1
|
Bejarano DH, Martínez RA, Rocha JF. Genome-wide association study for growth traits in Blanco Orejinegro and Romosinuano cattle. Trop Anim Health Prod 2023; 55:358. [PMID: 37848724 PMCID: PMC10581918 DOI: 10.1007/s11250-023-03743-9] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Accepted: 09/12/2023] [Indexed: 10/19/2023]
Abstract
Growth traits are economically important characteristics for the genetic improvement of local cattle breeds. Genome-wide association studies (GWAS) provide valuable information to enhance the understanding on the genetics of complex traits. The aim of this study was to perform a GWAS to identify genomic regions and genes associated to birth weight, weaning weight adjusted for 240 days, 16 months, and 24 months weight in Romosinuano (ROMO) and Blanco Orejinegro (BON) cattle. A single-step genomic-BLUP was implemented using 596 BON and 569 ROMO individuals that were genotyped with an Illumina BovineSNP50 BeadChip. There were 25 regions of interest identified on different chromosomes, with few of them simultaneously associated with two or more growth traits and some were common to both breeds. The gene mapping allowed to find 173 annotations on these regions, from which 49 represent potential candidate genes with known growth-related functions in cattle and other species. Among the regions that were associated with several growth traits, that at 24 - 27 MB of BTA14, has important candidate genes such as LYPLA1, XKR4, TMEM68 and PLAG1. Another region of interest at 0.40-0.77 Mb of BTA23 was identified in both breeds, containing KHDRBS2 as a potential candidate gene influencing body weight. Future studies targeting these regions could provide more knowledge to uncover the genetic architecture underlying growth traits in BON and ROMO cattle. The genomic regions and genes identified in this study could be used to improve the prediction of genetic merit for growth traits in these creole cattle breeds.
Collapse
Affiliation(s)
- Diego H Bejarano
- Corporación Colombiana de Investigación Agropecuaria -AGROSAVIA. Centro de Investigación Tibaitatá, Km. 14, Mosquera, Cundinamarca, Colombia
| | - Rodrigo A Martínez
- Corporación Colombiana de Investigación Agropecuaria -AGROSAVIA. Centro de Investigación Tibaitatá, Km. 14, Mosquera, Cundinamarca, Colombia
| | - Juan F Rocha
- Corporación Colombiana de Investigación Agropecuaria -AGROSAVIA. Centro de Investigación Tibaitatá, Km. 14, Mosquera, Cundinamarca, Colombia.
| |
Collapse
|
2
|
Zhang T, Keele GR, Gyuricza IG, Vincent M, Brunton C, Bell TA, Hock P, Shaw GD, Munger SC, de Villena FPM, Ferris MT, Paulo JA, Gygi SP, Churchill GA. Multi-omics analysis identifies drivers of protein phosphorylation. Genome Biol 2023; 24:52. [PMID: 36944993 PMCID: PMC10031968 DOI: 10.1186/s13059-023-02892-2] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Accepted: 03/09/2023] [Indexed: 03/23/2023] Open
Abstract
BACKGROUND Phosphorylation of proteins is a key step in the regulation of many cellular processes including activation of enzymes and signaling cascades. The abundance of a phosphorylated peptide (phosphopeptide) is determined by the abundance of its parent protein and the proportion of target sites that are phosphorylated. RESULTS We quantified phosphopeptides, proteins, and transcripts in heart, liver, and kidney tissue samples of mice from 58 strains of the Collaborative Cross strain panel. We mapped ~700 phosphorylation quantitative trait loci (phQTL) across the three tissues and applied genetic mediation analysis to identify causal drivers of phosphorylation. We identified kinases, phosphatases, cytokines, and other factors, including both known and potentially novel interactions between target proteins and genes that regulate site-specific phosphorylation. Our analysis highlights multiple targets of pyruvate dehydrogenase kinase 1 (PDK1), a regulator of mitochondrial function that shows reduced activity in the NZO/HILtJ mouse, a polygenic model of obesity and type 2 diabetes. CONCLUSIONS Together, this integrative multi-omics analysis in genetically diverse CC strains provides a powerful tool to identify regulators of protein phosphorylation. The data generated in this study provides a resource for further exploration.
Collapse
Affiliation(s)
- Tian Zhang
- Harvard Medical School, Boston, MA, 02115, USA
| | | | | | | | | | - Timothy A Bell
- Department of Genetics, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Pablo Hock
- Department of Genetics, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Ginger D Shaw
- Department of Genetics, University of North Carolina, Chapel Hill, NC, 27599, USA
| | | | - Fernando Pardo-Manuel de Villena
- Department of Genetics, University of North Carolina, Chapel Hill, NC, 27599, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Martin T Ferris
- Department of Genetics, University of North Carolina, Chapel Hill, NC, 27599, USA
| | | | | | | |
Collapse
|
3
|
Mohd Sanusi NSN, Rosli R, Chan KL, Halim MAA, Ting NC, Singh R, Low ETL. Integrated consensus genetic map and genomic scaffold re-ordering of oil palm (Elaeis guineensis) genome. Comput Biol Chem 2023; 102:107801. [PMID: 36528019 DOI: 10.1016/j.compbiolchem.2022.107801] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 07/21/2022] [Accepted: 12/05/2022] [Indexed: 12/13/2022]
Abstract
A high-quality reference genome is an important resource that can help decipher the genetic basis of traits in combination with linkage or association analyses. The publicly available oil palm draft genome sequence of AVROS pisifera (EG5) accounts for 1.535 Gb of the 1.8 Gb oil palm genome. However, the assemblies are fragmented, and the earlier assembly only had 43% of the sequences placed on pseudo-chromosomes. By integrating a number of SNP and SSR-based genetic maps, a consensus map (AM_EG5.1), comprising of 828.243 Mb genomic scaffolds anchored to 16 pseudo-chromosomes, was generated. This accounted for 54% of the genome assembly, which is a significant improvement to the original assembly. The total length of N50 scaffolds anchored to the pseudo-chromosomes increased by ∼18% compared to the previous assembly. A total of 139 quantitative trait loci for agronomically important quantitative traits, sourced from literature, were successfully mapped on the new pseudo-chromosomes. The improved assembly could also be used as a reference to identify potential errors in placement of specific markers in the linkage groups of the genetic maps used to assemble the consensus map. The 3422 unique markers from five genetic maps, anchored to the pseudo-chromosomes of AM_EG5.1, are an important resource that can be used preferentially to either construct new maps or fill gaps in existing genetic maps. Synteny analysis further revealed that the AM_EG5.1 had high collinearity with the date palm genome cultivar 'Barhee BC4' and shared most of its segmental duplications. This improved chromosomal-level genome is a valuable resource for genetic research in oil palm.
Collapse
Affiliation(s)
| | - Rozana Rosli
- Malaysian Palm Oil Board, 6 Persiaran Institusi, Bandar Baru Bangi, 43000 Kajang, Selangor, Malaysia
| | - Kuang-Lim Chan
- Malaysian Palm Oil Board, 6 Persiaran Institusi, Bandar Baru Bangi, 43000 Kajang, Selangor, Malaysia
| | - Mohd Amin Ab Halim
- Malaysian Palm Oil Board, 6 Persiaran Institusi, Bandar Baru Bangi, 43000 Kajang, Selangor, Malaysia
| | - Ngoot-Chin Ting
- Malaysian Palm Oil Board, 6 Persiaran Institusi, Bandar Baru Bangi, 43000 Kajang, Selangor, Malaysia
| | - Rajinder Singh
- Malaysian Palm Oil Board, 6 Persiaran Institusi, Bandar Baru Bangi, 43000 Kajang, Selangor, Malaysia
| | - Eng-Ti Leslie Low
- Malaysian Palm Oil Board, 6 Persiaran Institusi, Bandar Baru Bangi, 43000 Kajang, Selangor, Malaysia.
| |
Collapse
|
4
|
Alsaleh A. SSR-based genome-wide association study in turkish durum wheat germplasms revealed novel QTL of accumulated platinum. Mol Biol Rep 2022; 49:11289-11300. [PMID: 35819556 DOI: 10.1007/s11033-022-07720-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [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: 02/25/2022] [Revised: 06/05/2022] [Accepted: 06/14/2022] [Indexed: 11/28/2022]
Abstract
BACKGROUND Durum wheat has a genetic capacity to accumulate toxic metals that can exceed the safety limit of the international standards, which may seriously affect human health. Identifying germplasms with low, nontoxic accumulated metal contents is important to select and develop new varieties. Thus, the objective of this study is to identify the levels of accumulated platinum in durum wheat and detect novel QTL. METHODS AND RESULTS Platinum contents were determined using 130 durum genotypes. Results generally showed low values of accumulated Pt and significantly less than the maximum grain's Pt content determined by international standards. Pt contents among genotypes varied from ≤ 0.001 to 0.72 µg/kg with an average of 0.02. Landraces showed the lowest average accumulated Pt. GWAS was then performed with 780 SSR markers. Five QTL were detected and explained 14.4-23.1% of the total phenotypic variation. Chromosomes 3 A, 3B, and 5B appear to be hotspots and may play a crucial role in accumulated Pt and were harbored in 1, 3, and 1 QTL, respectively. CONCLUSIONS This assessment of accumulated Pt within a unique panel included accessions mostly from Turkish regions, and GWAS used is the first study regarding accumulated Pt indices to reveal novel QTL. It will allow breeders to accelerate their selection of proper genotypes according to desired alleles and offer an opportunity to apply MAS to minimize Pt toxicity in durum wheat. Results indicated that the significance of genome (B) regions are likely related to the inheritance control of Pt content and may play a pivotal role regarding durum wheat's Pt contents. Nonetheless, these novel QTL should be validated in independent populations in numerous environments.
Collapse
Affiliation(s)
- Ahmad Alsaleh
- Department of Agriculture and Food, Institute of Hemp Research, Yozgat Bozok University, 66200, Yozgat, Turkey.
| |
Collapse
|
5
|
Cunicelli M, Olukolu BA, Sams C, Schneider L, West D, Pantalone V. Mapping and identification of QTL in 5601T × U99-310255 RIL population using SNP genotyping: soybean seed quality traits. Mol Biol Rep 2022; 49:6623-6632. [PMID: 35618938 DOI: 10.1007/s11033-022-07505-y] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Accepted: 04/22/2022] [Indexed: 10/18/2022]
Abstract
BACKGROUND Molecular markers have played and will continue to play a major role in the genetic characterization and improvement of soybeans. They have helped identify major loci for tolerance to abiotic stressors, disease resistance, herbicide resistance, soybean seed quality traits, and yield. However, most yield quantitative trait loci (QTL) are specific to a certain population, and the genetic variation found in the specific bi-parental population is not always shared in other populations. A major objective in soybean breeding is to develop high yielding cultivars. Unfortunately, soybean seed yield, as well as protein and oil content, are complex quantitative traits to characterize from the phenotypic and genotypic perspectives. The objectives of this study are to detect soybean genomic regions that increase protein content, while maintaining oil content and seed yield and to successfully identify soybean QTL associated with these seed quality traits. METHODS AND RESULTS To achieve these objectives, data from the 138 recombinant inbred lines grown in six environments were used to perform QTL detection analyses in search of significant genomic regions affecting soybean seed protein, oil, and yield. CONCLUSIONS A total of 21 QTL were successfully identified for yield, protein, oil, methionine, threonine, lodging, maturity, and meal. Knowledge of their locations and flanking markers will aid in marker assisted selection for plant breeders. This will lead to a more valuable soybean for farmers, processors, and animal nutritionists.
Collapse
Affiliation(s)
| | - Bode A Olukolu
- Department of Entomology and Plant Pathology, University of Tennessee, 352 Plant Biotechnology Bldg. 2505 EJ Chapman Dr., Knoxville, TN, 37996, USA
| | - Carl Sams
- Department of Plant Sciences, University of Tennessee, 112 Plant Biotechnology Bldg. 2505 EJ Chapman Dr., Knoxville, TN, 37996, USA
| | - Liesel Schneider
- Department of Animal Sciences, University of Tennessee, 232 Brehm Animal Science Bldg. 2506 River Dr., Knoxville, TN, 37996, USA
| | - Dennis West
- Department of Plant Sciences, University of Tennessee, 112 Plant Biotechnology Bldg. 2505 EJ Chapman Dr., Knoxville, TN, 37996, USA
| | - Vincent Pantalone
- Department of Plant Sciences, University of Tennessee, 112 Plant Biotechnology Bldg. 2505 EJ Chapman Dr., Knoxville, TN, 37996, USA
| |
Collapse
|
6
|
Sun S, Wang Z, Xiang S, Lv M, Zhou K, Li J, Liang P, Li M, Li R, Ling Y, He G, Zhao F. Identification, pyramid, and candidate gene of QTL for yield-related traits based on rice CSSLs in indica Xihui18 background. Mol Breed 2022; 42:19. [PMID: 37309460 PMCID: PMC10248596 DOI: 10.1007/s11032-022-01284-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Accepted: 02/10/2022] [Indexed: 06/14/2023]
Abstract
Chromosome segment substitution line (CSSL) is important for functional analysis and design breeding of target genes. Here, a novel rice CSSL-Z431 was identified from indica restorer line Xihui18 as recipient and japonica Huhan3 as donor. Z431 contained six segments from Huhan3, with average substitution length of 2.12 Mb. Compared with Xihui18, Z431 increased panicle number per plant (PN) and displayed short-wide grains. The short-wide grain of Z431 was caused by decreased length and increased width of glume cell. Then, thirteen QTLs were identified in secondary F2 population from Xihui18/Z431. Again, eleven QTLs (qPL3, qPN3, qGPP12, qSPP12, qGL3, qGW5, qRLW2, qRLW3, qRLW5, qGWT3, qGWT5-2) were validated by six single-segment substitution lines (SSSLs, S1-S6) developed in F3. In addition, fifteen QTLs (qPN5, qGL1, qGL2, qGL5, qGW1, qGW5-1, qRLW1, qRLW5-2, qGWT1, qGWT2, qYD1, qYD2, qYD3, qYD5, qYD12) were detected by these SSSLs, while not be identified in the F2 population. Multiple panicles of Z431 were controlled by qPN3 and qPN5. OsIAGLU should be the candidate gene for qPN3. The short-wide grain of Z431 was controlled by qGL3, qGW5, etc. By DNA sequencing and qRT-PCR analysis, two best candidate genes for qGL3 and qGW5 were identified, respectively. In addition, pyramid of different QTLs in D1-D3 and T1-T2 showed independent inheritance or various epistatic effects. So, it is necessary to understand all genetic effects of target QTLs for designing breeding. Furthermore, these secondary substitution lines improved the deficiencies of Xihui18 to some extent, especially increasing yield per plant in S1, S3, S5, D1-D3, T1, and T2. Supplementary Information The online version contains supplementary material available at 10.1007/s11032-022-01284-x.
Collapse
Affiliation(s)
- Shuangfei Sun
- Rice Research Institute, Academy of Agricultural Science,, Southwest University, Chongqing, 400715 People’s Republic of China
| | - Zongbing Wang
- Rice Research Institute, Academy of Agricultural Science,, Southwest University, Chongqing, 400715 People’s Republic of China
| | - Siqian Xiang
- Rice Research Institute, Academy of Agricultural Science,, Southwest University, Chongqing, 400715 People’s Republic of China
| | - Meng Lv
- Rice Research Institute, Academy of Agricultural Science,, Southwest University, Chongqing, 400715 People’s Republic of China
| | - Kai Zhou
- Rice Research Institute, Academy of Agricultural Science,, Southwest University, Chongqing, 400715 People’s Republic of China
| | - Juan Li
- Rice Research Institute, Academy of Agricultural Science,, Southwest University, Chongqing, 400715 People’s Republic of China
| | - Peixuan Liang
- Rice Research Institute, Academy of Agricultural Science,, Southwest University, Chongqing, 400715 People’s Republic of China
| | - Miaomiao Li
- Rice Research Institute, Academy of Agricultural Science,, Southwest University, Chongqing, 400715 People’s Republic of China
| | - Ruxiang Li
- Rice Research Institute, Academy of Agricultural Science,, Southwest University, Chongqing, 400715 People’s Republic of China
| | - Yinghua Ling
- Rice Research Institute, Academy of Agricultural Science,, Southwest University, Chongqing, 400715 People’s Republic of China
| | - Guanghua He
- Rice Research Institute, Academy of Agricultural Science,, Southwest University, Chongqing, 400715 People’s Republic of China
| | - Fangming Zhao
- Rice Research Institute, Academy of Agricultural Science,, Southwest University, Chongqing, 400715 People’s Republic of China
| |
Collapse
|
7
|
Feng L, Su Q, Yue H, Wang L, Gao J, Xing L, Xu M, Zhou C, Yang Y, Zhou B. TIP41L, a putative candidate gene conferring both seed size and boll weight, was fine-mapped in an introgression line of Gossypium hirsutum-Gossypium arboreum. Plant Sci 2022; 317:111197. [PMID: 35193746 DOI: 10.1016/j.plantsci.2022.111197] [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] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2021] [Revised: 01/12/2022] [Accepted: 01/22/2022] [Indexed: 06/14/2023]
Abstract
QTLs for yield-related traits in tetraploid cotton have been widely mapped, but QTLs introduced from diploid species into tetraploid cotton background remain uninvolved. Here, a stable introgression line with the traits of small boll and seed on Chr. A12, IL197 derived from Gossypium hirsutum (2n = AADD = 52) × Gossypium arboreum (2n = AA = 26), was employed to construct the F2 and F3 secondary populations for fine-mapping QTLs of yield-related traits. QTL analysis showed eight QTLs were detected for three traits, boll weight (BW), seed index (SI, one-hundred-seed weight in g), and lint percentage, with 3.94-28.13 % of the phenotypic variance explained. Of them, a stable major QTL, q(BW + SI)-A12-1 controlling both BW and SI and covering the shortest region in Chr. A12, was further narrowed into a 60.09 kb-interval through substitution mapping. Finally, five candidate genes were detected in the interval. The qRT-PCR analysis revealed only TIP41-like family protein (TIP41L) kept up-regulated expression and significantly lower in TM-1 than that in IL197 from -1 DPA to 15 DPA during cotton boll rapid developmental stage. Therefore, TIP41L gene is speculated as the most likely candidate gene. Comparative analysis with the other four allotetraploid species showed TIP41L gene was probably diverged after the formation of allotetraploid cotton, which may be selected and swept during domestication of modern upland cotton because small boll and seed are detrimental to fibre yield of cotton. This research would lay a solid foundation for further elucidating the molecular mechanism of cotton boll and seed development.
