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Yu T, Zhang J, Cao J, Li S, Cai Q, Li X, Li S, Li Y, He C, Ma X. Identification of Multiple Genetic Loci Related to Low-Temperature Tolerance during Germination in Maize ( Zea maize L.) through a Genome-Wide Association Study. Curr Issues Mol Biol 2023; 45:9634-9655. [PMID: 38132448 PMCID: PMC10742315 DOI: 10.3390/cimb45120602] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 11/13/2023] [Accepted: 11/21/2023] [Indexed: 12/23/2023] Open
Abstract
Low-temperature stress during the germination stage is an important abiotic stress that affects the growth and development of northern spring maize and seriously restricts maize yield and quality. Although some quantitative trait locis (QTLs) related to low-temperature tolerance in maize have been detected, only a few can be commonly detected, and the QTL intervals are large, indicating that low-temperature tolerance is a complex trait that requires more in-depth research. In this study, 296 excellent inbred lines from domestic and foreign origins (America and Europe) were used as the study materials, and a low-coverage resequencing method was employed for genome sequencing. Five phenotypic traits related to low-temperature tolerance were used to assess the genetic diversity of maize through a genome-wide association study (GWAS). A total of 14 SNPs significantly associated with low-temperature tolerance were detected (-log10(P) > 4), and an SNP consistently linked to low-temperature tolerance in the field and indoors during germination was utilized as a marker. This SNP, 14,070, was located on chromosome 5 at position 2,205,723, which explained 4.84-9.68% of the phenotypic variation. The aim of this study was to enrich the genetic theory of low-temperature tolerance in maize and provide support for the innovation of low-temperature tolerance resources and the breeding of new varieties.
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Affiliation(s)
- Tao Yu
- Maize Research Institute of Heilongjiang Academy of Agricultural Sciences, Harbin 150086, China; (J.C.); (Q.C.); (X.L.); (X.M.)
- Key Laboratory of Biology and Genetics Improvement of Maize in Northern Northeast Region, Ministry of Agriculture and Rural Affairs, Harbin 150086, China
- Key Laboratory of Germplasm Resources Creation and Utilization of Maize, Harbin 150086, China
| | - Jianguo Zhang
- Maize Research Institute of Heilongjiang Academy of Agricultural Sciences, Harbin 150086, China; (J.C.); (Q.C.); (X.L.); (X.M.)
- Key Laboratory of Biology and Genetics Improvement of Maize in Northern Northeast Region, Ministry of Agriculture and Rural Affairs, Harbin 150086, China
- Key Laboratory of Germplasm Resources Creation and Utilization of Maize, Harbin 150086, China
| | - Jingsheng Cao
- Maize Research Institute of Heilongjiang Academy of Agricultural Sciences, Harbin 150086, China; (J.C.); (Q.C.); (X.L.); (X.M.)
- Key Laboratory of Biology and Genetics Improvement of Maize in Northern Northeast Region, Ministry of Agriculture and Rural Affairs, Harbin 150086, China
- Key Laboratory of Germplasm Resources Creation and Utilization of Maize, Harbin 150086, China
| | - Shujun Li
- Maize Research Institute of Heilongjiang Academy of Agricultural Sciences, Harbin 150086, China; (J.C.); (Q.C.); (X.L.); (X.M.)
- Key Laboratory of Biology and Genetics Improvement of Maize in Northern Northeast Region, Ministry of Agriculture and Rural Affairs, Harbin 150086, China
- Key Laboratory of Germplasm Resources Creation and Utilization of Maize, Harbin 150086, China
| | - Quan Cai
- Maize Research Institute of Heilongjiang Academy of Agricultural Sciences, Harbin 150086, China; (J.C.); (Q.C.); (X.L.); (X.M.)
- Key Laboratory of Biology and Genetics Improvement of Maize in Northern Northeast Region, Ministry of Agriculture and Rural Affairs, Harbin 150086, China
- Key Laboratory of Germplasm Resources Creation and Utilization of Maize, Harbin 150086, China
| | - Xin Li
- Maize Research Institute of Heilongjiang Academy of Agricultural Sciences, Harbin 150086, China; (J.C.); (Q.C.); (X.L.); (X.M.)
