi-wild wheat Q1028 and Zhengmai 9023. A total of 15 QTLs on eight chromosomes were detected, including four major QTLs, QMrl.sau-7B, QTrl.sau-4B, QAd.sau-7A, and QSa.sau-4B. The phenotypic variation explained by each of these QTLs ranges from 5.67% to 16.68%. Positive alleles of six QTLs were derived from Q1028. Several novel QTLs for root traits were identified. In addition, significant correlations were detected amongst root traits and agronomic traits. Taken together, these results suggest that Tibetan semi-wild wheat and the newly identified novel QTLs could be useful in future breeding programs.
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Affiliation(s)
- Jian Ma
- Triticeae Research Institute, Sichuan Agricultural University, 211 Huimin Road, Wenjiang, Chengdu, Sichuan 611130, China.,Triticeae Research Institute, Sichuan Agricultural University, 211 Huimin Road, Wenjiang, Chengdu, Sichuan 611130, China
| | - Wei Luo
- Triticeae Research Institute, Sichuan Agricultural University, 211 Huimin Road, Wenjiang, Chengdu, Sichuan 611130, China.,Triticeae Research Institute, Sichuan Agricultural University, 211 Huimin Road, Wenjiang, Chengdu, Sichuan 611130, China
| | - Han Zhang
- Triticeae Research Institute, Sichuan Agricultural University, 211 Huimin Road, Wenjiang, Chengdu, Sichuan 611130, China.,Triticeae Research Institute, Sichuan Agricultural University, 211 Huimin Road, Wenjiang, Chengdu, Sichuan 611130, China
| | - Xiao-Hong Zhou
- Triticeae Research Institute, Sichuan Agricultural University, 211 Huimin Road, Wenjiang, Chengdu, Sichuan 611130, China.,Triticeae Research Institute, Sichuan Agricultural University, 211 Huimin Road, Wenjiang, Chengdu, Sichuan 611130, China
| | - Na-Na Qin
- Triticeae Research Institute, Sichuan Agricultural University, 211 Huimin Road, Wenjiang, Chengdu, Sichuan 611130, China.,Triticeae Research Institute, Sichuan Agricultural University, 211 Huimin Road, Wenjiang, Chengdu, Sichuan 611130, China
| | - Yu-Ming Wei
- Triticeae Research Institute, Sichuan Agricultural University, 211 Huimin Road, Wenjiang, Chengdu, Sichuan 611130, China.,Triticeae Research Institute, Sichuan Agricultural University, 211 Huimin Road, Wenjiang, Chengdu, Sichuan 611130, China
| | - Ya-Xi Liu
- Triticeae Research Institute, Sichuan Agricultural University, 211 Huimin Road, Wenjiang, Chengdu, Sichuan 611130, China.,Triticeae Research Institute, Sichuan Agricultural University, 211 Huimin Road, Wenjiang, Chengdu, Sichuan 611130, China
| | - Qian-Tao Jiang
- Triticeae Research Institute, Sichuan Agricultural University, 211 Huimin Road, Wenjiang, Chengdu, Sichuan 611130, China.,Triticeae Research Institute, Sichuan Agricultural University, 211 Huimin Road, Wenjiang, Chengdu, Sichuan 611130, China
| | - Guo-Yue Chen
- Triticeae Research Institute, Sichuan Agricultural University, 211 Huimin Road, Wenjiang, Chengdu, Sichuan 611130, China.,Triticeae Research Institute, Sichuan Agricultural University, 211 Huimin Road, Wenjiang, Chengdu, Sichuan 611130, China
| | - You-Liang Zheng
- Triticeae Research Institute, Sichuan Agricultural University, 211 Huimin Road, Wenjiang, Chengdu, Sichuan 611130, China.,Triticeae Research Institute, Sichuan Agricultural University, 211 Huimin Road, Wenjiang, Chengdu, Sichuan 611130, China
| | - Xiu-Jin Lan
- Triticeae Research Institute, Sichuan Agricultural University, 211 Huimin Road, Wenjiang, Chengdu, Sichuan 611130, China.,Triticeae Research Institute, Sichuan Agricultural University, 211 Huimin Road, Wenjiang, Chengdu, Sichuan 611130, China
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18
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Knoch D, Riewe D, Meyer RC, Boudichevskaia A, Schmidt R, Altmann T. Genetic dissection of metabolite variation in Arabidopsis seeds: evidence for mQTL hotspots and a master regulatory locus of seed metabolism. J Exp Bot 2017; 68:1655-1667. [PMID: 28338798 PMCID: PMC5444479 DOI: 10.1093/jxb/erx049] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
To gain insight into genetic factors controlling seed metabolic composition and its relationship to major seed properties, an Arabidopsis recombinant inbred line (RIL) population, derived from accessions Col-0 and C24, was studied using an MS-based metabolic profiling approach. Relative intensities of 311 polar primary metabolites were used to identify associated genomic loci and to elucidate their interactions by quantitative trait locus (QTL) mapping. A total of 786 metabolic QTLs (mQTLs) were unequally distributed across the genome, forming several hotspots. For the branched-chain amino acid leucine, mQTLs and candidate genes were elucidated in detail. Correlation studies displayed links between metabolite levels, seed protein content, and seed weight. Principal component analysis revealed a clustering of samples, with PC1 mapping to a region on the short arm of chromosome IV. The overlap of this region with mQTL hotspots indicates the presence of a potential master regulatory locus of seed metabolism. As a result of database queries, a series of candidate regulatory genes, including bZIP10, were identified within this region. Depending on the search conditions, metabolic pathway-derived candidate genes for 40-61% of tested mQTLs could be determined, providing an extensive basis for further identification and characterization of hitherto unknown genes causal for natural variation of Arabidopsis seed metabolism.