Collapse
Affiliation(s)
- Liuchun Feng
- State Key Laboratory of Crop Genetics & Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, People's Republic of China; Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, 210014, People's Republic of China
| | - Qiao Su
- State Key Laboratory of Crop Genetics & Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, People's Republic of China
| | - Haoran Yue
- State Key Laboratory of Crop Genetics & Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, People's Republic of China
| | - Liang Wang
- State Key Laboratory of Crop Genetics & Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, People's Republic of China
| | - Jianbo Gao
- State Key Laboratory of Crop Genetics & Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, People's Republic of China
| | - Liangshuai Xing
- State Key Laboratory of Crop Genetics & Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, People's Republic of China
| | - Min Xu
- State Key Laboratory of Crop Genetics & Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, People's Republic of China
| | - Chenhui Zhou
- State Key Laboratory of Crop Genetics & Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, People's Republic of China
| | - Ying Yang
- State Key Laboratory of Crop Genetics & Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, People's Republic of China
| | - Baoliang Zhou
- State Key Laboratory of Crop Genetics & Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, People's Republic of China.
| |
Collapse
|
8
|
Fei J, Lu J, Jiang Q, Liu Z, Yao D, Qu J, Liu S, Guan S, Ma Y. Maize plant architecture trait QTL mapping and candidate gene identification based on multiple environments and double populations. BMC Plant Biol 2022; 22:110. [PMID: 35277127 PMCID: PMC8915473 DOI: 10.1186/s12870-022-03470-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Accepted: 02/10/2022] [Indexed: 06/14/2023]
Abstract
BACKGROUND The plant architecture traits of maize determine the yield. Plant height, ear position, leaf angle above the primary ear and internode length above the primary ear together determine the canopy structure and photosynthetic efficiency of maize and at the same time affect lodging and disease resistance. A flat and tall plant architecture confers an obvious advantage in the yield of a single plant but is not conducive to dense planting and results in high rates of lodging; thus, it has been gradually eliminated in production. Although using plants that are too compact, short and density tolerant can increase the yield per unit area to a certain extent, the photosynthetic efficiency of such plants is low, ultimately limiting yield increases. Genetic mapping is an effective method for the improvement of plant architecture to identify candidate genes for regulating plant architecture traits. RESULTS To find the best balance between the yield per plant and the yield per unit area of maize, in this study, the F2:3 pedigree population and a RIL population with the same male parent were used to identify QTL for plant height (PH), ear height (EH), leaf angle and internode length above the primary ear (LAE and ILE) in Changchun and Gongzhuling for 5 consecutive years (2016-2020). A total of 11, 13, 23 and 13 QTL were identified for PH, EH, LAE, and ILE, respectively. A pleiotropic consistent QTL for PH overlapped with that for EH on chromosome 3, with a phenotypic variation explanation rate from 6.809% to 21.96%. In addition, there were major consistent QTL for LAE and ILE, and the maximum phenotypic contribution rates were 24.226% and 30.748%, respectively. Three candidate genes were mined from the three consistent QTL regions and were involved in the gibberellin-activated signal pathway, brassinolide signal transduction pathway and auxin-activated signal pathway, respectively. Analysis of the expression levels of the three genes showed that they were actively expressed during the jointing stage of vigorous maize growth. CONCLUSIONS In this study, three consistent major QTL related to plant type traits were identified and three candidate genes were screened. These results lay a foundation for the cloning of related functional genes and marker-assisted breeding of related functional genes.
Collapse
Affiliation(s)
- Jianbo Fei
- College of Bioscience, Jilin Agricultural University, Changchun, 130118, China
| | - Jianyu Lu
- College of Bioscience, Jilin Agricultural University, Changchun, 130118, China
| | - Qingping Jiang
- College of Bioscience, Jilin Agricultural University, Changchun, 130118, China
| | - Zhibo Liu
- College of Bioscience, Jilin Agricultural University, Changchun, 130118, China
| | - Dan Yao
- College of Bioscience, Jilin Agricultural University, Changchun, 130118, China
| | - Jing Qu
- College of Agriculture, Jilin Agricultural University, Changchun, 130118, China
| | - Siyan Liu
- College of Agriculture, Jilin Agricultural University, Changchun, 130118, China
| | - Shuyan Guan
- College of Agriculture, Jilin Agricultural University, Changchun, 130118, China.
| | - Yiyong Ma
- College of Agriculture, Jilin Agricultural University, Changchun, 130118, China
| |
Collapse
|
9
|
Schilder BM, Navarro E, Raj T. Multi-omic insights into Parkinson's Disease: From genetic associations to functional mechanisms. Neurobiol Dis 2021; 163:105580. [PMID: 34871738 PMCID: PMC10101343 DOI: 10.1016/j.nbd.2021.105580] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 11/17/2021] [Accepted: 12/02/2021] [Indexed: 02/07/2023] Open
Abstract
Genome-Wide Association Studies (GWAS) have elucidated the genetic components of Parkinson's Disease (PD). However, because the vast majority of GWAS association signals fall within non-coding regions, translating these results into an interpretable, mechanistic understanding of the disease etiology remains a major challenge in the field. In this review, we provide an overview of the approaches to prioritize putative causal variants and genes as well as summarise the primary findings of previous studies. We then discuss recent efforts to integrate multi-omics data to identify likely pathogenic cell types and biological pathways implicated in PD pathogenesis. We have compiled full summary statistics of cell-type, tissue, and phentoype enrichment analyses from multiple studies of PD GWAS and provided them in a standardized format as a resource for the research community (https://github.com/RajLabMSSM/PD_omics_review). Finally, we discuss the experimental, computational, and conceptual advances that will be necessary to fully elucidate the effects of functional variants and genes on cellular dysregulation and disease risk.
Collapse
Affiliation(s)
- Brian M Schilder
- Nash Family Department of Neuroscience & Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States; Ronald M. Loeb Center for Alzheimer's disease, Icahn School of Medicine at Mount Sinai, New York, NY, United States; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States; Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, United States; Estelle and Daniel Maggin Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, United States; Department of Brain Sciences, Faculty of Medicine, Imperial College London, London, United Kingdom; UK Dementia Research Institute at Imperial College London, London, United Kingdom.
| | - Elisa Navarro
- Nash Family Department of Neuroscience & Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States; Ronald M. Loeb Center for Alzheimer's disease, Icahn School of Medicine at Mount Sinai, New York, NY, United States; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States; Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, United States; Estelle and Daniel Maggin Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, United States; Sección Departamental de Bioquímica y Biología Molecular, Facultad de Medicina, Universidad Complutense de Madrid, Madrid, Spain
| | - Towfique Raj
- Nash Family Department of Neuroscience & Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States; Ronald M. Loeb Center for Alzheimer's disease, Icahn School of Medicine at Mount Sinai, New York, NY, United States; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States; Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, United States; Estelle and Daniel Maggin Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, United States.
| |
Collapse
|
10
|
Pan Y, Zhu J, Hong Y, Zhang M, Lv C, Guo B, Shen H, Xu X, Xu R. Identification of novel QTL contributing to barley yellow mosaic resistance in wild barley (Hordeum vulgare spp. spontaneum). BMC Plant Biol 2021; 21:560. [PMID: 34823470 PMCID: PMC8613928 DOI: 10.1186/s12870-021-03321-x] [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] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Accepted: 11/08/2021] [Indexed: 05/14/2023]
Abstract
BACKGROUND Barley yellow mosaic disease (BYMD) caused by Barley yellow mosaic virus (BaYMV) and Barley mild mosaic virus (BaMMV) seriously threatens the production of winter barley. Cultivating and promoting varieties that carry disease-resistant genes is one of the most powerful ways to minimize the disease's effect on yield. However, as the BYMD virus mutates rapidly, resistance conferred by the two cloned R genes to the virus had been overcome by new virus strains. There is an urgent need for novel resistance genes in barley that convey sustainable resistance to newly emerging virus strains causing BYMD. RESULTS A doubled haploid (DH) population derived from a cross of SRY01 (BYMD resistant wild barley) and Gairdner (BYMD susceptible barley cultivar) was used to explore for QTL of resistance to BYMD in barley. A total of six quantitative trait loci (qRYM-1H, qRYM-2Ha, qRYM-2Hb, qRYM-3H, qRYM-5H, and qRYM-7H) related to BYMD resistance were detected, which were located on chromosomes 1H, 2H, 3H, 5H, and 7H. Both qRYM-1H and qRYM-2Ha were detected in all environments. qRYM-1H was found to be overlapped with rym7, a known R gene to the disease, whereas qRYM-2Ha is a novel QTL on chromosome 2H originated from SRY01, explaining phenotypic variation from 9.8 to 17.8%. The closely linked InDel markers for qRYM-2Ha were developed which could be used for marker-assisted selection in barley breeding. qRYM-2Hb and qRYM-3H were stable QTL for specific resistance to Yancheng and Yangzhou virus strains, respectively. qRYM-5H and qRYM-7H identified in Yangzhou were originated from Gairdner. CONCLUSIONS Our work is focusing on a virus disease (barley yellow mosaic) of barley. It is the first report on BYMD-resistant QTL from wild barley accessions. One novel major QTL (qRYM-2Ha) for the resistance was detected. The consistently detected new genes will potentially serve as novel sources for achieving pre-breeding barley materials with resistance to BYMD.
Collapse
Affiliation(s)
- Yuhan Pan
- Key Laboratory of Plant Functional Genomics of the Ministry of Education / Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding / Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops / Institutes of Agricultural Science and Technology Development, Yangzhou University, Yangzhou, 225009, Jiangsu, China
| | - Juan Zhu
- Key Laboratory of Plant Functional Genomics of the Ministry of Education / Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding / Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops / Institutes of Agricultural Science and Technology Development, Yangzhou University, Yangzhou, 225009, Jiangsu, China
| | - Yi Hong
- Key Laboratory of Plant Functional Genomics of the Ministry of Education / Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding / Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops / Institutes of Agricultural Science and Technology Development, Yangzhou University, Yangzhou, 225009, Jiangsu, China
| | - Mengna Zhang
- Key Laboratory of Plant Functional Genomics of the Ministry of Education / Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding / Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops / Institutes of Agricultural Science and Technology Development, Yangzhou University, Yangzhou, 225009, Jiangsu, China
| | - Chao Lv
- Key Laboratory of Plant Functional Genomics of the Ministry of Education / Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding / Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops / Institutes of Agricultural Science and Technology Development, Yangzhou University, Yangzhou, 225009, Jiangsu, China
| | - Baojian Guo
- Key Laboratory of Plant Functional Genomics of the Ministry of Education / Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding / Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops / Institutes of Agricultural Science and Technology Development, Yangzhou University, Yangzhou, 225009, Jiangsu, China
| | - Huiquan Shen
- Jiangsu Institute for Seaside Agricultural Sciences and Yancheng Academy of Agricultural Science, Yancheng, 224002, Jiangsu, China
| | - Xiao Xu
- Jiangsu Institute for Seaside Agricultural Sciences and Yancheng Academy of Agricultural Science, Yancheng, 224002, Jiangsu, China
| | - Rugen Xu
- Key Laboratory of Plant Functional Genomics of the Ministry of Education / Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding / Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops / Institutes of Agricultural Science and Technology Development, Yangzhou University, Yangzhou, 225009, Jiangsu, China.
| |
Collapse
|
11
|
Wang J, Mao L, Zeng Z, Yu X, Lian J, Feng J, Yang W, An J, Wu H, Zhang M, Liu L. Genetic mapping high protein content QTL from soybean 'Nanxiadou 25' and candidate gene analysis. BMC Plant Biol 2021; 21:388. [PMID: 34416870 PMCID: PMC8377855 DOI: 10.1186/s12870-021-03176-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [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: 12/25/2020] [Accepted: 08/13/2021] [Indexed: 06/12/2023]
Abstract
BACKGROUND Soybean is a globally important legume crop that provides a primary source of high-quality vegetable protein and oil. Seed protein content (SPC) is a valuable quality trait controlled by multiple genes in soybean. RESULTS In this study, we performed quantitative trait loci (QTL) mapping, QTL-seq, and RNA sequencing (RNA-seq) to reveal the genes controlling protein content in the soybean by using the high protein content variety Nanxiadou 25. A total of 50 QTL for SPC distributed on 14 chromosomes except chromosomes 4, 12, 14, 17, 18, and 19 were identified by QTL mapping using 178 recombinant inbred lines (RILs). Among these QTL, the major QTL qSPC_20-1 and qSPC_20-2 on chromosome 20 were repeatedly detected across six tested environments, corresponding to the location of the major QTL detected using whole-genome sequencing-based QTL-seq. 329 candidate DEGs were obtained within the QTL region of qSPC_20-1 and qSPC_20-2 via gene expression profile analysis. Nine of which were associated with SPC, potentially representing candidate genes. Clone sequencing results showed that different single nucleotide polymorphisms (SNPs) and indels between high and low protein genotypes in Glyma.20G088000 and Glyma.16G066600 may be the cause of changes in this trait. CONCLUSIONS These results provide the basis for research on candidate genes and marker-assisted selection (MAS) in soybean breeding for seed protein content.
Collapse
Affiliation(s)
- Jia Wang
- Nanchong Academy of Agricultural Sciences, Nanchong, 637000, Sichuan, China.
- Southwest University, Chongqing, 400715, China.
| | - Lin Mao
- Southwest University, Chongqing, 400715, China
| | - Zhaoqiong Zeng
- Nanchong Academy of Agricultural Sciences, Nanchong, 637000, Sichuan, China
| | - Xiaobo Yu
- Nanchong Academy of Agricultural Sciences, Nanchong, 637000, Sichuan, China
| | - Jianqiu Lian
- Nanchong Academy of Agricultural Sciences, Nanchong, 637000, Sichuan, China
| | - Jun Feng
- Nanchong Academy of Agricultural Sciences, Nanchong, 637000, Sichuan, China
| | - Wenying Yang
- Nanchong Academy of Agricultural Sciences, Nanchong, 637000, Sichuan, China
| | - Jiangang An
- Nanchong Academy of Agricultural Sciences, Nanchong, 637000, Sichuan, China
| | - Haiying Wu
- Nanchong Academy of Agricultural Sciences, Nanchong, 637000, Sichuan, China
| | - Mingrong Zhang
- Nanchong Academy of Agricultural Sciences, Nanchong, 637000, Sichuan, China.
| | - Liezhao Liu
- Southwest University, Chongqing, 400715, China.
| |
Collapse
|
12
|
Xie H, Hou J, Fu N, Wei M, Li Y, Yu K, Song H, Li S, Liu J. Identification of QTL related to anther color and hull color by RAD sequencing in a RIL population of Setaria italica. BMC Genomics 2021; 22:556. [PMID: 34281524 PMCID: PMC8290542 DOI: 10.1186/s12864-021-07882-x] [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: 04/18/2021] [Accepted: 06/30/2021] [Indexed: 11/13/2022] Open
Abstract
Background Foxtail millet (Setaria italica) is one of the oldest domesticated crops and has been considered as an ideal model plant for C4 grasses. It has abundant type of anther and hull colors which is not only a most intuitive morphological marker for color selection in seed production, but also has very important biological significance for the study of molecular mechanism of regulating the synthesis and metabolism of flavonoids and lignin. However, only a few genetic studies have been reported for anther color and hull color in foxtail millet. Results Quantitative trait loci (QTL) analysis for anther color and hull color was conducted using 400 F6 and F7 recombinant inbreed lines (RILs) derived from a cross between parents Yugu18 and Jigu19. Using restriction-site associated DNA sequencing, 43,001 single-nucleotide polymorphisms (SNPs) and 3,022 indels were identified between both the parents and the RILs. A total of 1,304 bin markers developed from the SNPs and indels were used to construct a genetic map that spanned 2196 cM of the foxtail millet genome with an average of 1.68 cM/bin. Combined with this genetic map and the phenotypic data observed in two locations for two years, two QTL located on chromosome 6 (Chr6) in a 1.215-Mb interval (33,627,819–34,877,940 bp) for anther color (yellow - white) and three QTL located on Chr1 in a 6.23-Mb interval (1–6,229,734 bp) for hull color (gold-reddish brown) were detected. To narrow the QTL regions identified from the genetic map and QTL analysis, we developed a new method named “inconsistent rate analysis” and efficiently narrowed the QTL regions of anther color into a 60-kb interval (34.13–34.19 Mb) in Chr6, and narrowed the QTL regions of hull color into 70-kb (5.43–5.50 Mb) and 30-kb (5.69–5.72 Mb) intervals in Chr1. Two genes (Seita.6G228600.v2.2 and Seita.6G228700.v2.2) and a cinnamyl alcohol dehydrogenase (CAD) gene (Seita.1G057300.v2.2) with amino acid changes between the parents detected by whole-genome resequencing were identified as candidate genes for anther and hull color, respectively. Conclusions This work presents the related QTL and candidate genes of anther and hull color in foxtail millet and developed a new method named inconsistent rate analysis to detect the chromosome fragments linked with the quality trait in RILs. This is the first study of the QTL related to hull color in foxtail millet and clarifying that the CAD gene (Seita.1G057300.v2.2) is the key gene responsible for this trait. It lays the foundation for further cloning of the functional genes and provides a powerful tool to detect the chromosome fragments linked with quality traits in RILs. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07882-x.
