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Li S, Zhang C, Lu M, Yang D, Qian Y, Yue Y, Zhang Z, Jin F, Wang M, Liu X, Liu W, Li X. QTL mapping and GWAS for field kernel water content and kernel dehydration rate before physiological maturity in maize. Sci Rep 2020; 10:13114. [PMID: 32753586 PMCID: PMC7403598 DOI: 10.1038/s41598-020-69890-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Accepted: 07/20/2020] [Indexed: 11/09/2022] Open
Abstract
Kernel water content (KWC) and kernel dehydration rate (KDR) are two main factors affecting maize seed quality and have a decisive influence on the mechanical harvest. It is of great importance to map and mine candidate genes related to KWCs and KDRs before physiological maturity in maize. 120 double-haploid (DH) lines constructed from Si287 with low KWC and JiA512 with high KWC were used as the mapping population. KWCs were measured every 5 days from 10 to 40 days after pollination, and KDRs were calculated. A total of 1702 SNP markers were used to construct a linkage map, with a total length of 1,309.02 cM and an average map distance of 0.77 cM. 10 quantitative trait loci (QTLs) and 27 quantitative trait nucleotides (QTNs) were detected by genome-wide composite interval mapping (GCIM) and multi-locus random-SNP-effect mixed linear model (mrMLM), respectively. One and two QTL hotspot regions were found on Chromosome 3 and 7, respectively. Analysis of the Gene Ontology showed that 2 GO terms of biological processes (BP) were significantly enriched (P ≤ 0.05) and 6 candidate genes were obtained. This study provides theoretical support for marker-assisted breeding of mechanical harvest variety in maize.
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Affiliation(s)
- Shufang Li
- Crop Germplasm Resources Institute, Jilin Academy of Agricultural Sciences, Kemaoxi Street 303, Gongzhuling, 136100, Jilin Province, China
| | - Chunxiao Zhang
- Crop Germplasm Resources Institute, Jilin Academy of Agricultural Sciences, Kemaoxi Street 303, Gongzhuling, 136100, Jilin Province, China
| | - Ming Lu
- Maize Research Institute, Jilin Academy of Agricultural Sciences, Gongzhuling, 136100, China
| | - Deguang Yang
- College of Agronomy, Northeast Agricultural University, Harbin, 150030, China
| | - Yiliang Qian
- Maize Research Center, Anhui Academy of Agricultural Science, Hefei, 230001, China
| | - Yaohai Yue
- Maize Research Institute, Jilin Academy of Agricultural Sciences, Gongzhuling, 136100, China
| | - Zhijun Zhang
- Maize Research Institute, Jilin Academy of Agricultural Sciences, Gongzhuling, 136100, China
| | - Fengxue Jin
- Crop Germplasm Resources Institute, Jilin Academy of Agricultural Sciences, Kemaoxi Street 303, Gongzhuling, 136100, Jilin Province, China
| | - Min Wang
- Maize Research Institute, Jilin Academy of Agricultural Sciences, Gongzhuling, 136100, China
| | - Xueyan Liu
- Crop Germplasm Resources Institute, Jilin Academy of Agricultural Sciences, Kemaoxi Street 303, Gongzhuling, 136100, Jilin Province, China
| | - Wenguo Liu
- Maize Research Institute, Jilin Academy of Agricultural Sciences, Gongzhuling, 136100, China.
| | - Xiaohui Li
- Crop Germplasm Resources Institute, Jilin Academy of Agricultural Sciences, Kemaoxi Street 303, Gongzhuling, 136100, Jilin Province, China.
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Zuo JF, Niu Y, Cheng P, Feng JY, Han SF, Zhang YH, Shu G, Wang Y, Zhang YM. Effect of marker segregation distortion on high density linkage map construction and QTL mapping in Soybean (Glycine max L.). Heredity (Edinb) 2019; 123:579-592. [PMID: 31152165 PMCID: PMC6972858 DOI: 10.1038/s41437-019-0238-7] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2019] [Revised: 05/16/2019] [Accepted: 05/17/2019] [Indexed: 02/01/2023] Open
Abstract
Marker segregation distortion is a natural phenomenon. Severely distorted markers are usually excluded in the construction of linkage maps. We investigated the effect of marker segregation distortion on linkage map construction and quantitative trait locus (QTL) mapping. A total of 519 recombinant inbred lines of soybean from orthogonal and reciprocal crosses between LSZZH and NN493-1 were genotyped by specific length amplified fragment markers and seed linoleic acid content was measured in three environments. As a result, twenty linkage groups were constructed with 11,846 markers, including 1513 (12.77%) significantly distorted markers, on 20 chromosomes, and the map length was 2475.86 cM with an average marker-interval of 0.21 cM. The inclusion of distorted markers in the analysis was shown to not only improve the grouping of the markers from the same chromosomes, and the consistency of linkage maps with genome, but also increase genome coverage by markers. Combining genotypic data from both orthogonal and reciprocal crosses decreased the proportion of distorted markers and then improved the quality of linkage maps. Validation of the linkage maps was confirmed by the high collinearity between positions of markers in the soybean reference genome and in linkage maps and by the high consistency of 24 QTL regions in this study compared with the previously reported QTLs and lipid metabolism related genes. Additionally, linkage maps that include distorted markers could add more information to the outputs from QTL mapping. These results provide important information for linkage mapping, gene cloning and marker-assisted selection in soybean.