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Affiliation(s)
- Dominic Knoch
- Department of Molecular Genetics/Heterosis, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, D-06466 Seeland/OT Gatersleben, Germany
| | - David Riewe
- Department of Molecular Genetics/Heterosis, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, D-06466 Seeland/OT Gatersleben, Germany
| | - Rhonda Christiane Meyer
- Department of Molecular Genetics/Heterosis, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, D-06466 Seeland/OT Gatersleben, Germany
| | - Anastassia Boudichevskaia
- Department of Breeding Research/Genome Plasticity, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, D-06466 Seeland/OT Gatersleben, Germany
| | - Renate Schmidt
- Department of Breeding Research/Genome Plasticity, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, D-06466 Seeland/OT Gatersleben, Germany
| | - Thomas Altmann
- Department of Molecular Genetics/Heterosis, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, D-06466 Seeland/OT Gatersleben, Germany
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19
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Teraishi M, Tojo Y, Yamada N, Okumoto Y. Identification of environmentally stable QTLs controlling Saponin content in Glycine max. Breed Sci 2017; 67:123-128. [PMID: 28588388 PMCID: PMC5445963 DOI: 10.1270/jsbbs.16086] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/26/2016] [Accepted: 11/20/2016] [Indexed: 06/07/2023]
Abstract
Saponins are secondary metabolites that are widely distributed in plants. There are two major saponin precursors in soybean: soyasapogenol A, contributing to the undesirable taste, and soyasapogenol B, some of which have health benefits. It is important to control the ratio and content of the two major saponin groups to enhance the appeal of soybean as a health food. The structural diversity of saponin in the sugar chain composition makes it hard to quantify the saponin content. We measured the saponin content in soybean by removing the sugar chain from the saponin using acidic hydrolysis and detected novel quantitative trait loci (QTLs) for saponin content. Major QTLs in the hypocotyl were identified on chromosome 5 near the SSR marker, Satt 384, while those in the cotyledon were on chromosome 6 near Sat_312, which is linked to the T and E1 loci. Our results suggest that saponin contents in the hypocotyl and cotyledon are controlled by different genes and that it is difficult to increase the beneficial group B saponin and to decrease the undesirable group A saponin at the same time.
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Affiliation(s)
- Masayoshi Teraishi
- Graduate School of Agriculture, Kyoto University,
Oiwake, Kitashirakawa, Sakyo, Kyoto 606-8502,
Japan
| | - Yuka Tojo
- Graduate School of Agriculture, Kyoto University,
Oiwake, Kitashirakawa, Sakyo, Kyoto 606-8502,
Japan
| | - Naohiro Yamada
- Nagano Vegetable and Ornamental Crops Experiment Station,
1066-1 Soga, Shiojiri, Nagano 399-6461,
Japan
| | - Yutaka Okumoto
- Graduate School of Agriculture, Kyoto University,
Oiwake, Kitashirakawa, Sakyo, Kyoto 606-8502,
Japan
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20
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Shang L, Wang Y, Wang X, Liu F, Abduweli A, Cai S, Li Y, Ma L, Wang K, Hua J. Genetic Analysis and QTL Detection on Fiber Traits Using Two Recombinant Inbred Lines and Their Backcross Populations in Upland Cotton. G3 (Bethesda) 2016. [PMID: 27342735 DOI: 10.1111/pbr.12352] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
Cotton fiber, a raw natural fiber material, is widely used in the textile industry. Understanding the genetic mechanism of fiber traits is helpful for fiber quality improvement. In the present study, the genetic basis of fiber quality traits was explored using two recombinant inbred lines (RILs) and corresponding backcross (BC) populations under multiple environments in Upland cotton based on marker analysis. In backcross populations, no significant correlation was observed between marker heterozygosity and fiber quality performance and it suggested that heterozygosity was not always necessarily advantageous for the high fiber quality. In two hybrids, 111 quantitative trait loci (QTL) for fiber quality were detected using composite interval mapping, in which 62 new stable QTL were simultaneously identified in more than one environment or population. QTL detected at the single-locus level mainly showed additive effect. In addition, a total of 286 digenic interactions (E-QTL) and their environmental interactions [QTL × environment interactions (QEs)] were detected for fiber quality traits by inclusive composite interval mapping. QE effects should be considered in molecular marker-assisted selection breeding. On average, the E-QTL explained a larger proportion of the phenotypic variation than the main-effect QTL did. It is concluded that the additive effect of single-locus and epistasis with few detectable main effects play an important role in controlling fiber quality traits in Upland cotton.