Collapse
Affiliation(s)
- Huifang Xie
- Anyang Academy of Agriculture Sciences, 455000, Anyang, Henan, China
| | - Junliang Hou
- BGI Institute of Applied Agriculture, BGI-Shenzhen, 518120, Shenzhen, Guangdong, China
| | - Nan Fu
- Anyang Academy of Agriculture Sciences, 455000, Anyang, Henan, China
| | - Menghan Wei
- Anyang Academy of Agriculture Sciences, 455000, Anyang, Henan, China
| | - Yunfei Li
- BGI Institute of Applied Agriculture, BGI-Shenzhen, 518120, Shenzhen, Guangdong, China
| | - Kang Yu
- BGI Institute of Applied Agriculture, BGI-Shenzhen, 518120, Shenzhen, Guangdong, China
| | - Hui Song
- Anyang Academy of Agriculture Sciences, 455000, Anyang, Henan, China
| | - Shiming Li
- BGI Institute of Applied Agriculture, BGI-Shenzhen, 518120, Shenzhen, Guangdong, China.
| | - Jinrong Liu
- Anyang Academy of Agriculture Sciences, 455000, Anyang, Henan, China.
| |
Collapse
|
13
|
Soto-Cerda BJ, Aravena G, Cloutier S. Genetic dissection of flowering time in flax (Linum usitatissimum L.) through single- and multi-locus genome-wide association studies. Mol Genet Genomics 2021; 296:877-891. [PMID: 33903955 DOI: 10.1007/s00438-021-01785-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Accepted: 04/09/2021] [Indexed: 01/19/2023]
Abstract
In a rapidly changing climate, flowering time (FL) adaptation is important to maximize seed yield in flax (Linum usitatissimum L.). However, our understanding of the genetic mechanism underlying FL in this multipurpose crop remains limited. With the aim of dissecting the genetic architecture of FL in flax, a genome-wide association study (GWAS) was performed on 200 accessions of the flax core collection evaluated in four environments. Two single-locus and six multi-locus models were applied using 70,935 curated single nucleotide polymorphism (SNP) markers. A total of 40 quantitative trait nucleotides (QTNs) associated with 27 quantitative trait loci (QTL) were identified in at least two environments. The number of QTL with positive-effect alleles in accessions was significantly correlated with FL (r = 0.77 to 0.82), indicating principally additive gene actions. Nine QTL were significant in at least three of the four environments accounting for 3.06-14.71% of FL variation. These stable QTL spanned regions that harbored 27 Arabidopsis thaliana and Oryza sativa FL-related orthologous genes including FLOWERING LOCUS T (Lus10013532), FLOWERING LOCUS D (Lus10028817), transcriptional regulator SUPERMAN (Lus10021215), and gibberellin 2-beta-dioxygenase 2 (Lus10037816). In silico gene expression analysis of the 27 FL candidate gene orthologous suggested that they might play roles in the transition from vegetative to reproductive phase, flower development and fertilization. Our results provide new insights into the QTL architecture of flowering time in flax, identify potential candidate genes for further studies, and demonstrate the effectiveness of combining different GWAS models for the genetic dissection of complex traits.
Collapse
Affiliation(s)
- Braulio J Soto-Cerda
- Agriaquaculture Nutritional Genomic Center (CGNA), Las Heras 350, 4781158, Temuco, Chile.
| | - Gabriela Aravena
- Agriaquaculture Nutritional Genomic Center (CGNA), Las Heras 350, 4781158, Temuco, Chile
| | - Sylvie Cloutier
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, 960 Carling Avenue, Ottawa, ON, K1A 0C6, Canada.
| |
Collapse
|
14
|
Yi Q, Álvarez-Iglesias L, Malvar RA, Romay MC, Revilla P. A worldwide maize panel revealed new genetic variation for cold tolerance. Theor Appl Genet 2021; 134:1083-1094. [PMID: 33582854 DOI: 10.1007/s00122-020-03753-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [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: 08/19/2020] [Accepted: 12/12/2020] [Indexed: 05/21/2023]
Abstract
A large association panel of 836 maize inbreds revealed a broader genetic diversity of cold tolerance, as predominantly favorable QTL with small effects were identified, indicating that genomic selection is the most promising option for breeding maize for cold tolerance. Maize (Zea mays L.) has limited cold tolerance, and breeding for cold tolerance is a noteworthy bottleneck for reaching the high potential of maize production in temperate areas. In this study, we evaluate a large panel of 836 maize inbred lines to detect genetic loci and candidate genes for cold tolerance at the germination and seedling stages. Genetic variation for cold tolerance was larger than in previous reports with moderately high heritability for most traits. We identified 187 significant single-nucleotide polymorphisms (SNPs) that were integrated into 159 quantitative trait loci (QTL) for emergence and traits related to early growth. Most of the QTL have small effects and are specific for each environment, with the majority found under control conditions. Favorable alleles are more frequent in 120 inbreds including all germplasm groups, but mainly from Minnesota and Spain. Therefore, there is a large, potentially novel, genetic variability in the germplasm groups represented by these inbred lines. Most of the candidate genes are involved in metabolic processes and intracellular membrane-bounded organelles. We expect that further evaluations of germplasm with broader genetic diversity could identify additional favorable alleles for cold tolerance. However, it is not likely that further studies will find favorable alleles with large effects for improving cold tolerance in maize.
Collapse
Affiliation(s)
- Q Yi
- Misión Biológica de Galicia (CSIC), Apartado 28, E-36080, Pontevedra, Spain
- College of Agriculture, Guizhou University, Guiyang, 550025, China
| | - L Álvarez-Iglesias
- Misión Biológica de Galicia (CSIC), Apartado 28, E-36080, Pontevedra, Spain
| | - R A Malvar
- Misión Biológica de Galicia (CSIC), Apartado 28, E-36080, Pontevedra, Spain
| | - M C Romay
- Institute for Genomic Diversity, Cornell University, Ithaca, NY14853, USA
| | - Pedro Revilla
- Misión Biológica de Galicia (CSIC), Apartado 28, E-36080, Pontevedra, Spain.
| |
Collapse
|
15
|
Chen H, Kumawat G, Yan Y, Fan B, Xu D. Mapping and validation of a major QTL for primary root length of soybean seedlings grown in hydroponic conditions. BMC Genomics 2021; 22:132. [PMID: 33622237 PMCID: PMC7903605 DOI: 10.1186/s12864-021-07445-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [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: 02/08/2021] [Accepted: 02/15/2021] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND The root system provides nutrient absorption and is closely related to abiotic stress tolerance, but it is difficult to study the roots under field conditions. This study was conducted to identify quantitative trait loci (QTL) associated with primary root length (PRL) during soybean seedling growth in hydroponic conditions. A total of 103 F7 recombinant inbred lines (RILs) derived from a cross between K099 (short primary root) and Fendou 16 (long primary root) were used to identify QTL for PRL in soybean. The RIL population was genotyped with 223 simple sequence repeats markers covering 20 chromosomes. Phenotyping for primary root length was performed for 3-weeks plants grown in hydoponic conditions. The identified QTL was validated in near isogenic lines and in a separate RIL population. RESULTS QTL analysis using inclusive composite interval mapping method identified a major QTL on Gm16 between SSR markers Sat_165 and Satt621, explaining 30.25 % of the total phenotypic variation. The identified QTL, qRL16.1, was further confirmed in a segregating population derived from a residual heterozygous line (RHLs-98). To validate qRL16.1 in a different genetic background, QTL analysis was performed in another F6 RIL population derived from a cross between Union (medium primary root) and Fendou 16, in which a major QTL was detected again in the same genomic region as qRL16.1, explaining 14 % of the total phenotypic variation for PRL. In addition, the effect of qRL16.1 was confirmed using two pair of near-isogenic lines (NILs). PRL was significantly higher in NILs possessing the qRL16.1 allele from Fendou 16 compared to allele from K099. CONCLUSIONS The qRL16.1 is a novel QTL for primary root length in soybean which provides important information on the genetic control of root development. Identification of this major QTL will facilitate positional cloning and DNA marker-assisted selection for root traits in soybean.
Collapse
Affiliation(s)
- Huatao Chen
- Japan International Research Center for Agricultural Sciences (JIRCAS), 1-1 Ohwashi, 305-8686, Tsukuba, Ibaraki, Japan
- Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, 210014, Nanjing, P.R. China
| | - Giriraj Kumawat
- Japan International Research Center for Agricultural Sciences (JIRCAS), 1-1 Ohwashi, 305-8686, Tsukuba, Ibaraki, Japan
- ICAR-Indian Institute of Soybean Research, 452001, Indore, Madhya Pradesh, India
| | - Yongliang Yan
- Japan International Research Center for Agricultural Sciences (JIRCAS), 1-1 Ohwashi, 305-8686, Tsukuba, Ibaraki, Japan
- Institute of Crop Germplasm Resources, Xinjiang Academy of Agricultural Sciences, 830000, Urumqi, Xinjiang, P. R. China
| | - Baojie Fan
- Japan International Research Center for Agricultural Sciences (JIRCAS), 1-1 Ohwashi, 305-8686, Tsukuba, Ibaraki, Japan
- Institute of Cereal and Oil Crops, Hebei Academy of Agricultural and Forestry Sciences, 050035, Shijiazhuang, Hebei, P. R. China
| | - Donghe Xu
- Japan International Research Center for Agricultural Sciences (JIRCAS), 1-1 Ohwashi, 305-8686, Tsukuba, Ibaraki, Japan.
| |
Collapse
|
16
|
Diaz S, Ariza-Suarez D, Izquierdo P, Lobaton JD, de la Hoz JF, Acevedo F, Duitama J, Guerrero AF, Cajiao C, Mayor V, Beebe SE, Raatz B. Genetic mapping for agronomic traits in a MAGIC population of common bean (Phaseolus vulgaris L.) under drought conditions. BMC Genomics 2020; 21:799. [PMID: 33198642 PMCID: PMC7670608 DOI: 10.1186/s12864-020-07213-6] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [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: 03/30/2020] [Accepted: 11/05/2020] [Indexed: 01/06/2023] Open
Abstract
BACKGROUND Common bean is an important staple crop in the tropics of Africa, Asia and the Americas. Particularly smallholder farmers rely on bean as a source for calories, protein and micronutrients. Drought is a major production constraint for common bean, a situation that will be aggravated with current climate change scenarios. In this context, new tools designed to understand the genetic basis governing the phenotypic responses to abiotic stress are required to improve transfer of desirable traits into cultivated beans. RESULTS A multiparent advanced generation intercross (MAGIC) population of common bean was generated from eight Mesoamerican breeding lines representing the phenotypic and genotypic diversity of the CIAT Mesoamerican breeding program. This population was assessed under drought conditions in two field trials for yield, 100 seed weight, iron and zinc accumulation, phenology and pod harvest index. Transgressive segregation was observed for most of these traits. Yield was positively correlated with yield components and pod harvest index (PHI), and negative correlations were found with phenology traits and micromineral contents. Founder haplotypes in the population were identified using Genotyping by Sequencing (GBS). No major population structure was observed in the population. Whole Genome Sequencing (WGS) data from the founder lines was used to impute genotyping data for GWAS. Genetic mapping was carried out with two methods, using association mapping with GWAS, and linkage mapping with haplotype-based interval screening. Thirteen high confidence QTL were identified using both methods and several QTL hotspots were found controlling multiple traits. A major QTL hotspot located on chromosome Pv01 for phenology traits and yield was identified. Further hotspots affecting several traits were observed on chromosomes Pv03 and Pv08. A major QTL for seed Fe content was contributed by MIB778, the founder line with highest micromineral accumulation. Based on imputed WGS data, candidate genes are reported for the identified major QTL, and sequence changes were identified that could cause the phenotypic variation. CONCLUSIONS This work demonstrates the importance of this common bean MAGIC population for genetic mapping of agronomic traits, to identify trait associations for molecular breeding tool design and as a new genetic resource for the bean research community.
Collapse
Affiliation(s)
- Santiago Diaz
- Bean Program, Agrobiodiversity Area, International Center for Tropical Agriculture (CIAT), Cali, Colombia
| | - Daniel Ariza-Suarez
- Bean Program, Agrobiodiversity Area, International Center for Tropical Agriculture (CIAT), Cali, Colombia
| | - Paulo Izquierdo
- Bean Program, Agrobiodiversity Area, International Center for Tropical Agriculture (CIAT), Cali, Colombia.,Present Address: Department of Plant Soil and Microbial Sciences, Michigan State University, East Lansing, MI, USA
| | - Juan David Lobaton
- Bean Program, Agrobiodiversity Area, International Center for Tropical Agriculture (CIAT), Cali, Colombia.,Present Address: School of Environmental and Rural Sciences, University of New England, Armidale, SA, Australia
| | - Juan Fernando de la Hoz
- Bean Program, Agrobiodiversity Area, International Center for Tropical Agriculture (CIAT), Cali, Colombia.,Present Address: Bioinformatics Interdepartmental Ph.D. Program, University of California, Los Angeles, Los Angeles, CA, USA
| | - Fernando Acevedo
- Bean Program, Agrobiodiversity Area, International Center for Tropical Agriculture (CIAT), Cali, Colombia.,Departamento de Agronomía, Facultad de Ciencias Agrarias, Universidad Nacional de Colombia, Bogotá, Colombia
| | - Jorge Duitama
- Bean Program, Agrobiodiversity Area, International Center for Tropical Agriculture (CIAT), Cali, Colombia.,Present Address: Systems and Computing Engineering Department, Universidad de los Andes, Bogotá, Colombia
| | - Alberto F Guerrero
- Bean Program, Agrobiodiversity Area, International Center for Tropical Agriculture (CIAT), Cali, Colombia
| | - Cesar Cajiao
- Bean Program, Agrobiodiversity Area, International Center for Tropical Agriculture (CIAT), Cali, Colombia
| | - Victor Mayor
- Bean Program, Agrobiodiversity Area, International Center for Tropical Agriculture (CIAT), Cali, Colombia.,Present Address: Progeny Breeding, Madrid, Colombia
| | - Stephen E Beebe
- Bean Program, Agrobiodiversity Area, International Center for Tropical Agriculture (CIAT), Cali, Colombia
| | - Bodo Raatz
- Bean Program, Agrobiodiversity Area, International Center for Tropical Agriculture (CIAT), Cali, Colombia.
| |
Collapse
|
17
|
Beji S, Fontaine V, Devaux R, Thomas M, Negro SS, Bahrman N, Siol M, Aubert G, Burstin J, Hilbert JL, Delbreil B, Lejeune-Hénaut I. Genome-wide association study identifies favorable SNP alleles and candidate genes for frost tolerance in pea. BMC Genomics 2020; 21:536. [PMID: 32753054 PMCID: PMC7430820 DOI: 10.1186/s12864-020-06928-w] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [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: 08/09/2019] [Accepted: 07/20/2020] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Frost is a limiting abiotic stress for the winter pea crop (Pisum sativum L.) and identifying the genetic determinants of frost tolerance is a major issue to breed varieties for cold northern areas. Quantitative trait loci (QTLs) have previously been detected from bi-parental mapping populations, giving an overview of the genome regions governing this trait. The recent development of high-throughput genotyping tools for pea brings the opportunity to undertake genetic association studies in order to capture a higher allelic diversity within large collections of genetic resources as well as to refine the localization of the causal polymorphisms thanks to the high marker density. In this study, a genome-wide association study (GWAS) was performed using a set of 365 pea accessions. Phenotyping was carried out by scoring frost damages in the field and in controlled conditions. The association mapping collection was also genotyped using an Illumina Infinium® BeadChip, which allowed to collect data for 11,366 single nucleotide polymorphism (SNP) markers. RESULTS GWAS identified 62 SNPs significantly associated with frost tolerance and distributed over six of the seven pea linkage groups (LGs). These results confirmed 3 QTLs that were already mapped in multiple environments on LG III, V and VI with bi-parental populations. They also allowed to identify one locus, on LG II, which has not been detected yet and two loci, on LGs I and VII, which have formerly been detected in only one environment. Fifty candidate genes corresponding to annotated significant SNPs, or SNPs in strong linkage disequilibrium with the formers, were found to underlie the frost damage (FD)-related loci detected by GWAS. Additionally, the analyses allowed to define favorable haplotypes of markers for the FD-related loci and their corresponding accessions within the association mapping collection. CONCLUSIONS This study led to identify FD-related loci as well as corresponding favorable haplotypes of markers and representative pea accessions that might to be used in winter pea breeding programs. Among the candidate genes highlighted at the identified FD-related loci, the results also encourage further attention to the presence of C-repeat Binding Factors (CBF) as potential genetic determinants of the frost tolerance locus on LG VI.