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Affiliation(s)
- Jian-Fang Zuo
- Crop Information Center, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yuan Niu
- College of Life Sciences and Food Engineering, Huaiyin Institute of Technology, Huaian, 223003, China
| | - Peng Cheng
- Crop Information Center, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Jian-Ying Feng
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
| | - Shi-Feng Han
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
| | - Ying-Hao Zhang
- Crop Information Center, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Guoping Shu
- Center of Molecular Breeding and Biotechnology, Beijing Lantron Seed Corp., Beijing, 100081, China
| | - Yibo Wang
- Center of Molecular Breeding and Biotechnology, Beijing Lantron Seed Corp., Beijing, 100081, China
| | - Yuan-Ming Zhang
- Crop Information Center, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China.
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Chattopadhyay K, Behera L, Bagchi TB, Sardar SS, Moharana N, Patra NR, Chakraborti M, Das A, Marndi BC, Sarkar A, Ngangkham U, Chakraborty K, Bose LK, Sarkar S, Ray S, Sharma S. Detection of stable QTLs for grain protein content in rice (Oryza sativa L.) employing high throughput phenotyping and genotyping platforms. Sci Rep 2019; 9:3196. [PMID: 30824776 PMCID: PMC6397320 DOI: 10.1038/s41598-019-39863-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Accepted: 01/30/2019] [Indexed: 11/10/2022] Open
Abstract
Lack of appropriate donors, non-utilization of high throughput phenotyping and genotyping platforms with high genotype × environment interaction restrained identification of robust QTLs for grain protein content (GPC) in rice. In the present investigation a BC3F4 mapping population was developed using grain protein donor, ARC10075 and high-yielding cultivar Naveen and 190 lines were genotyped using 40 K Affimetrix custom SNP array with the objective to identify stable QTLs for protein content. Three of the identified QTLs, one for GPC (qGPC1.1) and the other two for single grain protein content (qSGPC2.1, qSGPC7.1) were stable over the environments explaining 13%, 14% and 7.8% of the phenotypic variances, respectively. Stability and repeatability of these additive QTLs were supported by the synergistic additive effects of multi-environmental-QTLs. One epistatic-QTL, independent of the main effect QTL was detected over the environment for SGPC. A few functional genes governing seed storage protein were hypothesised inside these identified QTLs. The qGPC1.1 was validated by NIR Spectroscopy-based high throughput phenotyping in BC3F5 population. Higher glutelin content was estimated in high-protein lines with the introgression of qGPC1.1 in telomeric region of short arm of chromosome 1. This was supported by the postulation of probable candidate gene inside this QTL region encoding glutelin family proteins.