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Affiliation(s)
- Lianguang Shang
- Department of Plant Genetics and Breeding/Key Laboratory of Crop Heterosis and Utilization of Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Yumei Wang
- Institute of Cash Crops, Hubei Academy of Agricultural Sciences, Wuhan 430064, China
| | - Xiaocui Wang
- Department of Plant Genetics and Breeding/Key Laboratory of Crop Heterosis and Utilization of Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Fang Liu
- Institute of Cotton Research, Chinese Academy of Agricultural Sciences/State Key Laboratory of Cotton Biology, Anyang 455000, Henan, China
| | - Abdugheni Abduweli
- Department of Plant Genetics and Breeding/Key Laboratory of Crop Heterosis and Utilization of Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Shihu Cai
- Department of Plant Genetics and Breeding/Key Laboratory of Crop Heterosis and Utilization of Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Yuhua Li
- Department of Plant Genetics and Breeding/Key Laboratory of Crop Heterosis and Utilization of Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Lingling Ma
- Department of Plant Genetics and Breeding/Key Laboratory of Crop Heterosis and Utilization of Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Kunbo Wang
- Institute of Cotton Research, Chinese Academy of Agricultural Sciences/State Key Laboratory of Cotton Biology, Anyang 455000, Henan, China
| | - Jinping Hua
- Department of Plant Genetics and Breeding/Key Laboratory of Crop Heterosis and Utilization of Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
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21
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Shang L, Wang Y, Wang X, Liu F, Abduweli A, Cai S, Li Y, Ma L, Wang K, Hua J. Genetic Analysis and QTL Detection on Fiber Traits Using Two Recombinant Inbred Lines and Their Backcross Populations in Upland Cotton. G3 (Bethesda) 2016; 6:2717-24. [PMID: 27342735 DOI: 10.1534/g3.116.031302] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Cotton fiber, a raw natural fiber material, is widely used in the textile industry. Understanding the genetic mechanism of fiber traits is helpful for fiber quality improvement. In the present study, the genetic basis of fiber quality traits was explored using two recombinant inbred lines (RILs) and corresponding backcross (BC) populations under multiple environments in Upland cotton based on marker analysis. In backcross populations, no significant correlation was observed between marker heterozygosity and fiber quality performance and it suggested that heterozygosity was not always necessarily advantageous for the high fiber quality. In two hybrids, 111 quantitative trait loci (QTL) for fiber quality were detected using composite interval mapping, in which 62 new stable QTL were simultaneously identified in more than one environment or population. QTL detected at the single-locus level mainly showed additive effect. In addition, a total of 286 digenic interactions (E-QTL) and their environmental interactions [QTL × environment interactions (QEs)] were detected for fiber quality traits by inclusive composite interval mapping. QE effects should be considered in molecular marker-assisted selection breeding. On average, the E-QTL explained a larger proportion of the phenotypic variation than the main-effect QTL did. It is concluded that the additive effect of single-locus and epistasis with few detectable main effects play an important role in controlling fiber quality traits in Upland cotton.
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22
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Sahu R, Sharaff M, Pradhan M, Sethi A, Bandyopadhyay T, Mishra VK, Chand R, Chowdhury AK, Joshi AK, Pandey SP. Elucidation of defense-related signaling responses to spot blotch infection in bread wheat (Triticum aestivum L.). Plant J 2016; 86:35-49. [PMID: 26932764 DOI: 10.1111/tpj.13149] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2015] [Revised: 02/13/2016] [Accepted: 02/15/2016] [Indexed: 05/20/2023]
Abstract
Spot blotch disease, caused by Bipolaris sorokiniana, is an important threat to wheat, causing an annual loss of ~17%. Under epidemic conditions, these losses may be 100%, yet the molecular responses of wheat to spot blotch remain almost uncharacterized. Moreover, defense-related phytohormone signaling genes have been poorly characterized in wheat. Here, we have identified 18 central components of salicylic acid (SA), jasmonic acid (JA), ethylene (ET), and enhanced disease susceptibility 1 (EDS1) signaling pathways as well as the genes of the phenylpropanoid pathway in wheat. In time-course experiments, we characterized the reprogramming of expression of these pathways in two contrasting genotypes: Yangmai #6 (resistant to spot blotch) and Sonalika (susceptible to spot blotch). We further evaluated the performance of a population of recombinant inbred lines (RILs) by crossing Yangmai#6 and Sonalika (parents) and subsequent selfing to F10 under field conditions in trials at multiple locations. We characterized the reprogramming of defense-related signaling in these RILs as a consequence of spot blotch attack. During resistance to spot blotch attack, wheat strongly elicits SA signaling (SA biogenesis as well as the NPR1-dependent signaling pathway), along with WRKY33 transcription factor, followed by an enhanced expression of phenylpropanoid pathway genes. These may lead to accumulation of phenolics-based defense metabolites that may render resistance against spot blotch. JA signaling may synergistically contribute to the resistance. Failure to elicit SA (and possibly JA) signaling may lead to susceptibility against spot blotch infection in wheat.
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Affiliation(s)
- Ranabir Sahu
- Department of Biological Sciences, Indian Institute of Science Education and Research - Kolkata, Mohanpur Campus, Mohanpur, 741246, West Bengal, India
| | - Murali Sharaff
- Department of Biological Sciences, Indian Institute of Science Education and Research - Kolkata, Mohanpur Campus, Mohanpur, 741246, West Bengal, India
| | - Maitree Pradhan
- Department of Biological Sciences, Indian Institute of Science Education and Research - Kolkata, Mohanpur Campus, Mohanpur, 741246, West Bengal, India
| | - Avinash Sethi
- Department of Biological Sciences, Indian Institute of Science Education and Research - Kolkata, Mohanpur Campus, Mohanpur, 741246, West Bengal, India
| | - Tirthankar Bandyopadhyay
- Department of Biological Sciences, Indian Institute of Science Education and Research - Kolkata, Mohanpur Campus, Mohanpur, 741246, West Bengal, India
| | - Vinod K Mishra
- Department of Genetics and Plant Breeding, Institute of Agricultural Sciences, Banaras Hindu University, Varanasi, 22105, India
| | - Ramesh Chand
- Department of Plant Pathology, Institute of Agricultural Sciences, Banaras Hindu University, Varanasi, 22105, India
| | - Apurba K Chowdhury
- Uttar Banga Krishi Viswavidyalaya, Cooch Behar, Varanasi, 736165, West Bengal, India