Collapse
Affiliation(s)
- Sana Beji
- BioEcoAgro, INRAE, Univ. Liège, Univ. Lille, Univ. Picardie Jules Verne, 2, Chaussée Brunehaut, F-80203 Estrées-Mons, France
| | - Véronique Fontaine
- BioEcoAgro, INRAE, Univ. Liège, Univ. Lille, Univ. Picardie Jules Verne, 2, Chaussée Brunehaut, F-80203 Estrées-Mons, France
| | | | | | - Sandra Silvia Negro
- GQE - Le Moulon, INRAE, Univ. Paris-Sud, CNRS, AgroParisTech, Univ. Paris-Saclay, F-91190 Gif-sur-Yvette, France
| | - Nasser Bahrman
- BioEcoAgro, INRAE, Univ. Liège, Univ. Lille, Univ. Picardie Jules Verne, 2, Chaussée Brunehaut, F-80203 Estrées-Mons, France
| | - Mathieu Siol
- Agroécologie, AgroSup Dijon, INRAE, Univ. Bourgogne, Univ. Bourgogne Franche-Comté, F-21000 Dijon, France
| | - Grégoire Aubert
- Agroécologie, AgroSup Dijon, INRAE, Univ. Bourgogne, Univ. Bourgogne Franche-Comté, F-21000 Dijon, France
| | - Judith Burstin
- Agroécologie, AgroSup Dijon, INRAE, Univ. Bourgogne, Univ. Bourgogne Franche-Comté, F-21000 Dijon, France
| | - Jean-Louis Hilbert
- BioEcoAgro, INRAE, Univ. Liège, Univ. Lille, Univ. Picardie Jules Verne, 2, Chaussée Brunehaut, F-80203 Estrées-Mons, France
| | - Bruno Delbreil
- BioEcoAgro, INRAE, Univ. Liège, Univ. Lille, Univ. Picardie Jules Verne, 2, Chaussée Brunehaut, F-80203 Estrées-Mons, France
| | - Isabelle Lejeune-Hénaut
- BioEcoAgro, INRAE, Univ. Liège, Univ. Lille, Univ. Picardie Jules Verne, 2, Chaussée Brunehaut, F-80203 Estrées-Mons, France
| |
Collapse
|
18
|
Zhu D, Li X, Wang Z, You C, Nie X, Sun J, Zhang X, Zhang D, Lin Z. Genetic dissection of an allotetraploid interspecific CSSLs guides interspecific genetics and breeding in cotton. BMC Genomics 2020; 21:431. [PMID: 32586283 PMCID: PMC7318736 DOI: 10.1186/s12864-020-06800-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [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: 02/26/2020] [Accepted: 06/02/2020] [Indexed: 01/07/2023] Open
Abstract
Background The low genetic diversity of Upland cotton limits the potential for genetic improvement. Making full use of the genetic resources of Sea-island cotton will facilitate genetic improvement of widely cultivated Upland cotton varieties. The chromosome segments substitution lines (CSSLs) provide an ideal strategy for mapping quantitative trait loci (QTL) in interspecific hybridization. Results In this study, a CSSL population was developed by PCR-based markers assisted selection (MAS), derived from the crossing and backcrossing of Gossypium hirsutum (Gh) and G. barbadense (Gb), firstly. Then, by whole genome re-sequencing, 11,653,661 high-quality single nucleotide polymorphisms (SNPs) were identified which ultimately constructed 1211 recombination chromosome introgression segments from Gb. The sequencing-based physical map provided more accurate introgressions than the PCR-based markers. By exploiting CSSLs with mutant morphological traits, the genes responding for leaf shape and fuzz-less mutation in the Gb were identified. Based on a high-resolution recombination bin map to uncover genetic loci determining the phenotypic variance between Gh and Gb, 64 QTLs were identified for 14 agronomic traits with an interval length of 158 kb to 27 Mb. Surprisingly, multiple alleles of Gb showed extremely high value in enhancing cottonseed oil content (SOC). Conclusions This study provides guidance for studying interspecific inheritance, especially breeding researchers, for future studies using the traditional PCR-based molecular markers and high-throughput re-sequencing technology in the study of CSSLs. Available resources include candidate position for controlling cotton quality and quantitative traits, and excellent breeding materials. Collectively, our results provide insights into the genetic effects of Gb alleles on the Gh, and provide guidance for the utilization of Gb alleles in interspecific breeding.
Collapse
Affiliation(s)
- De Zhu
- National Key Laboratory of Crop Genetic Improvement, College of Plant Sciences & Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Ximei Li
- National Key Laboratory of Crop Genetic Improvement, College of Plant Sciences & Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, China.,Shandong Key Laboratory of Dryland Farming Technology/Shandong Engineering Research Center of Germplasm Innovation and Utilization of Salt-tolerant Crops, College of Agronomy, Qingdao Agricultural University, Qingdao, 266109, Shandong, China
| | - Zhiwei Wang
- National Key Laboratory of Crop Genetic Improvement, College of Plant Sciences & Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, China.,Shandong Peanut Research Institute, Qingdao, 266109, Shangdong, China
| | - Chunyuan You
- Cotton Research Institute, Shihezi Academy of Agriculture Science, Shihezi, Xinjiang, 832003, China
| | - Xinhui Nie
- Key Laboratory of Oasis Ecology Agricultural of Xinjiang Bingtuan, Agricultural College, Shihezi University, Shihezi, Xinjiang, 832003, China
| | - Jie Sun
- Key Laboratory of Oasis Ecology Agricultural of Xinjiang Bingtuan, Agricultural College, Shihezi University, Shihezi, Xinjiang, 832003, China
| | - Xianlong Zhang
- National Key Laboratory of Crop Genetic Improvement, College of Plant Sciences & Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Dawei Zhang
- Institute of Industrial Crops, Xinjiang Academy of Agricultural Sciences, Urumqi, Xinjiang, 830091, China.
| | - Zhongxu Lin
- National Key Laboratory of Crop Genetic Improvement, College of Plant Sciences & Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, China.
| |
Collapse
|
19
|
Fauteux F, Wang Y, Rocheleau H, Liu Z, Pan Y, Fedak G, McCartney C, Ouellet T. Characterization of QTL and eQTL controlling early Fusarium graminearum infection and deoxynivalenol levels in a Wuhan 1 x Nyubai doubled haploid wheat population. BMC Plant Biol 2019; 19:536. [PMID: 31795937 PMCID: PMC6892237 DOI: 10.1186/s12870-019-2149-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [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: 04/05/2019] [Accepted: 11/19/2019] [Indexed: 05/28/2023]
Abstract
BACKGROUND Fusarium head blight (FHB) is a major disease of cereal crops, caused by the fungal pathogen Fusarium graminearum and related species. Breeding wheat for FHB resistance contributes to increase yields and grain quality and to reduce the use of fungicides. The identification of genes and markers for FHB resistance in different wheat genotypes has nevertheless proven challenging. RESULTS In this study, early infection by F. graminearum was analyzed in a doubled haploid population derived from the cross of the moderately resistant wheat genotypes Wuhan 1 and Nyubai. Three quantitative trait loci (QTL) were identified: 1AL was associated with lower deoxynivalenol content, and 4BS and 5A were associated with reduced F. graminearum infection at 2 days post inoculation. Early resistance alleles were inherited from Wuhan 1 for QTL 1AL and 4BS and inherited from Nyubai for the 5A QTL. Cis and trans expression QTL (eQTL) were identified using RNA-seq data from infected head samples. Hotspots for trans eQTL were identified in the vicinity of the 1AL and 4BS QTL peaks. Among differentially expressed genes with cis eQTL within the QTL support intervals, nine genes had higher expression associated with FHB early resistance, and four genes had higher expression associated with FHB early susceptibility. CONCLUSIONS Our analysis of genotype and gene expression data of wheat infected by F. graminearum identified three QTL associated with FHB early resistance, and linked genes with eQTL and differential expression patterns to those QTL. These findings may have applications in breeding wheat for early resistance to FHB.
Collapse
Affiliation(s)
- François Fauteux
- Digital Technologies Research Centre, National Research Council Canada, Ottawa, Ontario Canada
| | - Yunli Wang
- Digital Technologies Research Centre, National Research Council Canada, Ottawa, Ontario Canada
| | - Hélène Rocheleau
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, Ontario Canada
| | - Ziying Liu
- Digital Technologies Research Centre, National Research Council Canada, Ottawa, Ontario Canada
| | - Youlian Pan
- Digital Technologies Research Centre, National Research Council Canada, Ottawa, Ontario Canada
| | - George Fedak
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, Ontario Canada
| | - Curt McCartney
- Morden Research and Development Centre, Agriculture and Agri-Food Canada, Morden, Manitoba Canada
| | - Thérèse Ouellet
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, Ontario Canada
| |
Collapse
|
20
|
Odilbekov F, Armoniené R, Koc A, Svensson J, Chawade A. GWAS-Assisted Genomic Prediction to Predict Resistance to Septoria Tritici Blotch in Nordic Winter Wheat at Seedling Stage. Front Genet 2019; 10:1224. [PMID: 31850073 PMCID: PMC6901976 DOI: 10.3389/fgene.2019.01224] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [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: 06/01/2019] [Accepted: 11/05/2019] [Indexed: 02/01/2023] Open
Abstract
Septoria tritici blotch (STB) disease caused by Zymoseptoria tritici is one of the most damaging diseases of wheat causing significant yield losses worldwide. Identification and employment of resistant germplasm is the most cost-effective method to control STB. In this study, we characterized seedling stage resistance to STB in 175 winter wheat landraces and old cultivars of Nordic origin. The study revealed significant (p < 0.05) phenotypic differences in STB severity in the germplasm. Genome-wide association analysis (GWAS) using five different algorithms identified ten significant markers on five chromosomes. Six markers were localized within a region of 2 cM that contained seven candidate genes on chromosome 1B. Genomic prediction (GP) analysis resulted in a model with an accuracy of 0.47. To further improve the prediction efficiency, significant markers identified by GWAS were included as fixed effects in the GP model. Depending on the number of fixed effect markers, the prediction accuracy improved from 0.47 (without fixed effects) to 0.62 (all non-redundant GWAS markers as fixed effects), respectively. The resistant genotypes and single-nucleotide polymorphism (SNP) markers identified in the present study will serve as a valuable resource for future breeding for STB resistance in wheat. The results also highlight the benefits of integrating GWAS with GP to further improve the accuracy of GP.
Collapse
Affiliation(s)
- Firuz Odilbekov
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Alnarp, Sweden
| | - Rita Armoniené
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Alnarp, Sweden.,Institute of Agriculture, Lithuanian Research Centre for Agriculture and Forestry (LAMMC), Akademija, Lithuania
| | - Alexander Koc
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Alnarp, Sweden
| | | | - Aakash Chawade
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Alnarp, Sweden
| |
Collapse
|
21
|
Jiménez-Galindo JC, Malvar RA, Butrón A, Santiago R, Samayoa LF, Caicedo M, Ordás B. Mapping of resistance to corn borers in a MAGIC population of maize. BMC Plant Biol 2019; 19:431. [PMID: 31623579 PMCID: PMC6796440 DOI: 10.1186/s12870-019-2052-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [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: 09/12/2018] [Accepted: 09/24/2019] [Indexed: 05/05/2023]
Abstract
BACKGROUND Corn borers constitute an important pest of maize around the world; in particular Sesamia nonagrioides Lefèbvre, named Mediterranean corn borer (MCB), causes important losses in Southern Europe. Methods of selection can be combined with transgenic approaches to increase the efficiency and durability of the resistance to corn borers. Previous studies of the genetic factors involved in resistance to MCB have been carried out using bi-parental populations that have low resolution or using association inbred panels that have a low power to detect rare alleles. We developed a Multi-parent Advanced Generation InterCrosses (MAGIC) population to map with high resolution the genetic determinants of resistance to MCB. RESULTS We detected multiple single nucleotide polymorphisms (SNPs) of low effect associated with resistance to stalk tunneling by MCB. We dissected a wide region related to stalk tunneling in multiple studies into three smaller regions (at ~ 150, ~ 155, and ~ 165 Mb in chromosome 6) that closely overlap with regions associated with cell wall composition. We also detected regions associated with kernel resistance and agronomic traits, although the co-localization of significant regions between traits was very low. This indicates that it is possible the concurrent improvement of resistance and agronomic traits. CONCLUSIONS We developed a mapping population which allowed a finer dissection of the genetics of maize resistance to corn borers and a solid nomination of candidate genes based on functional information. The population, given its large variability, was also adequate to map multiple traits and study the relationship between them.
Collapse
Affiliation(s)
- José Cruz Jiménez-Galindo
- Misión Biológica de Galicia, Spanish National Research Council (CSIC), Apartado 28, 36080 Pontevedra, Spain
- National Institute of Forestry, Agriculture and Livestock Research (INIFAP), Ave. Hidalgo 1213, Cd. Cuauhtémoc, 31500 Chihuahua, Mexico
| | - Rosa Ana Malvar
- Misión Biológica de Galicia, Spanish National Research Council (CSIC), Apartado 28, 36080 Pontevedra, Spain
| | - Ana Butrón
- Misión Biológica de Galicia, Spanish National Research Council (CSIC), Apartado 28, 36080 Pontevedra, Spain
| | - Rogelio Santiago
- Departamento Biología Vegetal y Ciencias del Suelo, Unidad Asociada BVE1-UVIGO y MBG (CSIC), Facultad de Biología, Universidad de Vigo, Campus As Lagoas Marcosende, 36310 Vigo, Spain
| | - Luis Fernando Samayoa
- North Carolina State University, 4210 Williams Hall 101, Derieux Place, Raleigh, NC 27695 USA
- Department of Crop and Soil Sciences, North Carolina State University, Raleigh, NC 27695-7620 USA
| | - Marlon Caicedo
- Instituto Nacional de Investigaciones Agropecuarias (INIAP), 170315 Quito, Ecuador
| | - Bernardo Ordás
- Misión Biológica de Galicia, Spanish National Research Council (CSIC), Apartado 28, 36080 Pontevedra, Spain
| |
Collapse
|
22
|
Sannemann W, Lisker A, Maurer A, Léon J, Kazman E, Cöster H, Holzapfel J, Kempf H, Korzun V, Ebmeyer E, Pillen K. Adaptive selection of founder segments and epistatic control of plant height in the MAGIC winter wheat population WM-800. BMC Genomics 2018; 19:559. [PMID: 30064354 PMCID: PMC6069784 DOI: 10.1186/s12864-018-4915-3] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [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: 04/18/2018] [Accepted: 07/02/2018] [Indexed: 01/15/2023] Open
Abstract
BACKGROUND Multi-parent advanced generation intercross (MAGIC) populations are a newly established tool to dissect quantitative traits. We developed the high resolution MAGIC wheat population WM-800, consisting of 910 F4:6 lines derived from intercrossing eight recently released European winter wheat cultivars. RESULTS Genotyping WM-800 with 7849 SNPs revealed a low mean genetic similarity of 59.7% between MAGIC lines. WM-800 harbours distinct genomic regions exposed to segregation distortion. These are mainly located on chromosomes 2 to 6 of the wheat B genome where founder specific DNA segments were positively or negatively selected. This suggests adaptive selection of individual founder alleles during population development. The application of a genome-wide association study identified 14 quantitative trait loci (QTL) controlling plant height in WM-800, including the known semi-dwarf genes Rht-B1 and Rht-D1 and a potentially novel QTL on chromosome 5A. Additionally, epistatic effects controlled plant height. For example, two loci on chromosomes 2B and 7B gave rise to an additive epistatic effect of 13.7 cm. CONCLUSION The present study demonstrates that plant height in the MAGIC-WHEAT population WM-800 is mainly determined by large-effect QTL and di-genic epistatic interactions. As a proof of concept, our study confirms that WM-800 is a valuable tool to dissect the genetic architecture of important agronomic traits.