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Affiliation(s)
| | | | | | | | | | | | | | - Avijit Das
- ICAR-National Institute of Natural Fibre Engineering and Technology, Kolkata, India
| | | | - Ananta Sarkar
- ICAR- Central Institute for Women in Agriculture, Bhubaneswar, India
| | | | | | | | - Sutapa Sarkar
- ICAR-National Rice Research Institute, Cuttack, India
| | - Soham Ray
- ICAR-Central Research Institute for Jute and Allied Fibres, Barrackpore, India
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Paudel D, Kannan B, Yang X, Harris-Shultz K, Thudi M, Varshney RK, Altpeter F, Wang J. Surveying the genome and constructing a high-density genetic map of napiergrass (Cenchrus purpureus Schumach). Sci Rep 2018; 8:14419. [PMID: 30258215 PMCID: PMC6158254 DOI: 10.1038/s41598-018-32674-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Accepted: 09/13/2018] [Indexed: 01/17/2023] Open
Abstract
Napiergrass (Cenchrus purpureus Schumach) is a tropical forage grass and a promising lignocellulosic biofuel feedstock due to its high biomass yield, persistence, and nutritive value. However, its utilization for breeding has lagged behind other crops due to limited genetic and genomic resources. In this study, next-generation sequencing was first used to survey the genome of napiergrass. Napiergrass sequences displayed high synteny to the pearl millet genome and showed expansions in the pearl millet genome along with genomic rearrangements between the two genomes. An average repeat content of 27.5% was observed in napiergrass including 5,339 simple sequence repeats (SSRs). Furthermore, to construct a high-density genetic map of napiergrass, genotyping-by-sequencing (GBS) was employed in a bi-parental population of 185 F1 hybrids. A total of 512 million high quality reads were generated and 287,093 SNPs were called by using multiple de-novo and reference-based SNP callers. Single dose SNPs were used to construct the first high-density linkage map that resulted in 1,913 SNPs mapped to 14 linkage groups, spanning a length of 1,410 cM and a density of 1 marker per 0.73 cM. This map can be used for many further genetic and genomic studies in napiergrass and related species.
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Affiliation(s)
- Dev Paudel
- Agronomy Department, IFAS, University of Florida, Gainesville, FL, 32611, USA
| | - Baskaran Kannan
- Agronomy Department, IFAS, University of Florida, Gainesville, FL, 32611, USA
| | - Xiping Yang
- Agronomy Department, IFAS, University of Florida, Gainesville, FL, 32611, USA
| | - Karen Harris-Shultz
- Crop Genetics and Breeding Research Unit, USDA-Agricultural Research Service, 115 Coastal Way, Tifton, GA, 31793, USA
| | - Mahendar Thudi
- Center of Excellence in Genomics & Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, 502324, Telangana State, India
| | - Rajeev K Varshney
- Center of Excellence in Genomics & Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, 502324, Telangana State, India
| | - Fredy Altpeter
- Agronomy Department, IFAS, University of Florida, Gainesville, FL, 32611, USA.,Plant Molecular and Cellular Biology Program, Genetic Institute, University of Florida, Gainesville, FL, 32611, USA
| | - Jianping Wang
- Agronomy Department, IFAS, University of Florida, Gainesville, FL, 32611, USA. .,Plant Molecular and Cellular Biology Program, Genetic Institute, University of Florida, Gainesville, FL, 32611, USA. .,Center for Genomics and Biotechnology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Corps, Ministry of Education, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China.
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Wang X, Chen Z, Li Q, Zhang J, Liu S, Duan D. High-density SNP-based QTL mapping and candidate gene screening for yield-related blade length and width in Saccharina japonica (Laminariales, Phaeophyta). Sci Rep 2018; 8:13591. [PMID: 30206320 PMCID: PMC6133921 DOI: 10.1038/s41598-018-32015-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2017] [Accepted: 08/01/2018] [Indexed: 11/09/2022] Open
Abstract
Saccharina japonica is one of the most important marine crops in China, Japan and Korea. Candidate genes associated with blade length and blade width have not yet been reported. Here, based on SLAF-seq, the 7627 resulting SNP loci were selected for genetic linkage mapping to 31 linkage groups with an average spacing of 0.69 cM, and QTL analyses were performed to map the blade length and blade width phenotypes of S. japonica. In total, 12 QTLs contributing to blade length and 10 to width were detected. Some QTL intervals were detected for both blade length and width. Additive alleles for increasing blade length and width in S. japonica came from both parents. After the QTL interval regions were comparatively mapped to the current reference genome of S. japonica (MEHQ00000000), 14 Tic20 (translocon on the inner envelope membrane of chloroplast) genes and three peptidase genes were identified. RT-qPCR analysis showed that the transcription levels of four Tic20 genes were different not only in the two parent sporophytes but also at different cultivation times within one parent. The SNP markers closely associated with blade length and width could be used to improve the selection efficiency of S. japonica breeding.
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Affiliation(s)
- Xiuliang Wang
- Key Lab of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
- Lab for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, 7 Nanhai Road, Qingdao, 266071, China
| | - Zhihang Chen
- Key Lab of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
- Lab for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, China
- University of Chinese Academy of Sciences, Beijing, 100093, China
| | - Qiuying Li
- Key Lab of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
- Lab for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, China
- University of Chinese Academy of Sciences, Beijing, 100093, China
| | - Jie Zhang
- Key Lab of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
- Lab for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, 7 Nanhai Road, Qingdao, 266071, China
| | - Shun Liu
- Key Lab of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
- Lab for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, China
- University of Chinese Academy of Sciences, Beijing, 100093, China
| | - Delin Duan
- Key Lab of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China.