| | - Arun K Joshi
- Department of Genetics and Plant Breeding, Institute of Agricultural Sciences, Banaras Hindu University, Varanasi, 22105, India
- The International Maize and Wheat Improvement Center (CIMMYT) South Asia Office, Singh Durbar Plaza Marg, Kathmandu, Nepal
| | - Shree P Pandey
- Department of Biological Sciences, Indian Institute of Science Education and Research - Kolkata, Mohanpur Campus, Mohanpur, 741246, West Bengal, India
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Jamshed M, Jia F, Gong J, Palanga KK, Shi Y, Li J, Shang H, Liu A, Chen T, Zhang Z, Cai J, Ge Q, Liu Z, Lu Q, Deng X, Tan Y, Or Rashid H, Sarfraz Z, Hassan M, Gong W, Yuan Y. Identification of stable quantitative trait loci (QTLs) for fiber quality traits across multiple environments in Gossypium hirsutum recombinant inbred line population. BMC Genomics 2016; 17:197. [PMID: 26951621 PMCID: PMC4782318 DOI: 10.1186/s12864-016-2560-2] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2015] [Accepted: 02/29/2016] [Indexed: 01/13/2023] Open
Abstract
BACKGROUND The identification of quantitative trait loci (QTLs) that are stable and consistent across multiple environments and populations plays an essential role in marker-assisted selection (MAS). In the present study, we used 28,861 simple sequence repeat (SSR) markers, which included 12,560 Gossypium raimondii (D genome) sequence-based SSR markers to identify polymorphism between two upland cotton strains 0-153 and sGK9708. A total of 851 polymorphic primers were finally selected and used to genotype 196 recombinant inbred lines (RIL) derived from a cross between 0 and 153 and sGK9708 and used to construct a linkage map. The RIL population was evaluated for fiber quality traits in six locations in China for five years. Stable QTLs identified in this intraspecific cross could be used in future cotton breeding program and with fewer obstacles. RESULTS The map covered a distance of 4,110 cM, which represents about 93.2 % of the upland cotton genome, and with an average distance of 5.2 cM between adjacent markers. We identified 165 QTLs for fiber quality traits, of which 47 QTLs were determined to be stable across multiple environments. Most of these QTLs aggregated into clusters with two or more traits. A total of 30 QTL clusters were identified which consisted of 103 QTLs. Sixteen clusters in the At sub-genome comprised 44 QTLs, whereas 14 clusters in the Dt sub-genome that included 59 QTLs for fiber quality were identified. Four chromosomes, including chromosome 4 (c4), c7, c14, and c25 were rich in clusters harboring 5, 4, 5, and 6 clusters respectively. A meta-analysis was performed using Biomercator V4.2 to integrate QTLs from 11 environmental datasets on the RIL populations of the above mentioned parents and previous QTL reports. Among the 165 identified QTLs, 90 were identified as common QTLs, whereas the remaining 75 QTLs were determined to be novel QTLs. The broad sense heritability estimates of fiber quality traits were high for fiber length (0.93), fiber strength (0.92), fiber micronaire (0.85), and fiber uniformity (0.80), but low for fiber elongation (0.27). Meta-clusters on c4, c7, c14 and c25 were identified as stable QTL clusters and were considered more valuable in MAS for the improvement of fiber quality of upland cotton. CONCLUSION Multiple environmental evaluations of an intraspecific RIL population were conducted to identify stable QTLs. Meta-QTL analyses identified a common chromosomal region that plays an important role in fiber development. Therefore, QTLs identified in the present study are an ideal candidate for MAS in cotton breeding programs to improve fiber quality.
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Affiliation(s)
- Muhammad Jamshed
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China.
| | - Fei Jia
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China.
| | - Juwu Gong
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China.
- College of Agronomy, Xinjiang Agricultural University, Key Laboratory of Agro-Biotechnology, Urumqi, 830052, Xinjiang, China.
| | - Koffi Kibalou Palanga
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China.
| | - Yuzhen Shi
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China.
| | - Junwen Li
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China.
| | - Haihong Shang
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China.
| | - Aiying Liu
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China.
| | - Tingting Chen
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China.
| | - Zhen Zhang
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China.
| | - Juan Cai
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China.
| | - Qun Ge
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China.
| | - Zhi Liu
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, 410128, Hunan, China.
| | - Quanwei Lu
- Anyang College of Technology, Anyang, 455000, Henan, China.
| | - Xiaoying Deng
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China.
| | - Yunna Tan
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China.
| | - Harun Or Rashid
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China.
| | - Zareen Sarfraz
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China.
| | - Murtaza Hassan
- Department of Materials Science and Engineering, College of Engineering, Peking University, Beijing, 100871, China.
| | - Wankui Gong
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China.
| | - Youlu Yuan
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China.
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24
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Yu YH, Shao YF, Liu J, Fan YY, Sun CX, Cao ZY, Zhuang JY. Mapping of Quantitative Trait Loci for Contents of Macro- and Microelements in Milled Rice (Oryza sativa L.). J Agric Food Chem 2015; 63:7813-8. [PMID: 26301991 DOI: 10.1021/acs.jafc.5b02882] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Macro- and microelement contents are important traits for nutritional quality in rice. In this study, quantitative trait loci (QTLs) for the contents of seven mineral elements in milled rice were detected using recombinant inbred lines (RILs) of the indica rice cross Zhenshan 97/Milyang 46, followed by the validation and fine mapping of a QTL region on the short arm of chromosome 6. A total of 20 QTLs distributed on chromosomes 1, 3, 5, 6, 10, and 11 were detected in the RIL population. Co-localizations of QTLs for multiple traits were observed, of which the qP3/qMg3/qZn3 region was shown to have the largest effects for the contents of phosphorus, magnesium, and zinc, and the qK6.1/qCa6/qZn6/qMn6/qCu6 region was found to be responsible for five of the seven traits. Using near isogenic lines having sequential segregating region, the target QTL on chromosome 6 was delimitated to a 29.9 kb region flanked by RM19410 and Si2944. This QTL showed major effects for all seven traits, with the enhancing alleles derived from the male parent Milyang 46.