- Key Laboratory of Biology and Genetics Improvement of Maize in Northern Northeast Region, Ministry of Agriculture and Rural Affairs, Harbin 150086, China
| | - Sinan Li
- Maize Research Institute of Heilongjiang Academy of Agricultural Sciences, Harbin 150086, China; (J.C.); (Q.C.); (X.L.); (X.M.)
- Key Laboratory of Biology and Genetics Improvement of Maize in Northern Northeast Region, Ministry of Agriculture and Rural Affairs, Harbin 150086, China
| | - Yunlong Li
- Maize Research Institute of Heilongjiang Academy of Agricultural Sciences, Harbin 150086, China; (J.C.); (Q.C.); (X.L.); (X.M.)
- Key Laboratory of Biology and Genetics Improvement of Maize in Northern Northeast Region, Ministry of Agriculture and Rural Affairs, Harbin 150086, China
| | - Changan He
- Key Laboratory of Biology and Genetics Improvement of Maize in Northern Northeast Region, Ministry of Agriculture and Rural Affairs, Harbin 150086, China
- Keshan Branch of Heilongjiang Academy of Agricultural Sciences, Qiqihaer 161000, China
| | - Xuena Ma
- Maize Research Institute of Heilongjiang Academy of Agricultural Sciences, Harbin 150086, China; (J.C.); (Q.C.); (X.L.); (X.M.)
- Key Laboratory of Biology and Genetics Improvement of Maize in Northern Northeast Region, Ministry of Agriculture and Rural Affairs, Harbin 150086, China
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Wu L, Zheng Y, Jiao F, Wang M, Zhang J, Zhang Z, Huang Y, Jia X, Zhu L, Zhao Y, Guo J, Chen J. Identification of quantitative trait loci for related traits of stalk lodging resistance using genome-wide association studies in maize (Zea mays L.). BMC Genom Data 2022; 23:76. [PMID: 36319954 PMCID: PMC9623923 DOI: 10.1186/s12863-022-01091-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2021] [Accepted: 10/10/2022] [Indexed: 11/26/2022] Open
Abstract
BACKGROUND Stalk lodging is one of the main factors affecting maize (Zea mays L.) yield and limiting mechanized harvesting. Developing maize varieties with high stalk lodging resistance requires exploring the genetic basis of lodging resistance-associated agronomic traits. Stalk strength is an important indicator to evaluate maize lodging and can be evaluated by measuring stalk rind penetrometer resistance (RPR) and stalk buckling strength (SBS). Along with morphological traits of the stalk for the third internodes length (TIL), fourth internode length (FIL), third internode diameter (TID), and the fourth internode diameter (FID) traits are associated with stalk lodging resistance. RESULTS In this study, a natural population containing 248 diverse maize inbred lines genotyped with 83,057 single nucleotide polymorphism (SNP) markers was used for genome-wide association study (GWAS) for six stalk lodging resistance-related traits. The heritability of all traits ranged from 0.59 to 0.72 in the association mapping panel. A total of 85 significant SNPs were identified for the association mapping panel using best linear unbiased prediction (BLUP) values of all traits. Additionally, five candidate genes were associated with stalk strength traits, which were either directly or indirectly associated with cell wall components. CONCLUSIONS These findings contribute to our understanding of the genetic basis of maize stalk lodging and provide valuable theoretical guidance for lodging resistance in maize breeding in the future.