Collapse
Affiliation(s)
- Wiebke Sannemann
- Chair of Plant Breeding, Martin Luther University Halle-Wittenberg, Betty-Heimann Straße 3, 06120 Halle, Germany
| | - Antonia Lisker
- Chair of Plant Breeding, Martin Luther University Halle-Wittenberg, Betty-Heimann Straße 3, 06120 Halle, Germany
| | - Andreas Maurer
- Chair of Plant Breeding, Martin Luther University Halle-Wittenberg, Betty-Heimann Straße 3, 06120 Halle, Germany
| | - Jens Léon
- Institute of Crop Science and Resource Conservation, Crop Genetics and Biotechnology Unit, University of Bonn, Katzenburgweg 5, Bonn, Germany
| | - Ebrahim Kazman
- Syngenta Seeds GmbH, Kroppenstedter Straße 4, 39387 Oschersleben (Bode), Hadmersleben, Germany
| | - Hilmar Cöster
- RAGT 2n, Steinesche 5A, 38855 - Silstedt, Wernigerode, Germany
| | - Josef Holzapfel
- Secobra Saatzucht GmbH, Feldkirchen 3, 85368 Moosburg an der Isar, Germany
| | - Hubert Kempf
- Secobra Saatzucht GmbH, Feldkirchen 3, 85368 Moosburg an der Isar, Germany
| | - Viktor Korzun
- KWS SAAT SE, Grimsehlstraße 31, 37555 Einbeck, Germany
| | - Erhard Ebmeyer
- KWS LOCHOW GMBH, Ferdinand-Lochow-Straße 5, 29303 Bergen/Wohlde, Germany
| | - Klaus Pillen
- Chair of Plant Breeding, Martin Luther University Halle-Wittenberg, Betty-Heimann Straße 3, 06120 Halle, Germany
| |
Collapse
|
23
|
Zhao Z, Tseng YC, Peng Z, Lopez Y, Chen CY, Tillman BL, Dang P, Wang J. Refining a major QTL controlling spotted wilt disease resistance in cultivated peanut (Arachis hypogaea L.) and evaluating its contribution to the resistance variations in peanut germplasm. BMC Genet 2018; 19:17. [PMID: 29571286 PMCID: PMC5865372 DOI: 10.1186/s12863-018-0601-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [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: 09/08/2017] [Accepted: 03/09/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Spotted wilt, caused by tomato spotted wilt virus (TSWV), has been one of major diseases in cultivated peanut grown in the southeastern United States (US) since 1990. Previously a major quantitative trait locus (QTL) controlling spotted wilt disease resistance was mapped to an interval of 2.55 cM genetic distance corresponding to a physical distance of 14.4 Mb on chromosome A01 of peanut by using a segregating F2 population. The current study focuses on refining this major QTL region and evaluating its contributions in the US peanut mini-core germplasm. RESULTS Two simple sequence repeat (SSR) markers associated with the major QTL were used to genotype F5 individuals, and 25 heterozygous individuals were selected and developed into an F6 segregating population. Based on visual evaluation in the field, a total of 194 susceptible F6 individuals were selected and planted into F7 generation for phenotyping. Nine SSR markers were used to genotype the 194 F6 individuals, and QTL analysis revealed that a confidence interval of 15.2 Mb region had the QTL with 22.8% phenotypic variation explained (PVE). This QTL interval was further genotyped using the Amplicon-seq method. A total of 81 non-redundant single nucleotide polymorphism (SNP) and eight InDel markers were detected. No recombinant was detected among the F6 individuals. Two InDel markers were integrated into the linkage group and helped to refine the confidence interval of this QTL into a 0.8 Mb region. To test the QTL contributes to the resistance variance in US peanut mini-core germplasm, two flanking SSR markers were used to genotype 107 mini-core germplasm accessions. No statistically significant association was observed between the genotype at the QTL region and spotted wilt resistance in the mini-core germplasm, which indicated that the resistance allelic region at this QTL didn't contribute to the resistance variance in the US peanut mini-core germplasm, thus was a unique resistance source. CONCLUSION A major QTL related to spotted wilt disease resistance in peanut was refined to a 0.8 Mb region on A01 chromosome, which didn't relate to spotted wilt disease resistance in the US peanut mini-core germplasm and might be a unique genetic source.
Collapse
Affiliation(s)
- Zifan Zhao
- Agronomy Department, University of Florida, Gainesville, FL, 32610, USA
| | - Yu-Chien Tseng
- Agronomy Department, University of Florida, Gainesville, FL, 32610, USA.,North Florida Research and Education Center, University of Florida, Marianna, FL, 32446, USA
| | - Ze Peng
- Agronomy Department, University of Florida, Gainesville, FL, 32610, USA
| | - Yolanda Lopez
- Agronomy Department, University of Florida, Gainesville, FL, 32610, USA
| | - Charles Y Chen
- Department of Crop, Soil and Environmental Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Barry L Tillman
- Agronomy Department, University of Florida, Gainesville, FL, 32610, USA.,North Florida Research and Education Center, University of Florida, Marianna, FL, 32446, USA
| | - Phat Dang
- USDA-ARS National Peanut Research Laboratory, Dawson, GA, 39842, USA
| | - Jianping Wang
- Agronomy Department, University of Florida, Gainesville, FL, 32610, USA. .,Center for Genomics and Biotechnology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education; Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China.
| |
Collapse
|
24
|
Sivasakthi K, Thudi M, Tharanya M, Kale SM, Kholová J, Halime MH, Jaganathan D, Baddam R, Thirunalasundari T, Gaur PM, Varshney RK, Vadez V. Plant vigour QTLs co-map with an earlier reported QTL hotspot for drought tolerance while water saving QTLs map in other regions of the chickpea genome. BMC Plant Biol 2018; 18:29. [PMID: 29409451 PMCID: PMC5801699 DOI: 10.1186/s12870-018-1245-1] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [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: 07/13/2017] [Accepted: 01/21/2018] [Indexed: 05/20/2023]
Abstract
BACKGROUND Terminal drought stress leads to substantial annual yield losses in chickpea (Cicer arietinum L.). Adaptation to water limitation is a matter of matching water supply to water demand by the crop. Therefore, harnessing the genetics of traits contributing to plant water use, i.e. transpiration rate and canopy development dynamics, is important to design crop ideotypes suited to a varying range of water limited environments. With an aim of identifying genomic regions for plant vigour (growth and canopy size) and canopy conductance traits, 232 recombinant inbred lines derived from a cross between ICC 4958 and ICC 1882, were phenotyped at vegetative stage under well-watered conditions using a high throughput phenotyping platform (LeasyScan). RESULTS Twenty one major quantitative trait loci (M-QTLs) were identified for plant vigour and canopy conductance traits using an ultra-high density bin map. Plant vigour traits had 13 M-QTLs on CaLG04, with favourable alleles from high vigour parent ICC 4958. Most of them co-mapped with a previously fine mapped major drought tolerance "QTL-hotspot" region on CaLG04. One M-QTL was found for canopy conductance on CaLG03 with the ultra-high density bin map. Comparative analysis of the QTLs found across different density genetic maps revealed that QTL size reduced considerably and % of phenotypic variation increased as marker density increased. CONCLUSION Earlier reported drought tolerance hotspot is a vigour locus. The fact that canopy conductance traits, i.e. the other important determinant of plant water use, mapped on CaLG03 provides an opportunity to manipulate these loci to tailor recombinants having low/high transpiration rate and plant vigour, fitted to specific drought stress scenarios in chickpea.
Collapse
Affiliation(s)
- Kaliamoorthy Sivasakthi
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Greater Hyderabad, Telangana, India
- Bharathidasan University, Tiruchirappalli, Tamil Nadu India
| | - Mahendar Thudi
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Greater Hyderabad, Telangana, India
| | - Murugesan Tharanya
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Greater Hyderabad, Telangana, India
- Bharathidasan University, Tiruchirappalli, Tamil Nadu India
| | - Sandip M. Kale
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Greater Hyderabad, Telangana, India
| | - Jana Kholová
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Greater Hyderabad, Telangana, India
| | - Mahamat Hissene Halime
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Greater Hyderabad, Telangana, India
| | - Deepa Jaganathan
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Greater Hyderabad, Telangana, India
| | - Rekha Baddam
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Greater Hyderabad, Telangana, India
| | | | - Pooran M. Gaur
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Greater Hyderabad, Telangana, India
| | - Rajeev K. Varshney
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Greater Hyderabad, Telangana, India
| | - Vincent Vadez
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Greater Hyderabad, Telangana, India
- Institut de Recherche pour le Developpement (IRD), Université de Montpellier – UMR DIADE, 911 Avenue Agropolis, BP 64501, 34394 Montpellier cedex 5, France
| |
Collapse
|
25
|
Chaipanya C, Telebanco-Yanoria MJ, Quime B, Longya A, Korinsak S, Korinsak S, Toojinda T, Vanavichit A, Jantasuriyarat C, Zhou B. Dissection of broad-spectrum resistance of the Thai rice variety Jao Hom Nin conferred by two resistance genes against rice blast. Rice (N Y) 2017; 10:18. [PMID: 28493203 PMCID: PMC5425360 DOI: 10.1186/s12284-017-0159-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2016] [Accepted: 05/04/2017] [Indexed: 05/19/2023]
Abstract
BACKGROUND Rice (Oryza sativa) is one of the most important food crops in the world. Rice blast, caused by the fungal pathogen Magnaporthe oryzae, is one of the most destructive rice diseases worldwide. To effectively cope with this problem, the use of rice blast resistance varieties through innovative breeding programs is the best strategy to date. The Thai rice variety Jao Hom Nin (JHN) showed broad-spectrum resistance against Thai rice blast isolates. Two QTLs for blast resistance in JHN were reported on chromosome 1 (QTL1) and 11 (QTL11). RESULTS Monogenic lines of QTL1 (QTL1-C) and QTL11 (QTL11-C) in the CO39 genetic background were generated. Cluster analysis based on the disease reaction pattern of QTL1-C and QTL11-C, together with IRBLs, showed that those two monogenic lines were clustered with IRBLsh-S (Pish) and IRBL7-M (Pi7), respectively. Moreover, sequence analysis revealed that Pish and Pi7 were embedded within the QTL1 and QTL11 delimited genomic intervals, respectively. This study thus concluded that QTL1 and QTL11 could encode alleles of Pish and Pi7, designated as Pish-J and Pi7-J, respectively. To validate this hypothesis, the genomic regions of Pish-J and Pi7-J were cloned and sequenced. Protein sequence comparison revealed that Pish-J and Pi7-J were identical to Pish and Pi7, respectively. The holistic disease spectrum of JHN was found to be exactly attributed to the additive ones of both QTL1-C and QTL11-C. CONCLUSION JHN showed broad spectrum resistance against Thai and Philippine rice blast isolates. As this study demonstrated, the combination of two resistance genes, Pish-J and Pi7-J, in JHN, with each controlling broad-spectrum resistance to rice blast disease, explains the high level of resistance. Thus, the combination of Pish and Pi7 can provide a practical scheme for breeding durable resistance in rice against rice blast disease.
Collapse
Affiliation(s)
- Chaivarakun Chaipanya
- Department of Genetics, Faculty of Science, Kasetsart University, Chatuchak, Bangkok, 10900, Thailand
- Genetics and Biotechnology Division, International Rice Research Institute, Los Baños, Laguna, 4031, Philippines
| | | | - Berlaine Quime
- Genetics and Biotechnology Division, International Rice Research Institute, Los Baños, Laguna, 4031, Philippines
| | - Apinya Longya
- Department of Genetics, Faculty of Science, Kasetsart University, Chatuchak, Bangkok, 10900, Thailand
| | - Siripar Korinsak
- Rice Gene Discovery Laboratory, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, Pathum Thani, 12120, Thailand
| | - Siriporn Korinsak
- Rice Gene Discovery Laboratory, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, Pathum Thani, 12120, Thailand
| | - Theerayut Toojinda
- Plant Biotechnology Research Unit, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, Pathum Thani, 12120, Thailand
| | - Apichart Vanavichit
- Rice Science Center, Kasetsart University, Kamphaeng Saen, Nakhon Pathom, 73140, Thailand
- Agronomy Department Faculty of Agriculture at Kamphaeng Saen, Kasetsart University, Nakhon Pathom, 73140, Thailand
| | - Chatchawan Jantasuriyarat
- Department of Genetics, Faculty of Science, Kasetsart University, Chatuchak, Bangkok, 10900, Thailand.
- Center for Advanced Studies in Tropical Natural Resources, National Research University-Kasetsart University (CASNAR, NRU-KU), Chatuchak, Bangkok, 10900, Thailand.
| | - Bo Zhou
- Genetics and Biotechnology Division, International Rice Research Institute, Los Baños, Laguna, 4031, Philippines.
| |
Collapse
|
26
|
Bdeir R, Muchero W, Yordanov Y, Tuskan GA, Busov V, Gailing O. Quantitative trait locus mapping of Populus bark features and stem diameter. BMC Plant Biol 2017; 17:224. [PMID: 29179673 PMCID: PMC5704590 DOI: 10.1186/s12870-017-1166-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [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: 05/29/2017] [Accepted: 11/10/2017] [Indexed: 05/08/2023]
Abstract
BACKGROUND Bark plays important roles in photosynthate transport and storage, along with physical and chemical protection. Bark texture varies extensively among species, from smooth to fissured to deeply furrowed, but its genetic control is unknown. This study sought to determine the main genomic regions associated with natural variation in bark features and stem diameter. Quantitative trait loci (QTL) were mapped using an interspecific pseudo-backcross pedigree (Populus trichocarpa x P. deltoides and P. deltoides) for bark texture, bark thickness and diameter collected across three years, two sites and three biological replicates per site. RESULTS QTL specific to bark texture were highly reproducible in shared intervals across sites, years and replicates. Significant positive correlations and co-localization between trait QTL suggest pleiotropic regulators or closely linked genes. A list of candidate genes with related putative function, location close to QTL maxima and with the highest expression level in the phloem, xylem and cambium was identified. CONCLUSION Candidate genes for bark texture included an ortholog of Arabidopsis ANAC104 (PopNAC128), which plays a role in lignified fiber cell and ray development, as well as Pinin and Fasciclin (PopFLA) genes with a role in cell adhesion, cell shape and migration. The results presented in this study provide a basis for future genomic characterization of genes found within the QTL for bark texture, bark thickness and diameter in order to better understand stem and bark development in Populus and other woody perennial plants. The QTL mapping approach identified a list of prime candidate genes for further validation using functional genomics or forward genetics approaches.
Collapse
Affiliation(s)
- Roba Bdeir
- School of Forest Resources and Environmental Science, Michigan Technological University, 1400 Townsend Drive, Houghton, MI 49931 USA
| | - Wellington Muchero
- Biosciences Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 37831 USA
| | - Yordan Yordanov
- Departement of Biology, Eastern Illinois University, 600 Lincoln Ave, Charleston, IL 61920 USA
| | - Gerald A. Tuskan
- Biosciences Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 37831 USA
| | - Victor Busov
- School of Forest Resources and Environmental Science, Michigan Technological University, 1400 Townsend Drive, Houghton, MI 49931 USA
| | - Oliver Gailing
- School of Forest Resources and Environmental Science, Michigan Technological University, 1400 Townsend Drive, Houghton, MI 49931 USA
- Present address: Forest Genetics and Forest Tree Breeding, Faculty of Forest Sciences, University of Göttingen, Büsgenweg 2, 37077 Göttingen, Germany
| |
Collapse
|
27
|
Wang Q, Sun G, Ren X, Wang J, Du B, Li C, Sun D. Detection of QTLs for seedling characteristics in barley (Hordeum vulgare L.) grown under hydroponic culture condition. BMC Genet 2017; 18:94. [PMID: 29115942 PMCID: PMC5678765 DOI: 10.1186/s12863-017-0562-y] [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] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Accepted: 10/30/2017] [Indexed: 01/15/2023] Open
Abstract
BACKGROUND Seedling characteristics play significant roles in the growth and development of barley (Hordeum vulgare L.), including stable stand establishment, water and nutrients uptake, biotic resistance and abiotic stresses, and can influence yield and quality. However, the genetic mechanisms underlying seedling characteristics in barley are largely unknown and little research has been done. In the present work, 21 seedling-related characteristics are assessed in a barley double haploid (DH) population, grown under hydroponic conditions. Of them, leaf age (LAG), shoot height (SH), maximum root length (MRL), main root number (MRN) and seedling fresh weight (SFW) were investigated at the 13th, 20th, 27th, and 34th day after germination. The objectives were to identify quantitative trait loci (QTLs) underlying these seedling characteristics using a high-density linkage map and to reveal the QTL expression pattern by comparing the QTLs among four different seedling growth stages. RESULTS A total of 70 QTLs were distributed over all chromosomes except 4H, and, individually, accounted for 5.01%-77.78% of phenotypic variation. Out of the 70 detected QTLs, 23 showed a major effect on 14 seedling-related characteristics. Ten co-localized chromosomal regions on 2H (five regions), 3H (two regions) and 7H (three regions) involved 39 QTLs (55.71%), each simultaneously influenced more than one trait. Meanwhile, 9 co-localized genomic regions involving 22 QTLs for five seedling characteristics (LAG, SH, MRL, MRN and SFW) at the 13th, 20th, 27th and 34th day-old seedling were common for two or more growth stages of seedling. QTL in the vicinity of Vrs1 locus on chromosome 2H with the favorable alleles from Huadamai 6 was found to have the largest main effects on multiple seedling-related traits. CONCLUSIONS Six QTL cluster regions associated with 16 seedling-related characteristics were observed on chromosome 2H, 3H and 7H. The majority of the 29 regions identified for five seedling characteristics were selectively expressed at different developmental stages. The genetic effects of 9 consecutive expression regions displayed different developmental influences at different developmental stages. These findings enhanced our understanding of a genetic basis underlying seedling characteristics in barley. Some QTLs detected here could be used for marker-assisted selection (MAS) in barley breeding.