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Affiliation(s)
- Yong-Hong Yu
- China National Rice Research Institute , Hangzhou, Zhejiang 310006, People's Republic of China
| | - Ya-Fang Shao
- China National Rice Research Institute , Hangzhou, Zhejiang 310006, People's Republic of China
| | - Jie Liu
- China National Rice Research Institute , Hangzhou, Zhejiang 310006, People's Republic of China
| | - Ye-Yang Fan
- China National Rice Research Institute , Hangzhou, Zhejiang 310006, People's Republic of China
| | - Cheng-Xiao Sun
- China National Rice Research Institute , Hangzhou, Zhejiang 310006, People's Republic of China
| | - Zhao-Yun Cao
- China National Rice Research Institute , Hangzhou, Zhejiang 310006, People's Republic of China
| | - Jie-Yun Zhuang
- China National Rice Research Institute , Hangzhou, Zhejiang 310006, People's Republic of China
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25
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Abstract
Multiparental populations are of considerable interest in high-density genetic mapping due to their increased levels of polymorphism and recombination relative to biparental populations. However, errors in map construction can have significant impact on QTL discovery in later stages of analysis, and few methods have been developed to quantify the uncertainty attached to the reported order of markers or intermarker distances. Current methods are computationally intensive or limited to assessing uncertainty only for order or distance, but not both simultaneously. We derive the asymptotic joint distribution of maximum composite likelihood estimators for intermarker distances. This approach allows us to construct hypothesis tests and confidence intervals for simultaneously assessing marker-order instability and distance uncertainty. We investigate the effects of marker density, population size, and founder distribution patterns on map confidence in multiparental populations through simulations. Using these data, we provide guidelines on sample sizes necessary to map markers at sub-centimorgan densities with high certainty. We apply these approaches to data from a bread wheat Multiparent Advanced Generation Inter-Cross (MAGIC) population genotyped using the Illumina 9K SNP chip to assess regions of uncertainty and validate them against the recently released pseudomolecule for the wheat chromosome 3B.
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26
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Kato S, Fujii K, Yumoto S, Ishimoto M, Shiraiwa T, Sayama T, Kikuchi A, Nishio T. Seed yield and its components of indeterminate and determinate lines in recombinant inbred lines of soybean. Breed Sci 2015; 65:154-60. [PMID: 26069445 PMCID: PMC4430510 DOI: 10.1270/jsbbs.65.154] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2014] [Accepted: 12/10/2014] [Indexed: 05/18/2023]
Abstract
The present study was conducted to evaluate the benefits of indeterminate growth habit in breeding to improve yield potential of Japanese soybean varieties, which exclusively have determinate growth habit. Two populations of recombinant inbred lines (RILs) derived from crosses between determinate Japanese cultivars and indeterminate US cultivars were grown in Akita and Kyoto, and seed weight per plant (SW) and its components were compared between indeterminate and determinate RILs. The difference of SW between the two growth habits in RILs varied depending on maturation time. The SW of early indeterminate lines was significantly higher than that of early determinate ones in Akita, but not in Kyoto. Among yield components, the number of seeds per pod was constantly larger in indeterminate lines than that in determinate ones irrespective of maturation time. The number of seeds per plant and the number of pods per plant of the indeterminate lines were greater than those of the determinate lines in early maturation in Akita. These results suggest that the indeterminate growth habit is an advantageous characteristic in breeding for high yield of early maturing soybean varieties in the Tohoku region.
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Affiliation(s)
- Shin Kato
- National Agriculture and Food Research Organization (NARO) Tohoku Agricultural Research Center,
Uenodai, Kariwano, Daisen, Akita 019-2112,
Japan
| | - Kenichiro Fujii
- National Institute of Agrobiological Sciences (NIAS),
2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602,
Japan
| | - Setsuzo Yumoto
- NARO Institute of Crop Science,
2-1-18 Kannondai, Tsukuba, Ibaraki 305-8518,
Japan
| | - Masao Ishimoto
- National Institute of Agrobiological Sciences (NIAS),
2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602,
Japan
| | - Tatsuhiko Shiraiwa
- Graduate School of Agriculture, Kyoto University,
Oiwake, Kitashirakawa, Sakyo, Kyoto 606-8502,
Japan
| | - Takashi Sayama
- National Institute of Agrobiological Sciences (NIAS),
2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602,
Japan
| | - Akio Kikuchi
- National Agriculture and Food Research Organization (NARO) Tohoku Agricultural Research Center,
Uenodai, Kariwano, Daisen, Akita 019-2112,
Japan
| | - Takeshi Nishio
- Graduate School of Agricultural Science, Tohoku University,
1-1 Tsutsumidori-Amamiyamachi, Aoba, Sendai, Miyagi 981-8555,
Japan
- Corresponding author (e-mail: )
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27
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Wang X, Yu K, Li H, Peng Q, Chen F, Zhang W, Chen S, Hu M, Zhang J. High-Density SNP Map Construction and QTL Identification for the Apetalous Character in Brassica napus L. Front Plant Sci 2015; 6:1164. [PMID: 26779193 PMCID: PMC4688392 DOI: 10.3389/fpls.2015.01164] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2015] [Accepted: 12/07/2015] [Indexed: 05/09/2023]
Abstract
The apetalous genotype is a morphological ideotype for increasing seed yield and should be of considerable agricultural use; however, only a few studies have focused on the genetic control of this trait in Brassica napus. In the present study, a recombinant inbred line, the AH population, containing 189 individuals was derived from a cross between an apetalous line 'APL01' and a normally petalled variety 'Holly'. The Brassica 60 K Infinium BeadChip Array harboring 52,157 single nucleotide polymorphism (SNP) markers was used to genotype the AH individuals. A high-density genetic linkage map was constructed based on 2,755 bins involving 11,458 SNPs and 57 simple sequence repeats, and was used to identify loci associated with petalous degree (PDgr). The linkage map covered 2,027.53 cM, with an average marker interval of 0.72 cM. The AH map had good collinearity with the B. napus reference genome, indicating its high quality and accuracy. After phenotypic analyses across five different experiments, a total of 19 identified quantitative trait loci (QTLs) distributed across chromosomes A3, A5, A6, A9 and C8 were obtained, and these QTLs were further integrated into nine consensus QTLs by a meta-analysis. Interestingly, the major QTL qPD.C8-2 was consistently detected in all five experiments, and qPD.A9-2 and qPD.C8-3 were stably expressed in four experiments. Comparative mapping between the AH map and the B. napus reference genome suggested that there were 328 genes underlying the confidence intervals of the three steady QTLs. Based on the Gene Ontology assignments of 52 genes to the regulation of floral development in published studies, 146 genes were considered as potential candidate genes for PDgr. The current study carried out a QTL analysis for PDgr using a high-density SNP map in B. napus, providing novel targets for improving seed yield. These results advanced our understanding of the genetic control of PDgr regulation in B. napus.