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Affiliation(s)
- Lifen Wu
- State Key Laboratory of North China Crop Improvement and Regulation, Hebei Sub-Center for National Maize Improvement Center, College of Agronomy, Hebei Agricultural University, Hebei, Baoding 071001 China
| | - Yunxiao Zheng
- State Key Laboratory of North China Crop Improvement and Regulation, Hebei Sub-Center for National Maize Improvement Center, College of Agronomy, Hebei Agricultural University, Hebei, Baoding 071001 China
| | - Fuchao Jiao
- grid.412608.90000 0000 9526 6338College of Agronomy, Qingdao Agricultural University, Shandong, Qingdao 266109 China
| | - Ming Wang
- grid.412608.90000 0000 9526 6338College of Agronomy, Qingdao Agricultural University, Shandong, Qingdao 266109 China
| | - Jing Zhang
- State Key Laboratory of North China Crop Improvement and Regulation, Hebei Sub-Center for National Maize Improvement Center, College of Agronomy, Hebei Agricultural University, Hebei, Baoding 071001 China
| | - Zhongqin Zhang
- State Key Laboratory of North China Crop Improvement and Regulation, Hebei Sub-Center for National Maize Improvement Center, College of Agronomy, Hebei Agricultural University, Hebei, Baoding 071001 China
| | - Yaqun Huang
- State Key Laboratory of North China Crop Improvement and Regulation, Hebei Sub-Center for National Maize Improvement Center, College of Agronomy, Hebei Agricultural University, Hebei, Baoding 071001 China
| | - Xiaoyan Jia
- State Key Laboratory of North China Crop Improvement and Regulation, Hebei Sub-Center for National Maize Improvement Center, College of Agronomy, Hebei Agricultural University, Hebei, Baoding 071001 China
| | - Liying Zhu
- State Key Laboratory of North China Crop Improvement and Regulation, Hebei Sub-Center for National Maize Improvement Center, College of Agronomy, Hebei Agricultural University, Hebei, Baoding 071001 China
| | - Yongfeng Zhao
- State Key Laboratory of North China Crop Improvement and Regulation, Hebei Sub-Center for National Maize Improvement Center, College of Agronomy, Hebei Agricultural University, Hebei, Baoding 071001 China
| | - Jinjie Guo
- State Key Laboratory of North China Crop Improvement and Regulation, Hebei Sub-Center for National Maize Improvement Center, College of Agronomy, Hebei Agricultural University, Hebei, Baoding 071001 China
| | - Jingtang Chen
- State Key Laboratory of North China Crop Improvement and Regulation, Hebei Sub-Center for National Maize Improvement Center, College of Agronomy, Hebei Agricultural University, Hebei, Baoding 071001 China ,grid.412608.90000 0000 9526 6338College of Agronomy, Qingdao Agricultural University, Shandong, Qingdao 266109 China
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Li C, Jia Y, Zhou R, Liu L, Cao M, Zhou Y, Wang Z, Di H. GWAS and RNA-seq analysis uncover candidate genes associated with alkaline stress tolerance in maize ( Zea mays L.) seedlings. FRONTIERS IN PLANT SCIENCE 2022; 13:963874. [PMID: 35923879 PMCID: PMC9340071 DOI: 10.3389/fpls.2022.963874] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Accepted: 06/24/2022] [Indexed: 06/15/2023]
Abstract
Soil salt-alkalization is a common yet critical environmental stress factor for plant growth and development. Discovering and exploiting genes associated with alkaline tolerance in maize (Zea mays L.) is helpful for improving alkaline resistance. Here, an association panel consisting of 200 maize lines was used to identify the genetic loci responsible for alkaline tolerance-related traits in maize seedlings. A total of nine single-nucleotide polymorphisms (SNPs) and their associated candidate genes were found to be significantly associated with alkaline tolerance using a genome-wide association study (GWAS). An additional 200 genes were identified when the screen was extended to include a linkage disequilibrium (LD) decay distance of r2 ≥ 0.2 from the SNPs. RNA-sequencing (RNA-seq) analysis was then conducted to confirm the linkage between the candidate genes and alkali tolerance. From these data, a total of five differentially expressed genes (DEGs; |log2FC| ≥ 0.585, p < 0.05) were verified as the hub genes involved in alkaline tolerance. Subsequently, two candidate genes, Zm00001d038250 and Zm00001d001960, were verified to affect the alkaline tolerance of maize seedlings by qRT-PCR analysis. These genes were putatively involved protein binding and "flavonoid biosynthesis process," respectively, based on Kyoto Encyclopedia of Genes and Genomes (KEGG) and Gene Ontology (GO) enrichment analyses. Gene promoter region contains elements related to stress and metabolism. The results of this study will help further elucidate the mechanisms of alkaline tolerance in maize, which will provide the groundwork for future breeding projects.