- Lab for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, China.
- Center for Ocean Mega-Science, Chinese Academy of Sciences, 7 Nanhai Road, Qingdao, 266071, China.
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A high-density consensus linkage map of white lupin highlights synteny with narrow-leafed lupin and provides markers tagging key agronomic traits. Sci Rep 2017; 7:15335. [PMID: 29127429 PMCID: PMC5681670 DOI: 10.1038/s41598-017-15625-w] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Accepted: 10/30/2017] [Indexed: 11/15/2022] Open
Abstract
White lupin (Lupinus albus L.) is a valuable source of seed protein, carbohydrates and oil, but requires genetic improvement to attain its agronomic potential. This study aimed to (i) develop a new high-density consensus linkage map based on new, transcriptome-anchored markers; (ii) map four important agronomic traits, namely, vernalization requirement, seed alkaloid content, and resistance to anthracnose and Phomopsis stem blight; and, (iii) define regions of synteny between the L. albus and narrow-leafed lupin (L. angustifolius L.) genomes. Mapping of white lupin quantitative trait loci (QTLs) revealed polygenic control of vernalization responsiveness and anthracnose resistance, as well as a single locus regulating seed alkaloid content. We found high sequence collinearity between white and narrow-leafed lupin genomes. Interestingly, the white lupin QTLs did not correspond to previously mapped narrow-leafed lupin loci conferring vernalization independence, anthracnose resistance, low alkaloids and Phomopsis stem blight resistance, highlighting different genetic control of these traits. Our suite of allele-sequenced and PCR validated markers tagging these QTLs is immediately applicable for marker-assisted selection in white lupin breeding. The consensus map constitutes a platform for synteny-based gene cloning approaches and can support the forthcoming white lupin genome sequencing efforts.
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Zhao J, Han D, Shi K, Wang L, Gao J, Yang R. Influence of epistatic segregation distortion loci on genetic marker linkages in Japanese flounder. Genomics 2017; 110:59-66. [PMID: 28830780 DOI: 10.1016/j.ygeno.2017.08.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2017] [Revised: 08/11/2017] [Accepted: 08/18/2017] [Indexed: 11/28/2022]
Abstract
For genetic linkage analysis of Japanese flounder, 160 doubled haploids (DH) were artificially produced using mitotic gynogenesis and were genotyped for 458 simple sequence repeat (SSR) markers, 101 of which show distortional segregation. The genetic linkage map was constructed by modifying recombination fractions between the distorted markers. Between the corrected and uncorrected genetic maps, there were considerable differences in genetic distance, but not in relative locations among markers. Using a liability model, a segregation distortion locus (SDL), with an additive genetic effect of 1.772, was mapped between markers BDHYP387 and Poli56TUF of chromosome 24 in the corrected genetic map. Additionally, six pairs of epistatic SDLs were identified on chromosomes 1, 5, 8, 9, 23, and 24. Changes in genetic distances between markers did not occur on chromosome regions with main effect SDLs. However, most chromosome regions where genetic distances changed covered the detected epistatic SDLs. This study concluded that epistatic SDLs decrease linkages between markers and lengthen genetic distances in Japanese flounder. This finding has been partially validated in other DH populations derived from three female Japanese flounders.
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Affiliation(s)
- Jingli Zhao
- Key Laboratory of Aquatic Genomics, Ministry of Agriculture, Research Centre for Aquatic Biotechnology, Chinese Academy of Fishery Sciences, Beijing 100141, China
| | - Dandan Han
- Department of Biological Science and Technology, Heilongjiang Vocational College for Nationalities, Harbin 150066, China
| | - Kuntao Shi
- Division of Comprehensive Aquaculture, Shandong Weihai Institute of Ocean and Aquaculture, Weihai 264200, China
| | - Li Wang
- Division of Comprehensive Aquaculture, Shandong Weihai Institute of Ocean and Aquaculture, Weihai 264200, China
| | - Jin Gao
- Key Laboratory of Aquatic Genomics, Ministry of Agriculture, Research Centre for Aquatic Biotechnology, Chinese Academy of Fishery Sciences, Beijing 100141, China
| | - Runqing Yang
- Key Laboratory of Aquatic Genomics, Ministry of Agriculture, Research Centre for Aquatic Biotechnology, Chinese Academy of Fishery Sciences, Beijing 100141, China.
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