Collapse
Affiliation(s)
- Qifei Wang
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070 China
| | - Genlou Sun
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070 China
- Biology Department, Saint Mary’s University, 923 Robie Street, Halifax, NS B3H 3C3 Canada
| | - Xifeng Ren
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070 China
| | - Jibin Wang
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070 China
| | - Binbin Du
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070 China
| | - Chengdao Li
- Department of Agriculture & Food/Agricultural Research Western Australia, 3 Baron-Hay Court, South Perth, WA 6155 Australia
| | - Dongfa Sun
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070 China
- Hubei Collaborative Innovation Center for Grain Industry, Jingzhou, Hubei 434025 China
| |
Collapse
|
28
|
Li X, Wu M, Liu G, Pei W, Zhai H, Yu J, Zhang J, Yu S. Identification of candidate genes for fiber length quantitative trait loci through RNA-Seq and linkage and physical mapping in cotton. BMC Genomics 2017; 18:427. [PMID: 28569138 DOI: 10.1186/s12864-017-3812-5] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2016] [Accepted: 05/23/2017] [Indexed: 01/17/2023] Open
Abstract
BACKGROUND Cotton (Gossypium spp.) fibers are single-celled elongated trichomes, the molecular aspects of genetic variation in fiber length (FL) among genotypes are currently unknown. In this study, two backcross inbred lines (BILs), i.e., NMGA-062 ("Long") and NMGA-105 ("Short") with 32.1 vs. 27.2 mm in FL, respectively, were chosen to perform RNA-Seq on developing fibers at 10 days post anthesis (DPA). The two BILs differed in 4 quantitative trait loci (QTL) for FL and were developed from backcrosses between G. hirsutum as the recurrent parent and G. barbadense. RESULTS In total, 51.7 and 54.3 million reads were obtained and assembled to 49,508 and 49,448 transcripts in the two genotypes, respectively. Of 1551 differentially expressed genes (DEGs) between the two BILs, 678 were up-regulated and 873 down-regulated in "Long"; and 703 SNPs were identified in 339 DEGs. Further physical mapping showed that 8 DEGs were co-localized with the 4 FL QTL identified in the BIL population containing the two BILs. Four SNP markers in 3 DEGs that showed significant correlations with FL were developed. Among the three candidate genes encoding for proline-rich protein, D-cysteine desulfhydrase, and thaumatin-like protein, a SNP of thaumatin-like protein gene showed consistent correlations with FL across all testing environments. CONCLUSIONS This study represents one of the first investigations of positional candidate gene approach of QTL in cotton in integrating transcriptome and SNP identification based on RNA-Seq with linkage and physical mapping of QTL and genes, which will facilitate eventual cloning and identification of genes responsible for FL QTL. The candidate genes may serve as the foundation for further in-depth studies of the molecular mechanism of natural variation in fiber elongation.
Collapse
|
29
|
van der Weijde T, Kamei CLA, Severing EI, Torres AF, Gomez LD, Dolstra O, Maliepaard CA, McQueen-Mason SJ, Visser RGF, Trindade LM. Genetic complexity of miscanthus cell wall composition and biomass quality for biofuels. BMC Genomics 2017; 18:406. [PMID: 28545405 PMCID: PMC5445440 DOI: 10.1186/s12864-017-3802-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [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: 02/01/2017] [Accepted: 05/17/2017] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND Miscanthus sinensis is a high yielding perennial grass species with great potential as a bioenergy feedstock. One of the challenges that currently impedes commercial cellulosic biofuel production is the technical difficulty to efficiently convert lignocellulosic biomass into biofuel. The development of feedstocks with better biomass quality will improve conversion efficiency and the sustainability of the value-chain. Progress in the genetic improvement of biomass quality may be substantially expedited by the development of genetic markers associated to quality traits, which can be used in a marker-assisted selection program. RESULTS To this end, a mapping population was developed by crossing two parents of contrasting cell wall composition. The performance of 182 F1 offspring individuals along with the parents was evaluated in a field trial with a randomized block design with three replicates. Plants were phenotyped for cell wall composition and conversion efficiency characters in the second and third growth season after establishment. A new SNP-based genetic map for M. sinensis was built using a genotyping-by-sequencing (GBS) approach, which resulted in 464 short-sequence uniparental markers that formed 16 linkage groups in the male map and 17 linkage groups in the female map. A total of 86 QTLs for a variety of biomass quality characteristics were identified, 20 of which were detected in both growth seasons. Twenty QTLs were directly associated to different conversion efficiency characters. Marker sequences were aligned to the sorghum reference genome to facilitate cross-species comparisons. Analyses revealed that for some traits previously identified QTLs in sorghum occurred in homologous regions on the same chromosome. CONCLUSION In this work we report for the first time the genetic mapping of cell wall composition and bioconversion traits in the bioenergy crop miscanthus. These results are a first step towards the development of marker-assisted selection programs in miscanthus to improve biomass quality and facilitate its use as feedstock for biofuel production.
Collapse
Affiliation(s)
- Tim van der Weijde
- Wageningen UR Plant Breeding, Wageningen University and Research, PO Box 386, 6700 AJ, Wageningen, Netherlands.,Graduate School Experimental Plant Sciences, Wageningen University, 6708 PB, Wageningen, Netherlands.,Present address: Research, Barenbrug Holland B.V, Duitsekampweg 60, 6748 ZB, Wolfheze, Netherlands
| | - Claire L Alvim Kamei
- Wageningen UR Plant Breeding, Wageningen University and Research, PO Box 386, 6700 AJ, Wageningen, Netherlands.,Present address: Department of Comparative Development and Genetics, Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829, Cologne, Germany
| | - Edouard I Severing
- Wageningen UR Plant Breeding, Wageningen University and Research, PO Box 386, 6700 AJ, Wageningen, Netherlands.,Present address: Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829, Cologne, Germany
| | - Andres F Torres
- Wageningen UR Plant Breeding, Wageningen University and Research, PO Box 386, 6700 AJ, Wageningen, Netherlands
| | - Leonardo D Gomez
- Center for Novel Agricultural Products, University of York, YO10 5 DD, York, UK
| | - Oene Dolstra
- Wageningen UR Plant Breeding, Wageningen University and Research, PO Box 386, 6700 AJ, Wageningen, Netherlands
| | - Chris A Maliepaard
- Wageningen UR Plant Breeding, Wageningen University and Research, PO Box 386, 6700 AJ, Wageningen, Netherlands
| | | | - Richard G F Visser
- Wageningen UR Plant Breeding, Wageningen University and Research, PO Box 386, 6700 AJ, Wageningen, Netherlands
| | - Luisa M Trindade
- Wageningen UR Plant Breeding, Wageningen University and Research, PO Box 386, 6700 AJ, Wageningen, Netherlands.
| |
Collapse
|
30
|
Krystkowiak K, Langner M, Adamski T, Salmanowicz BP, Kaczmarek Z, Krajewski P, Surma M. Interactions between Glu-1 and Glu-3 loci and associations of selected molecular markers with quality traits in winter wheat (Triticum aestivum L.) DH lines. J Appl Genet 2017; 58:37-48. [PMID: 27502940 PMCID: PMC5243893 DOI: 10.1007/s13353-016-0362-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2016] [Revised: 07/10/2016] [Accepted: 07/13/2016] [Indexed: 11/04/2022]
Abstract
The quality of wheat depends on a large complex of genes and environmental factors. The objective of this study was to identify quantitative trait loci controlling technological quality traits and their stability across environments, and to assess the impact of interaction between alleles at loci Glu-1 and Glu-3 on grain quality. DH lines were evaluated in field experiments over a period of 4 years, and genotyped using simple sequence repeat markers. Lines were analysed for grain yield (GY), thousand grain weight (TGW), protein content (PC), starch content (SC), wet gluten content (WG), Zeleny sedimentation value (ZS), alveograph parameter W (APW), hectolitre weight (HW), and grain hardness (GH). A number of QTLs for these traits were identified in all chromosome groups. The Glu-D1 locus influenced TGW, PC, SC, WG, ZS, APW, GH, while locus Glu-B1 affected only PC, ZS, and WG. Most important marker-trait associations were found on chromosomes 1D and 5D. Significant effects of interaction between Glu-1 and Glu-3 loci on technological properties were recorded, and in all types of this interaction positive effects of Glu-D1 locus on grain quality were observed, whereas effects of Glu-B1 locus depended on alleles at Glu-3 loci. Effects of Glu-A3 and Glu-D3 loci per se were not significant, while their interaction with alleles present at other loci encoding HMW and LMW were important. These results indicate that selection of wheat genotypes with predicted good bread-making properties should be based on the allelic composition both in Glu-1 and Glu-3 loci, and confirm the predominant effect of Glu-D1d allele on technological properties of wheat grains.
Collapse
Affiliation(s)
- Karolina Krystkowiak
- Institute of Plant Genetics, Polish Academy of Sciences, Strzeszyńska 34, 60-479, Poznań, Poland.
| | - Monika Langner
- Institute of Plant Genetics, Polish Academy of Sciences, Strzeszyńska 34, 60-479, Poznań, Poland.
| | - Tadeusz Adamski
- Institute of Plant Genetics, Polish Academy of Sciences, Strzeszyńska 34, 60-479, Poznań, Poland
| | - Bolesław P Salmanowicz
- Institute of Plant Genetics, Polish Academy of Sciences, Strzeszyńska 34, 60-479, Poznań, Poland
| | - Zygmunt Kaczmarek
- Institute of Plant Genetics, Polish Academy of Sciences, Strzeszyńska 34, 60-479, Poznań, Poland
| | - Paweł Krajewski
- Institute of Plant Genetics, Polish Academy of Sciences, Strzeszyńska 34, 60-479, Poznań, Poland
| | - Maria Surma
- Institute of Plant Genetics, Polish Academy of Sciences, Strzeszyńska 34, 60-479, Poznań, Poland
| |
Collapse
|
31
|
Ereful NC, Liu LY, Tsai E, Kao SM, Dixit S, Mauleon R, Malabanan K, Thomson M, Laurena A, Lee D, Mackay I, Greenland A, Powell W, Leung H. Analysis of Allelic Imbalance in Rice Hybrids Under Water Stress and Association of Asymmetrically Expressed Genes with Drought-Response QTLs. Rice (N Y) 2016; 9:50. [PMID: 27671164 PMCID: PMC5037104 DOI: 10.1186/s12284-016-0123-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/21/2016] [Accepted: 09/18/2016] [Indexed: 06/06/2023]
Abstract
BACKGROUND Information on the effect of stress on the allele-specific expression (ASE) profile of rice hybrids is limited. More so, the association of allelically imbalanced genes to important traits is yet to be understood. Here we assessed allelic imbalance (AI) in the heterozygote state of rice under non- and water-stress treatments and determined association of asymmetrically expressed genes with grain yield (GY) under drought stress by in-silico co-localization analysis and selective genotyping. The genotypes IR64, Apo and their F1 hybrid (IR64 × Apo) were grown under normal and water-limiting conditions. We sequenced the total RNA transcripts for all genotypes then reconstructed the two chromosomes in the heterozygote. RESULTS We are able to estimate the transcript abundance of and the differential expression (DE) between the two parent-specific alleles in the rice hybrids. The magnitude and direction of AI are classified into two categories: (1) symmetrical or biallelic and (2) asymmetrical. The latter can be further classified as either IR64- or Apo-favoring gene. Analysis showed that in the hybrids grown under non-stress conditions, 179 and 183 favor Apo- and IR64-specific alleles, respectively. Hence, the number of IR64- and Apo-favoring genes is relatively equal. Under water-stress conditions, 179 and 255 favor Apo- and IR64-specific alleles, respectively, indicating that the number of allelically imbalanced genes is skewed towards IR64. This is nearly 40-60 % preference for Apo and IR64 alleles, respectively, to the hybrid transcriptome. We also observed genes which exhibit allele preference switching when exposed to water-stress conditions. Results of in-silico co-localization procedure and selective genotyping of Apo/IR64 F3:5 progenies revealed significant association of several asymmetrically expressed genes with GY under drought stress conditions. CONCLUSION Our data suggest that water stress skews AI on a genome-wide scale towards the IR64 allele, the cross-specific maternal allele. Several asymmetrically expressed genes are strongly associated with GY under drought stress which may shed hints that genes associated with important traits are allelically imbalanced. Our approach of integrating hybrid expression analysis and QTL mapping analysis may be an efficient strategy for shortlisting candidate genes for gene discovery.
Collapse
Affiliation(s)
- Nelzo C. Ereful
- Genetics and Biotechnology Division, International Rice Research Institute (IRRI), Los Baños, Laguna Philippines
- The John Bingham Laboratory, National Institute of Agricultural Botany (NIAB), Huntingdon Road, Cambridge, CB3 0LE UK
| | - Li-Yu Liu
- Department of Agronomy, National Taiwan University (NTU), Taipei City, 100 Taiwan
| | - Eric Tsai
- Department of Agronomy, National Taiwan University (NTU), Taipei City, 100 Taiwan
| | - Shu-Min Kao
- Department of Agronomy, National Taiwan University (NTU), Taipei City, 100 Taiwan
| | - Shalabh Dixit
- Genetics and Biotechnology Division, International Rice Research Institute (IRRI), Los Baños, Laguna Philippines
| | - Ramil Mauleon
- Genetics and Biotechnology Division, International Rice Research Institute (IRRI), Los Baños, Laguna Philippines
| | - Katrina Malabanan
- Genetics and Biotechnology Division, International Rice Research Institute (IRRI), Los Baños, Laguna Philippines
- Crop Science Cluster, College of Agriculture, University of the Philippines, Los Baños, Laguna 4031 Philippines
| | - Michael Thomson
- Genetics and Biotechnology Division, International Rice Research Institute (IRRI), Los Baños, Laguna Philippines
- Texas A &M, Department of Soil and Crop Sciences 2474 TAMU, College Station, TX 77843-2474 USA
| | - Antonio Laurena
- Institute of Plant Breeding, University of the Philippines, Los Baños, Laguna Philippines
| | - David Lee
- The John Bingham Laboratory, National Institute of Agricultural Botany (NIAB), Huntingdon Road, Cambridge, CB3 0LE UK
| | - Ian Mackay
- The John Bingham Laboratory, National Institute of Agricultural Botany (NIAB), Huntingdon Road, Cambridge, CB3 0LE UK
| | - Andy Greenland
- The John Bingham Laboratory, National Institute of Agricultural Botany (NIAB), Huntingdon Road, Cambridge, CB3 0LE UK
| | - Wayne Powell
- SRUC, Peter Wilson Building, West Mains Road, Edinburgh, EH9 3JG UK
| | - Hei Leung
- Genetics and Biotechnology Division, International Rice Research Institute (IRRI), Los Baños, Laguna Philippines
| |
Collapse
|
32
|
Wang YH, Wu DH, Huang JH, Tsao SJ, Hwu KK, Lo HF. Mapping quantitative trait loci for fruit traits and powdery mildew resistance in melon (Cucumis melo). Bot Stud 2016; 57:19. [PMID: 28597428 PMCID: PMC5430578 DOI: 10.1186/s40529-016-0130-1] [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] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2016] [Accepted: 06/23/2016] [Indexed: 05/06/2023]
Abstract
BACKGROUND Fruit characters affect consumer preferences and the market value of melons is determined by fruit quality. Most fruit quality-related traits are controlled by multiple genes, and are influenced by environmental factors. Furthermore, powdery mildew is another limiting factor in melon production. To develop new melon cultivars with disease resistance and high quality fruits using the molecular marker-assisted breeding strategy, identification of quantitative trait loci for fruit quality and disease resistance is required. RESULTS The F2 populations from the cross of TARI-08874 (Cucumis melo ssp. melo) and 'Bai-li-gua' (C. melo ssp. agrestis) were used to map the quantitative trait loci (QTLs) for fruit-related traits and powdery mildew resistance in two trials. All traits were significantly different (P < 0.05) between parents. The generated linkage map consisted of twelve major linkage groups (LGs), spanning 626.1 cM in total, with an average distance of 8.3 cM between flanking markers. Nineteen QTLs were detected for seven melon traits, among which ten QTLs were localized to the same positions as the corresponding QTLs described in other studies. Four of these QTLs were detected in both trials. The results of identified QTLs in this study suggested that fruit size in the tested populations were mainly determined by fruit diameter and flesh thickness. All of the major QTLs for fruit diameter and flesh thickness were identified on LG5 and LG11. Four QTLs identified responsible for netting width of fruit rind were co-localized with the QTLs for netting density, suggesting similar genetic mechanisms affecting these two traits. Additionally, only one major QTL for powdery mildew resistance was detected on LG2, and it was closely linked to a simple sequence repeat (SSR) marker CMBR120 which was identified in a previous study. CONCLUSION Because the netting feature is a crucial factor for external appearance of fruits in Asia market, we focus on mining the genetic information of fruit netting. This is the first report of QTL mapping to netting width. Furthermore, new QTLs were identified for netting density (qND4, qND6, and qND7) and netting width (qNW2, qNW4, qNW6, and qNW7) successfully. In addition, novel QTLs for fruit diameter (qFD5), flesh thickness (qFT11) were also detected.