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Lacasa J, Ciampitti IA, Amas JI, Curín F, Luque SF, Otegui ME. Breeding effects on canopy light attenuation in maize: a retrospective and prospective analysis. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:1301-1311. [PMID: 34939088 DOI: 10.1093/jxb/erab503] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2021] [Accepted: 11/15/2021] [Indexed: 06/14/2023]
Abstract
The light attenuation process within a plant canopy defines energy capture and vertical distribution of light and nitrogen (N). The vertical light distribution can be quantitatively described with the extinction coefficient (k), which associates the fraction of intercepted photosynthetically active radiation (fPARi) with the leaf area index (LAI). Lower values of k correspond to upright leaves and homogeneous vertical light distribution, increasing radiation use efficiency (RUE). Yield gains in maize (Zea mays L.) were accompanied by increases in optimum plant density and leaf erectness. Thus, the yield-driven breeding programs and management changes, such as reduced row spacing, selected a more erect leaf habit under different maize production systems (e.g., China and the USA). In this study, data from Argentina revealed that k decreased at a rate of 1.1% year-1 since 1989, regardless of plant density and in agreement with Chinese reports (1.0% year-1 since 1981). A reliable assessment of changes in k over time is critical for predicting (i) modifications in resource use efficiency (e.g. radiation, water, and N), improving estimations derived from crop simulation models; (ii) differences in productivity caused by management practices; and (iii) limitations to further exploit this trait with breeding.
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Affiliation(s)
- Josefina Lacasa
- Department of Agronomy, Kansas State University, 2004 Throckmorton Plant Science Center, Manhattan, KS, USA
- Dpto. de Producción Vegetal, Facultad de Agronomía, Universidad de Buenos Aires, Av. San Martín 4453 (C1417DSE), Ciudad de Buenos Aires, Argentina
| | - Ignacio A Ciampitti
- Department of Agronomy, Kansas State University, 2004 Throckmorton Plant Science Center, Manhattan, KS, USA
| | - Juan I Amas
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) en INTA, Centro Regional Buenos Aires Norte, Estación Experimental Agropecuaria, Ruta 32 km 4.5, Pergamino (C2700), Provincia de Buenos Aires, Argentina
| | - Facundo Curín
- Centro de Investigaciones y Transferencia del noroeste de la Provincia de Buenos Aires (CIT-NOBA-CONICET), Argentina
| | - Sergio F Luque
- Cátedra de Cereales y Oleaginosas, Facultad de Ciencias Agropecuarias, Universidad Nacional de Córdoba, Córdoba, Argentina
| | - María E Otegui
- Dpto. de Producción Vegetal, Facultad de Agronomía, Universidad de Buenos Aires, Av. San Martín 4453 (C1417DSE), Ciudad de Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) en INTA, Centro Regional Buenos Aires Norte, Estación Experimental Agropecuaria, Ruta 32 km 4.5, Pergamino (C2700), Provincia de Buenos Aires, Argentina
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Rida S, Maafi O, López-Malvar A, Revilla P, Riache M, Djemel A. Genetics of Germination and Seedling Traits under Drought Stress in a MAGIC Population of Maize. PLANTS (BASEL, SWITZERLAND) 2021; 10:1786. [PMID: 34579319 PMCID: PMC8468063 DOI: 10.3390/plants10091786] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 08/23/2021] [Accepted: 08/24/2021] [Indexed: 01/31/2023]
Abstract
Drought is one of the most detrimental abiotic stresses hampering seed germination, development, and productivity. Maize is more sensitive to drought than other cereals, especially at seedling stage. Our objective was to study genetic regulation of drought tolerance at germination and during seedling growth in maize. We evaluated 420 RIL with their parents from a multi-parent advanced generation inter-cross (MAGIC) population with PEG-induced drought at germination and seedling establishment. A genome-wide association study (GWAS) was carried out to identify genomic regions associated with drought tolerance. GWAS identified 28 and 16 SNPs significantly associated with germination and seedling traits under stress and well-watered conditions, respectively. Among the SNPs detected, two SNPs had significant associations with several traits with high positive correlations, suggesting a pleiotropic genetic control. Other SNPs were located in regions that harbored major QTLs in previous studies, and co-located with QTLs for cold tolerance previously published for this MAGIC population. The genomic regions comprised several candidate genes related to stresses and plant development. These included numerous drought-responsive genes and transcription factors implicated in germination, seedling traits, and drought tolerance. The current analyses provide information and tools for subsequent studies and breeding programs for improving drought tolerance.