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Affiliation(s)
- Xiaodong Wang
- Key Laboratory of Cotton and Rapeseed, Ministry of Agriculture, Institute of Industrial Crops, Jiangsu Academy of Agricultural SciencesNanjing, China
- Jiangsu Collaborative Innovation Center for Modern Crop ProductionNanjing, China
| | - Kunjiang Yu
- Key Laboratory of Cotton and Rapeseed, Ministry of Agriculture, Institute of Industrial Crops, Jiangsu Academy of Agricultural SciencesNanjing, China
| | - Hongge Li
- Key Laboratory of Cotton and Rapeseed, Ministry of Agriculture, Institute of Industrial Crops, Jiangsu Academy of Agricultural SciencesNanjing, China
| | - Qi Peng
- Key Laboratory of Cotton and Rapeseed, Ministry of Agriculture, Institute of Industrial Crops, Jiangsu Academy of Agricultural SciencesNanjing, China
| | - Feng Chen
- Key Laboratory of Cotton and Rapeseed, Ministry of Agriculture, Institute of Industrial Crops, Jiangsu Academy of Agricultural SciencesNanjing, China
- Provincial Key Laboratory of Agrobiology, Jiangsu Academy of Agricultural SciencesNanjing, China
| | - Wei Zhang
- Key Laboratory of Cotton and Rapeseed, Ministry of Agriculture, Institute of Industrial Crops, Jiangsu Academy of Agricultural SciencesNanjing, China
| | - Song Chen
- Key Laboratory of Cotton and Rapeseed, Ministry of Agriculture, Institute of Industrial Crops, Jiangsu Academy of Agricultural SciencesNanjing, China
| | - Maolong Hu
- Key Laboratory of Cotton and Rapeseed, Ministry of Agriculture, Institute of Industrial Crops, Jiangsu Academy of Agricultural SciencesNanjing, China
| | - Jiefu Zhang
- Key Laboratory of Cotton and Rapeseed, Ministry of Agriculture, Institute of Industrial Crops, Jiangsu Academy of Agricultural SciencesNanjing, China
- Jiangsu Collaborative Innovation Center for Modern Crop ProductionNanjing, China
- *Correspondence: Jiefu Zhang,
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Jiang G, Zeng J, He Y. Analysis of quantitative trait loci affecting chlorophyll content of rice leaves in a double haploid population and two backcross populations. Gene 2013; 536:287-95. [PMID: 24361205 DOI: 10.1016/j.gene.2013.12.010] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2013] [Revised: 12/07/2013] [Accepted: 12/09/2013] [Indexed: 02/04/2023]
Abstract
Chlorophyll content, one of the most important physiological parameters related to plant photosynthesis, is usually used to predict yield potential. To map the quantitative trait loci (QTLs) underlying the chlorophyll content of rice leaves, a double haploid (DH) population was developed from an indica/japonica (Zhenshan 97/Wuyujing 2) crossing and two backcross populations were established subsequently by backcrossing DH lines with each of their parents. The contents of chlorophyll a and chlorophyll b were determined by using a spectrophotometer to directly measure the leaf chlorophyll extracts. To determine the leaf chlorophyll retention along with maturation, all measurements were performed on the day of heading and were repeated 30 days later. A total of 60 QTLs were resolved for all the traits using these three populations. These QTLs were distributed on 10 rice chromosomes, except chromosomes 5 and 10; the closer the traits, the more clustering of the QTLs residing on common rice chromosomal regions. In general, the majority of QTLs that specify chlorophyll a content also play a role in determining chlorophyll b content. Strangely, chlorophyll content in this study was found mostly to be lacking or to have a negative correlation with yield. In both backcross F1 populations, overdominant (or underdominant) loci were more important than complete or partially dominant loci for main-effect QTLs and epistatic QTLs, thereby supporting previous findings that overdominant effects are the primary genetic basis for depression in inbreeding and heterosis in rice.
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Affiliation(s)
- Gonghao Jiang
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research and National Center of Crop Molecular Breeding, Huazhong Agricultural University, Wuhan 430070, PR China; College of Life Science, Heilongjiang University, Haerbin 150080, China
| | - Jing Zeng
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research and National Center of Crop Molecular Breeding, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Yuqing He
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research and National Center of Crop Molecular Breeding, Huazhong Agricultural University, Wuhan 430070, PR China.