Collapse
Affiliation(s)
- Yu-Hua Wang
- Crop Science Division, Taiwan Agricultural Research Institute, Council of Agriculture (COA), Taichung, Taiwan
- Department of Horticulture and Landscape Architecture, National Taiwan University, Taipei, Taiwan
| | - Dong-Hong Wu
- Crop Science Division, Taiwan Agricultural Research Institute, Council of Agriculture (COA), Taichung, Taiwan
| | - Jin-Hsing Huang
- Plant Pathology Division, Taiwan Agricultural Research Institute, Council of Agriculture (COA), Taichung, Taiwan
| | - Shing-Jy Tsao
- Department of Horticulture and Landscape Architecture, National Taiwan University, Taipei, Taiwan
| | - Kae-Kang Hwu
- Department of Agronomy, National Taiwan University, Taipei, Taiwan
| | - Hsiao-Feng Lo
- Department of Horticulture and Landscape Architecture, National Taiwan University, Taipei, Taiwan
| |
Collapse
|
33
|
Shi Y, Zhang B, Liu A, Li W, Li J, Lu Q, Zhang Z, Li S, Gong W, Shang H, Gong J, Chen T, Ge Q, Wang T, Zhu H, Liu Z, Yuan Y. Quantitative trait loci analysis of Verticillium wilt resistance in interspecific backcross populations of Gossypium hirsutum × Gossypium barbadense. BMC Genomics 2016; 17:877. [PMID: 27814678 DOI: 10.1186/s12864-016-3128-x] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2015] [Accepted: 09/27/2016] [Indexed: 11/17/2022] Open
Abstract
Background Verticillium wilt (VW) caused by Verticillium dahliae (Kleb) is one of the most destructive diseases of cotton. The identification of highly resistant QTLs or genes in the whole cotton genome is quite important for developing a VW-resistant variety and for further molecular design breeding. Results In the present study, BC1F1, BC1S1, and BC2F1 populations derived from an interspecific backcross between the highly resistant line Hai1 (Gossypium barbadense L.) and the susceptible variety CCRI36 (G. hirsutum L.) as the recurrent parent were constructed. Quantitative trait loci (QTL) related to VW resistance were detected in the whole cotton genome using a high-density simple sequence repeat (SSR) genetic linkage map from the BC1F1 population, with 2292 loci covering 5115.16 centiMorgan (cM) of the cotton (AD) genome, and the data concerning VW resistance that were obtained from four dates of BC2F1 in the artificial disease nursery and one date of BC1S1 and BC2F1 in the field. A total of 48 QTLs for VW resistance were identified, and 37 of these QTLs had positive additive effects, which indicated that the G. barbadense alleles increased resistance to VW and decreased the disease index (DI) by about 2.2–10.7. These QTLs were located on 19 chromosomes, in which 33 in the A subgenome and 15 QTLs in the D subgenome. The 6 QTLs were found to be stable. The 6 QTLs were consistent with those identified previously, and another 42 were new, unreported QTLs, of which 31 QTLs were from G. barbadense. By meta-analysis, 17 QTL hotspot regions were identified and 10 of them were new, unreported hotspot regions. 29 QTLs in this paper were in 12 hotspot regions and were all from G. barbadense. Conclusions These stable or consensus QTL regions warrant further investigation to better understand the genetics and molecular mechanisms underlying VW resistance. This study provides useful information for further comparative analysis and marker-assisted selection in the breeding of disease-resistant cotton. It may also lay an important foundation for gene cloning and further molecular design breeding for the entire cotton genome. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-3128-x) contains supplementary material, which is available to authorized users.
Collapse
|
34
|
Racedo J, Gutiérrez L, Perera MF, Ostengo S, Pardo EM, Cuenya MI, Welin B, Castagnaro AP. Genome-wide association mapping of quantitative traits in a breeding population of sugarcane. BMC Plant Biol 2016; 16:142. [PMID: 27342657 PMCID: PMC4921039 DOI: 10.1186/s12870-016-0829-x] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [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: 04/28/2015] [Accepted: 06/14/2016] [Indexed: 05/22/2023]
Abstract
BACKGROUND Molecular markers associated with relevant agronomic traits could significantly reduce the time and cost involved in developing new sugarcane varieties. Previous sugarcane genome-wide association analyses (GWAS) have found few molecular markers associated with relevant traits at plant-cane stage. The aim of this study was to establish an appropriate GWAS to find molecular markers associated with yield related traits consistent across harvesting seasons in a breeding population. Sugarcane clones were genotyped with DArT (Diversity Array Technology) and TRAP (Target Region Amplified Polymorphism) markers, and evaluated for cane yield (CY) and sugar content (SC) at two locations during three successive crop cycles. GWAS mapping was applied within a novel mixed-model framework accounting for population structure with Principal Component Analysis scores as random component. RESULTS A total of 43 markers significantly associated with CY in plant-cane, 42 in first ratoon, and 41 in second ratoon were detected. Out of these markers, 20 were associated with CY in 2 years. Additionally, 38 significant associations for SC were detected in plant-cane, 34 in first ratoon, and 47 in second ratoon. For SC, one marker-trait association was found significant for the 3 years of the study, while twelve markers presented association for 2 years. In the multi-QTL model several markers with large allelic substitution effect were found. Sequences of four DArT markers showed high similitude and e-value with coding sequences of Sorghum bicolor, confirming the high gene microlinearity between sorghum and sugarcane. CONCLUSIONS In contrast with other sugarcane GWAS studies reported earlier, the novel methodology to analyze multi-QTLs through successive crop cycles used in the present study allowed us to find several markers associated with relevant traits. Combining existing phenotypic trial data and genotypic DArT and TRAP marker characterizations within a GWAS approach including population structure as random covariates may prove to be highly successful. Moreover, sequences of DArT marker associated with the traits of interest were aligned in chromosomal regions where sorghum QTLs has previously been reported. This approach could be a valuable tool to assist the improvement of sugarcane and better supply sugarcane demand that has been projected for the upcoming decades.
Collapse
Affiliation(s)
- Josefina Racedo
- />Estación Experimental Agroindustrial Obispo Colombres (EEAOC)- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Instituto de Tecnología Agroindustrial del Noroeste Argentino (ITANOA), Av. William Cross 3150, Las Talitas, T4101XAC Tucumán Argentina
| | - Lucía Gutiérrez
- />Departamento de Biometría, Estadística y Cómputos, Facultad de Agronomía, Universidad de la República, Garzón 780, 12900 Montevideo, Uruguay
- />Agronomy Department, University of Wisconsin – Madison, 1575 Linden Dr., Madison, WI 53706 USA
| | - María Francisca Perera
- />Estación Experimental Agroindustrial Obispo Colombres (EEAOC)- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Instituto de Tecnología Agroindustrial del Noroeste Argentino (ITANOA), Av. William Cross 3150, Las Talitas, T4101XAC Tucumán Argentina
| | - Santiago Ostengo
- />Estación Experimental Agroindustrial Obispo Colombres (EEAOC)- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Instituto de Tecnología Agroindustrial del Noroeste Argentino (ITANOA), Av. William Cross 3150, Las Talitas, T4101XAC Tucumán Argentina
| | - Esteban Mariano Pardo
- />Estación Experimental Agroindustrial Obispo Colombres (EEAOC)- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Instituto de Tecnología Agroindustrial del Noroeste Argentino (ITANOA), Av. William Cross 3150, Las Talitas, T4101XAC Tucumán Argentina
| | - María Inés Cuenya
- />Estación Experimental Agroindustrial Obispo Colombres (EEAOC)- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Instituto de Tecnología Agroindustrial del Noroeste Argentino (ITANOA), Av. William Cross 3150, Las Talitas, T4101XAC Tucumán Argentina
| | - Bjorn Welin
- />Estación Experimental Agroindustrial Obispo Colombres (EEAOC)- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Instituto de Tecnología Agroindustrial del Noroeste Argentino (ITANOA), Av. William Cross 3150, Las Talitas, T4101XAC Tucumán Argentina
| | - Atilio Pedro Castagnaro
- />Estación Experimental Agroindustrial Obispo Colombres (EEAOC)- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Instituto de Tecnología Agroindustrial del Noroeste Argentino (ITANOA), Av. William Cross 3150, Las Talitas, T4101XAC Tucumán Argentina
| |
Collapse
|
35
|
Liu D, Zhang J, Liu X, Wang W, Liu D, Teng Z, Fang X, Tan Z, Tang S, Yang J, Zhong J, Zhang Z. Fine mapping and RNA-Seq unravels candidate genes for a major QTL controlling multiple fiber quality traits at the T1 region in upland cotton. BMC Genomics 2016; 17:295. [PMID: 27094760 PMCID: PMC4837631 DOI: 10.1186/s12864-016-2605-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [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: 10/23/2015] [Accepted: 03/28/2016] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND Improving fiber quality is a major challenge in cotton breeding, since the molecular basis of fiber quality traits is poorly understood. Fine mapping and candidate gene prediction of quantitative trait loci (QTL) controlling cotton fiber quality traits can help to elucidate the molecular basis of fiber quality. In our previous studies, one major QTL controlling multiple fiber quality traits was identified near the T1 locus on chromosome 6 in Upland cotton. RESULTS To finely map this major QTL, the F2 population with 6975 individuals was established from a cross between Yumian 1 and a recombinant inbred line (RIL118) selected from a recombinant inbred line population (T586 × Yumian 1). The QTL was mapped to a 0.28-cM interval between markers HAU2119 and SWU2302. The QTL explained 54.7 % (LOD = 222.3), 40.5 % (LOD = 145.0), 50.0 % (LOD = 194.3) and 30.1 % (LOD = 100.4) of phenotypic variation with additive effects of 2.78, -0.43, 2.92 and 1.90 units for fiber length, micronaire, strength and uniformity, respectively. The QTL region corresponded to a 2.7-Mb interval on chromosome 10 in the G. raimondii genome sequence and a 5.3-Mb interval on chromosome A06 in G. hirsutum. The fiber of Yumian 1 was much longer than that of RIL118 from 3 DPA to 7 DPA. RNA-Seq of ovules at 0 DPA and fibers at 5 DPA from Yumian 1 and RIL118 showed four genes in the QTL region of the G. raimondii genome to be extremely differentially expressed. RT-PCR analysis showed three genes in the QTL region of the G. hirsutum genome to behave similarly. CONCLUSIONS This study mapped a major QTL influencing four fiber quality traits to a 0.28-cM interval and identified three candidate genes by RNA-Seq and RT-PCR analysis. Integration of fine mapping and RNA-Seq is a powerful strategy to uncover candidates for QTL in large genomes.
Collapse
Affiliation(s)
- Dexin Liu
- Engineering Research Center of South Upland Agriculture, Ministry of Education, Southwest University, 400716, Chongqing, People's Republic of China
| | - Jian Zhang
- Engineering Research Center of South Upland Agriculture, Ministry of Education, Southwest University, 400716, Chongqing, People's Republic of China
| | - Xueying Liu
- Engineering Research Center of South Upland Agriculture, Ministry of Education, Southwest University, 400716, Chongqing, People's Republic of China
| | - Wenwen Wang
- Engineering Research Center of South Upland Agriculture, Ministry of Education, Southwest University, 400716, Chongqing, People's Republic of China
| | - Dajun Liu
- Engineering Research Center of South Upland Agriculture, Ministry of Education, Southwest University, 400716, Chongqing, People's Republic of China
| | - Zhonghua Teng
- Engineering Research Center of South Upland Agriculture, Ministry of Education, Southwest University, 400716, Chongqing, People's Republic of China
| | - Xiaomei Fang
- Engineering Research Center of South Upland Agriculture, Ministry of Education, Southwest University, 400716, Chongqing, People's Republic of China
| | - Zhaoyun Tan
- Engineering Research Center of South Upland Agriculture, Ministry of Education, Southwest University, 400716, Chongqing, People's Republic of China
| | - Shiyi Tang
- Engineering Research Center of South Upland Agriculture, Ministry of Education, Southwest University, 400716, Chongqing, People's Republic of China
| | - Jinghong Yang
- Engineering Research Center of South Upland Agriculture, Ministry of Education, Southwest University, 400716, Chongqing, People's Republic of China
| | - Jianwei Zhong
- Engineering Research Center of South Upland Agriculture, Ministry of Education, Southwest University, 400716, Chongqing, People's Republic of China
| | - Zhengsheng Zhang
- Engineering Research Center of South Upland Agriculture, Ministry of Education, Southwest University, 400716, Chongqing, People's Republic of China.
| |
Collapse
|
36
|
Singh R, Singh Y, Xalaxo S, Verulkar S, Yadav N, Singh S, Singh N, Prasad KSN, Kondayya K, Rao PVR, Rani MG, Anuradha T, Suraynarayana Y, Sharma PC, Krishnamurthy SL, Sharma SK, Dwivedi JL, Singh AK, Singh PK, Singh NK, Kumar R, Chetia SK, Ahmad T, Rai M, Perraju P, Pande A, Singh DN, Mandal NP, Reddy JN, Singh ON, Katara JL, Marandi B, Swain P, Sarkar RK, Singh DP, Mohapatra T, Padmawathi G, Ram T, Kathiresan RM, Paramsivam K, Nadarajan S, Thirumeni S, Nagarajan M, Singh AK, Vikram P, Kumar A, Septiningshih E, Singh US, Ismail AM, Mackill D, Singh NK. From QTL to variety-harnessing the benefits of QTLs for drought, flood and salt tolerance in mega rice varieties of India through a multi-institutional network. Plant Sci 2016; 242:278-287. [PMID: 26566845 DOI: 10.1016/j.plantsci.2015.08.008] [Citation(s) in RCA: 78] [Impact Index Per Article: 9.8] [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: 05/20/2015] [Revised: 08/10/2015] [Accepted: 08/13/2015] [Indexed: 05/21/2023]
Abstract
Rice is a staple cereal of India cultivated in about 43.5Mha area but with relatively low average productivity. Abiotic factors like drought, flood and salinity affect rice production adversely in more than 50% of this area. Breeding rice varieties with inbuilt tolerance to these stresses offers an economically viable and sustainable option to improve rice productivity. Availability of high quality reference genome sequence of rice, knowledge of exact position of genes/QTLs governing tolerance to abiotic stresses and availability of DNA markers linked to these traits has opened up opportunities for breeders to transfer the favorable alleles into widely grown rice varieties through marker-assisted backcross breeding (MABB). A large multi-institutional project, "From QTL to variety: marker-assisted breeding of abiotic stress tolerant rice varieties with major QTLs for drought, submergence and salt tolerance" was initiated in 2010 with funding support from Department of Biotechnology, Government of India, in collaboration with International Rice Research Institute, Philippines. The main focus of this project is to improve rice productivity in the fragile ecosystems of eastern, northeastern and southern part of the country, which bear the brunt of one or the other abiotic stresses frequently. Seven consistent QTLs for grain yield under drought, namely, qDTY1.1, qDTY2.1, qDTY2.2, qDTY3.1, qDTY3.2, qDTY9.1 and qDTY12.1 are being transferred into submergence tolerant versions of three high yielding mega rice varieties, Swarna-Sub1, Samba Mahsuri-Sub1 and IR 64-Sub1. To address the problem of complete submergence due to flash floods in the major river basins, the Sub1 gene is being transferred into ten highly popular locally adapted rice varieties namely, ADT 39, ADT 46, Bahadur, HUR 105, MTU 1075, Pooja, Pratikshya, Rajendra Mahsuri, Ranjit, and Sarjoo 52. Further, to address the problem of soil salinity, Saltol, a major QTL for salt tolerance is being transferred into seven popular locally adapted rice varieties, namely, ADT 45, CR 1009, Gayatri, MTU 1010, PR 114, Pusa 44 and Sarjoo 52. Genotypic background selection is being done after BC2F2 stage using an in-house designed 50K SNP chip on a set of twenty lines for each combination, identified with phenotypic similarity in the field to the recipient parent. Near-isogenic lines with more than 90% similarity to the recipient parent are now in advanced generation field trials. These climate smart varieties are expected to improve rice productivity in the adverse ecologies and contribute to the farmer's livelihood.