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Affiliation(s)
- Soumeya Rida
- Higher National Agronomic School (ENSA), L-RGB, Hassan Badi, El Harrach, Algiers 16004, Algeria; (S.R.); (O.M.); (M.R.); (A.D.)
| | - Oula Maafi
- Higher National Agronomic School (ENSA), L-RGB, Hassan Badi, El Harrach, Algiers 16004, Algeria; (S.R.); (O.M.); (M.R.); (A.D.)
| | - Ana López-Malvar
- Facultad de Biología, Departamento de Biología Vegetal y Ciencias del Suelo, Agrobiología Ambiental, Calidad de Suelos y Plantas, Universidad de Vigo, As Lagoas Marcosende, 36310 Vigo, Spain
| | - Pedro Revilla
- Misión Biológica de Galicia (CSIC), Apartado 28, E-36080 Pontevedra, Spain;
| | - Meriem Riache
- Higher National Agronomic School (ENSA), L-RGB, Hassan Badi, El Harrach, Algiers 16004, Algeria; (S.R.); (O.M.); (M.R.); (A.D.)
| | - Abderahmane Djemel
- Higher National Agronomic School (ENSA), L-RGB, Hassan Badi, El Harrach, Algiers 16004, Algeria; (S.R.); (O.M.); (M.R.); (A.D.)
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Dissecting the Genetic Basis of Flowering Time and Height Related-Traits Using Two Doubled Haploid Populations in Maize. PLANTS 2021; 10:plants10081585. [PMID: 34451629 PMCID: PMC8399143 DOI: 10.3390/plants10081585] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 07/23/2021] [Accepted: 07/27/2021] [Indexed: 11/16/2022]
Abstract
In the field, maize flowering time and height traits are closely linked with yield, planting density, lodging resistance, and grain fill. To explore the genetic basis of flowering time and height traits in maize, we investigated six related traits, namely, days to anthesis (AD), days to silking (SD), the anthesis-silking interval (ASI), plant height (PH), ear height (EH), and the EH/PH ratio (ER) in two locations for two years based on two doubled haploid (DH) populations. Based on the two high-density genetic linkage maps, 12 and 22 quantitative trait loci (QTL) were identified, respectively, for flowering time and height-related traits. Of these, ten QTLs had overlapping confidence intervals between the two populations and were integrated into three consensus QTLs (qFT_YZ1a, qHT_YZ5a, and qHT_YZ7a). Of these, qFT_YZ1a, conferring flowering time, is located at 221.1-277.0 Mb on chromosome 1 and explained 10.0-12.5% of the AD and SD variation, and qHT_YZ5a, conferring height traits, is located at 147.4-217.3 Mb on chromosome 5 and explained 11.6-15.3% of the PH and EH variation. These consensus QTLs, in addition to the other repeatedly detected QTLs, provide useful information for further genetic studies and variety improvements in flowering time and height-related traits.
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Adak A, Conrad C, Chen Y, Wilde SC, Murray SC, Anderson S, Subramanian NK. Validation of Functional Polymorphisms Affecting Maize Plant Height by Unoccupied Aerial Systems (UAS) Discovers Novel Temporal Phenotypes. G3-GENES GENOMES GENETICS 2021; 11:6211193. [PMID: 33822935 PMCID: PMC8495742 DOI: 10.1093/g3journal/jkab075] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/25/2020] [Accepted: 02/28/2021] [Indexed: 11/14/2022]
Abstract
Plant height (PHT) in maize (Zea mays L.) has been scrutinized genetically and phenotypically due to relationship with other agronomically valuable traits (e.g. yield). Heritable variation of PHT is determined by many discovered quantitative trait loci (QTLs); however, phenotypic effects of such loci often lack validation across environments and genetic backgrounds, especially in the hybrid state grown by farmers rather than the inbred state more often used by geneticists. A previous genome wide association study using a topcrossed hybrid diversity panel identified two novel quantitative trait variants (QTVs) controlling both PHT and grain yield. Here, heterogeneous inbred families demonstrated that these two loci, characterized by two single nucleotide polymorphisms (SNPs), cause phenotypic variation in inbred lines, but that size of these effects were variable across four different genetic backgrounds, ranging from 1 to 10 cm. Weekly unoccupied aerial system flights demonstrated the two SNPs had larger effects, varying from 10 to 25 cm, in early growth while effects decreased towards the end of the season. These results show that allelic effect sizes of economically valuable loci are both dynamic in temporal growth and dynamic across genetic backgrounds, resulting in informative phenotypic variability overlooked following traditional phenotyping methods. Public genotyping data shows recent favorable allele selection in elite temperate germplasm with little change across tropical backgrounds. As these loci remain rarer in tropical germplasm, with effects most visible early in growth, they are useful for breeding and selection to expand the genetic basis of maize.