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29
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Makumburage GB, Richbourg HL, LaTorre KD, Capps A, Chen C, Stapleton AE. Genotype to phenotype maps: multiple input abiotic signals combine to produce growth effects via attenuating signaling interactions in maize. G3 (Bethesda) 2013; 3:2195-204. [PMID: 24142926 DOI: 10.1534/g3.113.008573] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The complexity of allele interactions constrains crop improvement and the prediction of disease susceptibility. Additive allele effects are the foundation for selection in animal and plant breeding, and complex genetic and environmental interactions contribute to inefficient detection of desirable loci. Manipulation and modeling of other sources of variation, such as environmental variables, have the potential to improve our prediction of phenotype from genotype. As an example of our approach to analysis of the network linking environmental input to alleles, we mapped the genetic architecture of single and combined abiotic stress responses in two maize mapping populations and compared the observed genetic architecture patterns to simple theoretical predictions. Comparisons of single and combined stress effects on growth and biomass traits exhibit patterns of allele effects that suggest attenuating interactions among physiological signaling steps in drought and ultraviolet radiation stress responses. The presence of attenuating interactions implies that shared QTL found in sets of environments could be used to group environment types and identify underlying environmental similarities, and that patterns of stress-dependent genetic architecture should be studied as a way to prioritize prebreeding populations. A better understanding of whole-plant interactor pathways and genetic architecture of multiple-input environmental signaling has the potential to improve the prediction of genomic value in plant breeding and crop modeling.
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Gong L, Chen W, Gao Y, Liu X, Zhang H, Xu C, Yu S, Zhang Q, Luo J. Genetic analysis of the metabolome exemplified using a rice population. Proc Natl Acad Sci U S A 2013; 110:20320-5. [PMID: 24259710 DOI: 10.1073/pnas.1319681110] [Citation(s) in RCA: 131] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Plant metabolites are crucial for both plant life and human nutrition. Despite recent advance in metabolomics, the genetic control of plant metabolome remains largely unknown. Here, we performed a genetic analysis of the rice metabolome that provided over 2,800 highly resolved metabolic quantitative trait loci for 900 metabolites. Distinct and overlapping accumulation patterns of metabolites were observed and complex genetic regulation of metabolism was revealed in two different tissues. We associated 24 candidate genes to various metabolic quantitative trait loci by data mining, including ones regulating important morphological traits and biological processes. The corresponding pathways were reconstructed by updating in vivo functions of previously identified and newly assigned genes. This study demonstrated a powerful tool and provided a vast amount of high-quality data for understanding the plasticity of plant metabolome, which may help bridge the gap between the genome and phenome.
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31
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Liebe R, Hall RA, Williams RW, Dooley S, Lammert F. Systems genetics of hepatocellular damage in vivo and in vitro: identification of a critical network on chromosome 11 in mouse. Physiol Genomics 2013; 45:931-9. [PMID: 23943854 DOI: 10.1152/physiolgenomics.00078.2013] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Quantitative trait locus (QTL) mapping is a powerful method to find modifier loci that influence disease risk and progression without prior knowledge of underlying genetic mechanisms. The aim of this study is to identify gene loci that contribute to individual differences in liver fibrosis following chronic liver damage. For this purpose, we carried out a mapping study across a panel of 21 BXD recombinant inbred strains using primary hepatocytes challenged with transforming growth factor (TGF)-β for 48 h. We identified a 6 Mb interval on chromosome 11 that is a major modifier of TGF-β-induced hepatocyte injury. Corresponding in vivo genetic analysis of fibrosis after chronic hepatotoxic injury by carbon tetrachloride (CCl4 ip for 6 wk) highlighted the same locus. Expression QTL (eQTL) analysis in liver tissues in the BXD family identified six polymorphisms in this region that are associated with strong cis eQTLs and that correlate well with gene expression in liver after both 6 wk CCl4 treatment and acute ethanol damage of the liver. Within this interval we rank two genes containing coding sequence variants as strong candidates that may modulate the severity of liver fibrosis: 1) the extracellular proteinase inhibitor gene Expi (also known as Wdnm1 or Wfdc18) and 2) musashi RNA-binding protein 2 (Msi2). The powerful combination of experimental, genetics, and bioinformatics methods, as well as combined in vitro and in vivo approaches can be used to define QTLs, genes, and even candidate sequence variants linked to hepatotoxicity and fibrosis.
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Affiliation(s)
- Roman Liebe
- Department of Medicine II, Saarland University Medical Center, Homburg, Germany
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32
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Liang YS, Zhan XD, Wang HM, Gao ZQ, Lin ZC, Chen DB, Shen XH, Cao LY, Cheng SH. Locating QTLs controlling several adult root traits in an elite Chinese hybrid rice. Gene 2013; 526:331-5. [PMID: 23624393 DOI: 10.1016/j.gene.2013.04.010] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2012] [Revised: 04/11/2013] [Accepted: 04/12/2013] [Indexed: 11/29/2022]
Abstract
This study aimed to elucidate the genetics of the adult root system in elite Chinese hybrid rice. Several adult root traits in a recombinant inbred line (RIL) population of Xieyou 9308 and two backcross F1 (BCF1) populations derived from the RILs were phenotyped under hydroponic culture at heading stage for quantitative trait locus (QTL) mapping and other statistical analysis. There a total of eight QTLs detected for the root traits. Among of them, a pleiotropic QTL was repeatedly flanked by RM180 and RM5436 on the short arm of chromosome 7 for multiple traits across RILs and its BCF1 populations, accounting for 6.88% to 25.26% of the phenotypic variances. Only additive/dominant QTLs were detected for the root traits. These results can serve as a foundation for facilitating future cloning and molecular breeding.