Collapse
Affiliation(s)
- Renu Singh
- National Research Centre on Plant Biotechnology, New Delhi, India
| | - Yashi Singh
- National Research Centre on Plant Biotechnology, New Delhi, India
| | - Suchit Xalaxo
- Indira Gandhi Krishi Vishwavidyalaya, Raipur, Chhatisgarh, India
| | - S Verulkar
- Indira Gandhi Krishi Vishwavidyalaya, Raipur, Chhatisgarh, India
| | - Neera Yadav
- National Research Centre on Plant Biotechnology, New Delhi, India
| | - Shweta Singh
- National Research Centre on Plant Biotechnology, New Delhi, India
| | - Nisha Singh
- National Research Centre on Plant Biotechnology, New Delhi, India
| | - K S N Prasad
- Acharya N.G. Ranga Agricultural University, Maruteru, AP, India
| | - K Kondayya
- Acharya N.G. Ranga Agricultural University, Maruteru, AP, India
| | - P V Ramana Rao
- Acharya N.G. Ranga Agricultural University, Maruteru, AP, India
| | - M Girija Rani
- Acharya N.G. Ranga Agricultural University, Maruteru, AP, India
| | - T Anuradha
- Acharya N.G. Ranga Agricultural University, Maruteru, AP, India
| | - Y Suraynarayana
- Acharya N.G. Ranga Agricultural University, Maruteru, AP, India
| | - P C Sharma
- ICAR-Central Soil Salinity Research Institute, Karnal, Haryana, India
| | - S L Krishnamurthy
- ICAR-Central Soil Salinity Research Institute, Karnal, Haryana, India
| | - S K Sharma
- ICAR-Central Soil Salinity Research Institute, Karnal, Haryana, India
| | - J L Dwivedi
- Acharya Narendra Dev University of Agriculture and Technology, Faizabad, UP, India
| | - A K Singh
- Acharya Narendra Dev University of Agriculture and Technology, Faizabad, UP, India
| | - P K Singh
- Banaras Hindu University, Varanasi, UP, India
| | - N K Singh
- Rajendra Agricultural University, Samastipur, Bihar, India
| | - Rajesh Kumar
- Rajendra Agricultural University, Samastipur, Bihar, India
| | - S K Chetia
- Assam Agricultural University, Jorhat, Assam, India
| | - T Ahmad
- Assam Agricultural University, Jorhat, Assam, India
| | - M Rai
- Central Agricultural University, Umiam, Meghalaya, India
| | - P Perraju
- Jawahar Lal Nehru Krishi Vishwavidyalaya, Reewa, MP, India
| | - Anita Pande
- Birsa Agricultural University, Ranchi, Jharkhand, India
| | - D N Singh
- Birsa Agricultural University, Ranchi, Jharkhand, India
| | - N P Mandal
- ICAR-Central Rice Research Institute, Cuttack, Odisha, India
| | - J N Reddy
- ICAR-Central Rice Research Institute, Cuttack, Odisha, India
| | - O N Singh
- ICAR-Central Rice Research Institute, Cuttack, Odisha, India
| | - J L Katara
- ICAR-Central Rice Research Institute, Cuttack, Odisha, India
| | - B Marandi
- ICAR-Central Rice Research Institute, Cuttack, Odisha, India
| | - P Swain
- ICAR-Central Rice Research Institute, Cuttack, Odisha, India
| | - R K Sarkar
- ICAR-Central Rice Research Institute, Cuttack, Odisha, India
| | - D P Singh
- ICAR-Central Rice Research Institute, Cuttack, Odisha, India
| | - T Mohapatra
- ICAR-Central Rice Research Institute, Cuttack, Odisha, India
| | - G Padmawathi
- ICAR-Indian Institute of Rice Research, Hyderabad, India
| | - T Ram
- ICAR-Indian Institute of Rice Research, Hyderabad, India
| | | | - K Paramsivam
- Pandit Jawaharlal Nehru College of Agriculture & Research Institute, Karikal, Puducherry, India
| | - S Nadarajan
- Pandit Jawaharlal Nehru College of Agriculture & Research Institute, Karikal, Puducherry, India
| | - S Thirumeni
- Pandit Jawaharlal Nehru College of Agriculture & Research Institute, Karikal, Puducherry, India
| | - M Nagarajan
- ICAR-Indian Agricultural Research Institute, Aduthurai, TN, India
| | - A K Singh
- ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Prashant Vikram
- International Rice Research Institute, Los Banos, Philippines
| | - Arvind Kumar
- International Rice Research Institute, Los Banos, Philippines
| | - E Septiningshih
- International Rice Research Institute, Los Banos, Philippines
| | - U S Singh
- International Rice Research Institute, Los Banos, Philippines
| | - A M Ismail
- International Rice Research Institute, Los Banos, Philippines
| | - D Mackill
- International Rice Research Institute, Los Banos, Philippines
| | - Nagendra K Singh
- National Research Centre on Plant Biotechnology, New Delhi, India.
| |
Collapse
|
37
|
Sambucetti P, Loeschcke V, Norry FM. Patterns of longevity and fecundity at two temperatures in a set of heat-selected recombinant inbred lines of Drosophila melanogaster. Biogerontology 2015; 16:801-10. [PMID: 26404666 DOI: 10.1007/s10522-015-9606-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [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: 06/05/2015] [Accepted: 09/09/2015] [Indexed: 01/21/2023]
Abstract
Quantitative trait loci (QTL) were mapped for longevity and fecundity at two temperatures, 20 and 30 °C, in two sets of recombinant inbred lines (RIL) highly differing in thermotolerance. Early fecundity (EF) and longevity showed a negative association between temperatures. For instance, longevity was higher and fecundity was lower in the RIL panel showing higher life span at 30 °C. One X-linked QTL (7B3-12E) co-localized for longevity and EF at 20 °C, with one QTL allele showing a positive additive effect on longevity and a negative effect on EF. The across-RIL genetic correlation between longevity and EF was not significant within each temperature, and most QTL that affect life span have no effect on EF at each temperature. EF and longevity can mostly be genetically uncoupled in the thermotolerance-divergent RIL within each temperature as opposed to between temperatures. QTL were mostly temperature specific, although some trait-specific QTL showed possible antagonistic effects between temperatures.
Collapse
Affiliation(s)
- P Sambucetti
- Departamento de Ecología, Genética y Evolución, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires - IEGEBA (CONICET-UBA), C-1428-EHA, Buenos Aires, Argentina.
| | - V Loeschcke
- Department of Bioscience, Aarhus University, Ny Munkegade 114, Building 1540, 8000, Aarhus C, Denmark
| | - F M Norry
- Departamento de Ecología, Genética y Evolución, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires - IEGEBA (CONICET-UBA), C-1428-EHA, Buenos Aires, Argentina
| |
Collapse
|
38
|
Liu D, Liu F, Shan X, Zhang J, Tang S, Fang X, Liu X, Wang W, Tan Z, Teng Z, Zhang Z, Liu D. Construction of a high-density genetic map and lint percentage and cottonseed nutrient trait QTL identification in upland cotton (Gossypium hirsutum L.). Mol Genet Genomics 2015; 290:1683-700. [PMID: 25796191 DOI: 10.1007/s00438-015-1027-5] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2014] [Accepted: 03/03/2015] [Indexed: 12/19/2022]
Abstract
Upland cotton plays a critical role not only in the textile industry, but also in the production of important secondary metabolites, such as oil and proteins. Construction of a high-density linkage map and identifying yield and seed trait quantitative trail loci (QTL) are prerequisites for molecular marker-assisted selective breeding projects. Here, we update a high-density upland cotton genetic map from recombinant inbred lines. A total of 25,313 SSR primer pairs were screened for polymorphism between Yumian 1 and T586, and 1712 SSR primer pairs were used to genotype the mapping population and construct a map. An additional 1166 loci have been added to our previously published map with 509 SSR markers. The updated genetic map spans a total recombinant length of 3338.2 cM and contains 1675 SSR loci and nine morphological markers, with an average interval of 1.98 cM between adjacent markers. Green lint (Lg) mapped on chromosome 15 in a previous report is mapped in an interval of 2.6 cM on chromosome 21. Based on the map and phenotypic data from multiple environments, 79 lint percentage and seed nutrient trait QTL are detected. These include 8 lint percentage, 13 crude protein, 15 crude oil, 8 linoleic, 10 oleic, 13 palmitic, and 12 stearic acid content QTL. They explain 3.5-62.7 % of the phenotypic variation observed. Four morphological markers identified have a major impact on lint percentage and cottonseed nutrients traits. In this study, our genetic map provides new sights into the tetraploid cotton genome. Furthermore, the stable QTL and morphological markers could be used for fine-mapping and map-based cloning.
Collapse
|
39
|
Abstract
Displacement of the abomasum (DA) is a common inherited condition in Holstein cows. This article reviews the genetics of DA including risk factors, genetic parameters and molecular genetic results. Breeds other than Holsteins affected by DA include Guernseys, Jerseys, Brown Swiss, Ayrshires and Simmental-Red Holsteins. In most DA cases, left displacements of the abomasum (LDA) are seen. Lactation incidence rates are higher for DA in first lactation Holsteins compared to later lactations. For Holstein cows, heritability estimates for DA are between 0.03 and 0.53. Genetic correlation estimates among DA and milk production traits range from positive to negative. Genome-wide significant genomic regions associated with LDA are located on bovine chromosomes (BTA) 1, 3, 11, 20 and 23. Motilin-associated single nucleotide polymorphisms on BTA23 exhibit a functional relationship with LDA. Pathways for deposition of calcium, insulin-dependent diabetes mellitus and synaptic transmission are significantly related to LDA in Holsteins. Deciphering the DA-associated genomic regions and genes may be an important step in the quest to understand the underlying disease-causing mechanisms and in unravelling mutations with a causal relationship to DA.
Collapse
Affiliation(s)
- Ina Zerbin
- Institute for Animal Breeding and Genetics, University of Veterinary Medicine Hannover, Bünteweg 17p, Hannover 30559, Germany
| | - Stefanie Lehner
- Institute for Animal Breeding and Genetics, University of Veterinary Medicine Hannover, Bünteweg 17p, Hannover 30559, Germany
| | - Ottmar Distl
- Institute for Animal Breeding and Genetics, University of Veterinary Medicine Hannover, Bünteweg 17p, Hannover 30559, Germany.
| |
Collapse
|
40
|
Crespo ÂC, Silva B, Marques L, Marcelino E, Maruta C, Costa S, Timóteo A, Vilares A, Couto FS, Faustino P, Correia AP, Verdelho A, Porto G, Guerreiro M, Herrero A, Costa C, de Mendonça A, Costa L, Martins M. Genetic and biochemical markers in patients with Alzheimer's disease support a concerted systemic iron homeostasis dysregulation. Neurobiol Aging 2013; 35:777-85. [PMID: 24199959 DOI: 10.1016/j.neurobiolaging.2013.10.078] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.2] [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: 05/16/2013] [Revised: 10/01/2013] [Accepted: 10/12/2013] [Indexed: 11/24/2022]
Abstract
Alzheimer's disease (AD) is the most common form of dementia in the elderly individuals, resulting from a complex interaction between environmental and genetic factors. Impaired brain iron homeostasis has been recognized as an important mechanism underlying the pathogenesis of this disease. Nevertheless, the knowledge gathered so far at the systemic level is clearly insufficient. Herein, we used an integrative approach to study iron metabolism in the periphery, at both genotypic and phenotypic levels, in a sample of 116 patients with AD and 89 healthy control subjects. To assess the potential impact of iron metabolism on the risk of developing AD, genetic analyses were performed along with the evaluation of the iron status profile in peripheral blood by biochemical and gene expression studies. The results obtained showed a significant decrease of serum iron, ferritin, and transferrin concentrations in patients compared with the control subjects. Also, a significant decrease of ferroportin (SLC40A1) and both transferrin receptors TFRC and TFR2 transcripts was found in peripheral blood mononuclear cells from patients. At the genetic level, significant associations with AD were found for single nucleotide polymorphisms in TF, TFR2, ACO1, and SLC40A1 genes. Apolipoprotein E gene, a well-known risk factor for AD, was also found significantly associated with the disease in this study. Taken together, we hypothesize that the alterations on systemic iron status observed in patients could reflect an iron homeostasis dysregulation, particularly in cellular iron efflux. The intracellular iron accumulation would lead to a rise in oxidative damage, contributing to AD pathophysiology.
Collapse
Affiliation(s)
- Ângela C Crespo
- Health Promotion and Prevention of Noncommunicable Diseases Department, Instituto Nacional de Saúde Dr Ricardo Jorge, Lisboa, Portugal; Instituto Gulbenkian de Ciência, Oeiras, Portugal
| | - Bruno Silva
- Human Genetics Department, Instituto Nacional de Saúde Dr Ricardo Jorge, Lisboa, Portugal
| | - Liliana Marques
- Health Promotion and Prevention of Noncommunicable Diseases Department, Instituto Nacional de Saúde Dr Ricardo Jorge, Lisboa, Portugal; Center for Biodiversity, Functional and Integrative Genomics, Faculdade de Ciências da Universidade de Lisboa, Lisboa, Portugal
| | - Erica Marcelino
- Neurological Clinical Research Unit, Instituto de Medicina Molecular, Lisboa, Portugal
| | - Carolina Maruta
- Neurological Clinical Research Unit, Instituto de Medicina Molecular, Lisboa, Portugal
| | - Sónia Costa
- Neurology Department, Hospital Prof. Dr Fernando Fonseca, E.P.E., Amadora, Portugal
| | - Angela Timóteo
- Neurology Department, Hospital Prof. Dr Fernando Fonseca, E.P.E., Amadora, Portugal
| | - Arminda Vilares
- Health Promotion and Prevention of Noncommunicable Diseases Department, Instituto Nacional de Saúde Dr Ricardo Jorge, Lisboa, Portugal
| | | | - Paula Faustino
- Human Genetics Department, Instituto Nacional de Saúde Dr Ricardo Jorge, Lisboa, Portugal
| | | | - Ana Verdelho
- Neurological Clinical Research Unit, Instituto de Medicina Molecular, Lisboa, Portugal
| | - Graça Porto
- Center for Predictive and Preventive Genetics, Instituto de Biologia Molecular e Celular, Porto, Portugal
| | - Manuela Guerreiro
- Neurological Clinical Research Unit, Instituto de Medicina Molecular, Lisboa, Portugal
| | - Ana Herrero
- Neurology Department, Hospital Prof. Dr Fernando Fonseca, E.P.E., Amadora, Portugal
| | - Cristina Costa
- Neurology Department, Hospital Prof. Dr Fernando Fonseca, E.P.E., Amadora, Portugal
| | - Alexandre de Mendonça
- Neurological Clinical Research Unit, Instituto de Medicina Molecular, Lisboa, Portugal
| | - Luciana Costa
- Health Promotion and Prevention of Noncommunicable Diseases Department, Instituto Nacional de Saúde Dr Ricardo Jorge, Lisboa, Portugal; Center for Biodiversity, Functional and Integrative Genomics, Faculdade de Ciências da Universidade de Lisboa, Lisboa, Portugal
| | - Madalena Martins
- Neurological Clinical Research Unit, Instituto de Medicina Molecular, Lisboa, Portugal; Instituto Gulbenkian de Ciência, Oeiras, Portugal.
| |
Collapse
|
41
|
Xu Z, Nie Q, Zhang X. Overview of Genomic Insights into Chicken Growth Traits Based on Genome-Wide Association Study and microRNA Regulation. Curr Genomics 2013; 14:137-46. [PMID: 24082823 PMCID: PMC3637678 DOI: 10.2174/1389202911314020006] [Citation(s) in RCA: 17] [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: 10/09/2012] [Revised: 01/28/2013] [Accepted: 01/29/2013] [Indexed: 01/09/2023] Open
Abstract
Over the two past decades, a significant number of studies have observed animal growth traits to examine animal genetic mechanisms due to their ease of measurement and high heritability. Chicken which has a significant impact on fundamental biology is a major source of protein worldwide, making it an ideal model for examining animal growth trait development. The genetic mechanisms of chicken growth traits have been studied using quantitative trait loci mapping through genome-scan and candidate gene approaches, genome-wide association studies (GWAS), comparative genomic strategies, microRNA (miRNA) regulation of growth development analysis, and epigenomic analysis. This review focuses on chicken GWAS and miRNA regulation of growth traits. Several recently published GWAS reports showed that most genome-wide significant single nucleotide polymorphisms are located on chromosomes 1 and 4 in chickens. Chicken growth, particularly skeletal muscle growth and development, is greatly regulated by miRNA. Using dwarf and normal chickens, let-7b was found to be involved in determining chicken dwarf phenotypes by regulating growth hormone receptor gene expression.
Collapse
Affiliation(s)
- Zhenqiang Xu
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, South China Agricultural University, Guangzhou 510642, Guang-dong, China
| | | | | |
Collapse
|