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Affiliation(s)
- Alper Adak
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Clarissa Conrad
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yuanyuan Chen
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China.,Department of Environmental Horticulture, Institute of Food and Agricultural Sciences, Mid-Florida Research and Education Center, University of Florida, Apopka, FL, 32703, USA
| | - Scott C Wilde
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Seth C Murray
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Steven Anderson
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China.,Department of Soil and Crop Sciences, Texas A&M University, College Station, TX 77843-2474, USA
| | - Nithya K Subramanian
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
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Wang P, Sun X, Zhang K, Fang Y, Wang J, Yang C, Li WX, Ning H. Mapping QTL/QTN and mining candidate genes for plant height and its response to planting densities in soybean [ Glycine max (L.) Merr.] through a FW-RIL population. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2021; 41:12. [PMID: 37309477 PMCID: PMC10236039 DOI: 10.1007/s11032-021-01209-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Accepted: 01/26/2021] [Indexed: 06/13/2023]
Abstract
Plant height (PH) determines the morphology and seed yield of soybean, so it is an important breeding target, which is controlled by multiple genes and affected by plant density. In this research, it was used about a four-way recombinant inbred lines (FW-RIL) with 144 families constructed by double cross (Kenfeng 14 × Kenfeng 15) × (Heinong 48 × Kenfeng 19) as experimental materials, with the purpose to map QTL/QTN associated with PH under densities of 2.2×105 plant/ha (D1) and 3×105 plant/ha (D2) in five environments. The results showed that response of PH to densities varied in accordance to genotypes among environments. A total of 26 QTLs and 13 QTNs were identified specifically in D1; 20 QTLs and 21 QTNs were identified specifically in D2. Nine QTLs and one QTN were discovered commonly in two densities. Fifteen QTLs and 9 QTNs were repeatedly detected by multiple statistical methods, densities, or environments, which could be considered stable. Eighteen QTLs were detected, as well as 7 QTNs underlying responses of PH to density increment. Six QTNs, co-located in the interval of QTL, were detected in more than two environments or methods with a longer genome length over 3000 kb. Based on gene ontology (GO) enrichment analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis, five genes were predicted as candidates, which were likely to be involved in growth and development of PH. The results will help elucidate the genetic basis and improve molecular assistant selection of PH. Supplementary Information The online version contains supplementary material available at 10.1007/s11032-021-01209-0.
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Affiliation(s)
- Ping Wang
- Key Laboratory of Soybean Biology, Ministry of Education/Key Laboratory of Soybean Biology and Breeding/Genetics, Ministry of Agriculture, Northeast Agricultural University, Harbin, China
- Huaiyin Institute of Technology, Huai’an, China
| | - Xu Sun
- Key Laboratory of Soybean Biology, Ministry of Education/Key Laboratory of Soybean Biology and Breeding/Genetics, Ministry of Agriculture, Northeast Agricultural University, Harbin, China
| | - Kaixin Zhang
- Key Laboratory of Soybean Biology, Ministry of Education/Key Laboratory of Soybean Biology and Breeding/Genetics, Ministry of Agriculture, Northeast Agricultural University, Harbin, China
| | - Yanlong Fang
- Key Laboratory of Soybean Biology, Ministry of Education/Key Laboratory of Soybean Biology and Breeding/Genetics, Ministry of Agriculture, Northeast Agricultural University, Harbin, China
| | - Jiajing Wang
- Key Laboratory of Soybean Biology, Ministry of Education/Key Laboratory of Soybean Biology and Breeding/Genetics, Ministry of Agriculture, Northeast Agricultural University, Harbin, China
| | - Chang Yang
- Key Laboratory of Soybean Biology, Ministry of Education/Key Laboratory of Soybean Biology and Breeding/Genetics, Ministry of Agriculture, Northeast Agricultural University, Harbin, China
| | - Wen-Xia Li
- Key Laboratory of Soybean Biology, Ministry of Education/Key Laboratory of Soybean Biology and Breeding/Genetics, Ministry of Agriculture, Northeast Agricultural University, Harbin, China
| | - Hailong Ning
- Key Laboratory of Soybean Biology, Ministry of Education/Key Laboratory of Soybean Biology and Breeding/Genetics, Ministry of Agriculture, Northeast Agricultural University, Harbin, China
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Lu X, Wang J, Wang Y, Wen W, Zhang Y, Du J, Zhao Y, Guo X. Genome-Wide Association Study of Maize Aboveground Dry Matter Accumulation at Seedling Stage. Front Genet 2021; 11:571236. [PMID: 33519889 PMCID: PMC7838602 DOI: 10.3389/fgene.2020.571236] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Accepted: 11/30/2020] [Indexed: 11/13/2022] Open
Abstract