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Affiliation(s)
- Yong Shu Liang
- Chinese National Center for Rice Improvement, China National Rice Research Institute, Hangzhou 310006, PR China
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33
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Ding G, Zhao Z, Liao Y, Hu Y, Shi L, Long Y, Xu F. Quantitative trait loci for seed yield and yield-related traits, and their responses to reduced phosphorus supply in Brassica napus. Ann Bot 2012; 109:747-59. [PMID: 22234558 PMCID: PMC3286287 DOI: 10.1093/aob/mcr323] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2011] [Accepted: 12/07/2011] [Indexed: 05/06/2023]
Abstract
BACKGROUND AND AIMS One of the key targets of breeding programmes in rapeseed (Brassica napus) is to develop high-yield varieties. However, the lack of available phosphorus (P) in soils seriously limits rapeseed production. The aim of this study was to dissect the genetic control of seed yield and yield-related traits in B. napus grown with contrasting P supplies. METHODS Two-year field trials were conducted at one site with normal and low P treatments using a population of 124 recombinant inbred lines derived from a cross between 'B104-2' and 'Eyou Changjia'. Seed yield, seed weight, seed number, pod number, plant height, branch number and P efficiency coefficient (PEC) were investigated. Quantitative trait locus (QTL) analysis was performed by composite interval mapping. KEY RESULTS The phenotypic values of most of the tested traits were reduced under the low P conditions. In total, 74 putative QTLs were identified, contributing 7·3-25·4 % of the phenotypic variation. Of these QTLs, 16 (21·6 %) were detected in two seasons and in the mean value of two seasons, and eight QTLs for two traits were conserved across P levels. Low-P-specific QTLs were clustered on chromosomes A1, A6 and A8. By comparative mapping between Arabidopsis and B. napus, 161 orthologues of 146 genes involved in Arabidopsis P homeostasis and/or yield-related trait control were associated with 45 QTLs corresponding to 23 chromosomal regions. Four gene-based markers developed from genes involved in Arabidopsis P homeostasis were mapped to QTL intervals. CONCLUSIONS Different genetic determinants were involved in controlling seed yield and yield-related traits in B. napus under normal and low P conditions. The QTLs detected under reduced P supply may provide useful information for improving the seed yield of B. napus in soils with low P availability in marker-assisted selection.
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Affiliation(s)
- Guangda Ding
- National Key Laboratory of Crop Genetic Improvement
- Microelement Research Centre, Huazhong Agricultural University, Wuhan 430070, China
| | - Zunkang Zhao
- National Key Laboratory of Crop Genetic Improvement
- Microelement Research Centre, Huazhong Agricultural University, Wuhan 430070, China
| | - Yuan Liao
- National Key Laboratory of Crop Genetic Improvement
- Microelement Research Centre, Huazhong Agricultural University, Wuhan 430070, China
| | - Yifan Hu
- National Key Laboratory of Crop Genetic Improvement
- Microelement Research Centre, Huazhong Agricultural University, Wuhan 430070, China
| | - Lei Shi
- National Key Laboratory of Crop Genetic Improvement
- Microelement Research Centre, Huazhong Agricultural University, Wuhan 430070, China
| | - Yan Long
- National Key Laboratory of Crop Genetic Improvement
| | - Fangsen Xu
- National Key Laboratory of Crop Genetic Improvement
- Microelement Research Centre, Huazhong Agricultural University, Wuhan 430070, China
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34
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Ding G, Yang M, Hu Y, Liao Y, Shi L, Xu F, Meng J. Quantitative trait loci affecting seed mineral concentrations in Brassica napus grown with contrasting phosphorus supplies. Ann Bot 2010; 105:1221-34. [PMID: 20237116 PMCID: PMC2887070 DOI: 10.1093/aob/mcq050] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2009] [Revised: 12/14/2010] [Accepted: 02/09/2010] [Indexed: 05/18/2023]
Abstract
BACKGROUND AND AIMS Phosphorus (P) deficiency is one of the major limitations for crop production. A significant relationship exists between plant P uptake from soils and the accumulation of P and other mineral elements in seeds. The aims of this study were to identify and characterize genetic loci (QTLs) controlling the accumulation of mineral elements in seeds of Brassica napus grown with contrasting P availabilities. METHODS A population of 124 recombinant inbred lines derived from a cross between P-inefficient 'B104-2' and P-efficient 'Eyou Changjia' was used for phenotypic investigation and QTL analysis. Two-year field trials were conducted with two P treatments. Concentrations of mineral elements (P, Ca, Mg, Fe, Zn, Cu and Mn) in seeds were determined and QTLs were identified by composite interval mapping. KEY RESULTS There was significant genetic variation in seed concentrations of all mineral elements, and correlations between most elements were observed. A total of 78 putative QTLs (45 under the normal-P conditions and 33 under the low-P conditions) were detected, covering 17 linkage groups and accounting for 7.84-18.1 % of the phenotypic variation. Sixteen of these QTLs were identified in at least two environments, and co-location of QTLs for different mineral traits was found on several linkage groups. By in silico mapping, 21 genes involved in ion homeostasis in Arabidopsis were mapped to the QTL intervals identified in B. napus. CONCLUSIONS The accumulation of mineral elements in seeds is controlled by multiple genes. Common physiological and molecular mechanisms could be involved in the accumulation of several mineral elements, and genes involved in these processes in B. napus are suggested. These results offer insights to the genetic basis of seed mineral accumulation across different P levels in B. napus.
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Affiliation(s)
- Guangda Ding
- National Key Laboratory of Crop Genetic Improvement
- Microelement Research Centre, Huazhong Agricultural University, Wuhan 430070, China
| | - Mei Yang
- National Key Laboratory of Crop Genetic Improvement
- Microelement Research Centre, Huazhong Agricultural University, Wuhan 430070, China
| | - Yifan Hu
- Microelement Research Centre, Huazhong Agricultural University, Wuhan 430070, China
| | - Yuan Liao
- National Key Laboratory of Crop Genetic Improvement
- Microelement Research Centre, Huazhong Agricultural University, Wuhan 430070, China
| | - Lei Shi
- National Key Laboratory of Crop Genetic Improvement
- Microelement Research Centre, Huazhong Agricultural University, Wuhan 430070, China
| | - Fangsen Xu
- National Key Laboratory of Crop Genetic Improvement
- Microelement Research Centre, Huazhong Agricultural University, Wuhan 430070, China
- For correspondence. E-mail
| | - Jinling Meng
- National Key Laboratory of Crop Genetic Improvement
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