Dry matter accumulation and partitioning during the early phases of development could significantly affect crop growth and productivity. In this study, the aboveground dry matter (DM), the DM of different organs, and partition coefficients of a maize association mapping panel of 412 inbred lines were evaluated at the third and sixth leaf stages (V3 and V6). Further, the properties of these phenotypic traits were analyzed. Genome-wide association studies (GWAS) were conducted on the total aboveground biomass and the DM of different organs. Analysis of GWAS results identified a total of 1,103 unique candidate genes annotated by 678 significant SNPs (P value < 1.28e-6). A total of 224 genes annotated by SNPs at the top five of each GWAS method and detected by multiple GWAS methods were regarded as having high reliability. Pathway enrichment analysis was also performed to explore the biological significance and functions of these candidate genes. Several biological pathways related to the regulation of seed growth, gibberellin-mediated signaling pathway, and long-day photoperiodism were enriched. The results of our study could provide new perspectives on breeding high-yielding maize varieties.
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Affiliation(s)
- Xianju Lu
- Beijing Key Laboratory of Digital Plant, Beijing Research Center for Information Technology in Agriculture, National Engineering Research Center for Information Technology in Agriculture, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Jinglu Wang
- Beijing Key Laboratory of Digital Plant, Beijing Research Center for Information Technology in Agriculture, National Engineering Research Center for Information Technology in Agriculture, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Yongjian Wang
- Beijing Key Laboratory of Digital Plant, Beijing Research Center for Information Technology in Agriculture, National Engineering Research Center for Information Technology in Agriculture, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Weiliang Wen
- Beijing Key Laboratory of Digital Plant, Beijing Research Center for Information Technology in Agriculture, National Engineering Research Center for Information Technology in Agriculture, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Ying Zhang
- Beijing Key Laboratory of Digital Plant, Beijing Research Center for Information Technology in Agriculture, National Engineering Research Center for Information Technology in Agriculture, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Jianjun Du
- Beijing Key Laboratory of Digital Plant, Beijing Research Center for Information Technology in Agriculture, National Engineering Research Center for Information Technology in Agriculture, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Yanxin Zhao
- Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular Breeding, Maize Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Xinyu Guo
- Beijing Key Laboratory of Digital Plant, Beijing Research Center for Information Technology in Agriculture, National Engineering Research Center for Information Technology in Agriculture, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
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Zhang Y, Wang J, Du J, Zhao Y, Lu X, Wen W, Gu S, Fan J, Wang C, Wu S, Wang Y, Liao S, Zhao C, Guo X. Dissecting the phenotypic components and genetic architecture of maize stem vascular bundles using high-throughput phenotypic analysis. PLANT BIOTECHNOLOGY JOURNAL 2021; 19:35-50. [PMID: 32569428 PMCID: PMC7769239 DOI: 10.1111/pbi.13437] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Revised: 06/03/2020] [Accepted: 06/15/2020] [Indexed: 05/27/2023]
Abstract
High-throughput phenotyping is increasingly becoming an important tool for rapid advancement of genetic gain in breeding programmes. Manual phenotyping of vascular bundles is tedious and time-consuming, which lags behind the rapid development of functional genomics in maize. More robust and automated techniques of phenotyping vascular bundles traits at high-throughput are urgently needed for large crop populations. In this study, we developed a standard process for stem micro-CT data acquisition and an automatic CT image process pipeline to obtain vascular bundle traits of stems including geometry-related, morphology-related and distribution-related traits. Next, we analysed the phenotypic variation of stem vascular bundles between natural population subgroup (480 inbred lines) based on 48 comprehensively phenotypic information. Also, the first database for stem micro-phenotypes, MaizeSPD, was established, storing 554 pieces of basic information of maize inbred lines, 523 pieces of experimental information, 1008 pieces of CT scanning images and processed images, and 24 192 pieces of phenotypic data. Combined with genome-wide association studies (GWASs), a total of 1562 significant single nucleotide polymorphism (SNPs) were identified for 30 stem micro-phenotypic traits, and 84 unique genes of 20 traits such as VBNum, VBAvArea and PZVBDensity were detected. Candidate genes identified by GWAS mainly encode enzymes involved in cell wall metabolism, transcription factors, protein kinase and protein related to plant signal transduction and stress response. The results presented here will advance our knowledge about phenotypic trait components of stem vascular bundles and provide useful information for understanding the genetic controls of vascular bundle formation and development.
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Affiliation(s)
- Ying Zhang
- Beijing Key Lab of Digital PlantNational Engineering Research Center for Information Technology in AgricultureBeijing Research Center for Information Technology in AgricultureBeijing Academy of Agriculture and Forestry SciencesBeijingChina
| | - Jinglu Wang
- Beijing Key Lab of Digital PlantNational Engineering Research Center for Information Technology in AgricultureBeijing Research Center for Information Technology in AgricultureBeijing Academy of Agriculture and Forestry SciencesBeijingChina
| | - Jianjun Du
- Beijing Key Lab of Digital PlantNational Engineering Research Center for Information Technology in AgricultureBeijing Research Center for Information Technology in AgricultureBeijing Academy of Agriculture and Forestry SciencesBeijingChina
| | - Yanxin Zhao
- Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular BreedingMaize Research CenterBeijing Academy of Agriculture and Forestry SciencesBeijingChina
| | - Xianju Lu
- Beijing Key Lab of Digital PlantNational Engineering Research Center for Information Technology in AgricultureBeijing Research Center for Information Technology in AgricultureBeijing Academy of Agriculture and Forestry SciencesBeijingChina
| | - Weiliang Wen
- Beijing Key Lab of Digital PlantNational Engineering Research Center for Information Technology in AgricultureBeijing Research Center for Information Technology in AgricultureBeijing Academy of Agriculture and Forestry SciencesBeijingChina
| | - Shenghao Gu
- Beijing Key Lab of Digital PlantNational Engineering Research Center for Information Technology in AgricultureBeijing Research Center for Information Technology in AgricultureBeijing Academy of Agriculture and Forestry SciencesBeijingChina
| | - Jiangchuan Fan
- Beijing Key Lab of Digital PlantNational Engineering Research Center for Information Technology in AgricultureBeijing Research Center for Information Technology in AgricultureBeijing Academy of Agriculture and Forestry SciencesBeijingChina
| | - Chuanyu Wang
- Beijing Key Lab of Digital PlantNational Engineering Research Center for Information Technology in AgricultureBeijing Research Center for Information Technology in AgricultureBeijing Academy of Agriculture and Forestry SciencesBeijingChina
| | - Sheng Wu
- Beijing Key Lab of Digital PlantNational Engineering Research Center for Information Technology in AgricultureBeijing Research Center for Information Technology in AgricultureBeijing Academy of Agriculture and Forestry SciencesBeijingChina
| | - Yongjian Wang
- Beijing Key Lab of Digital PlantNational Engineering Research Center for Information Technology in AgricultureBeijing Research Center for Information Technology in AgricultureBeijing Academy of Agriculture and Forestry SciencesBeijingChina
| | - Shengjin Liao
- Beijing Key Lab of Digital PlantNational Engineering Research Center for Information Technology in AgricultureBeijing Research Center for Information Technology in AgricultureBeijing Academy of Agriculture and Forestry SciencesBeijingChina
| | - Chunjiang Zhao
- Beijing Key Lab of Digital PlantNational Engineering Research Center for Information Technology in AgricultureBeijing Research Center for Information Technology in AgricultureBeijing Academy of Agriculture and Forestry SciencesBeijingChina
| | - Xinyu Guo
- Beijing Key Lab of Digital PlantNational Engineering Research Center for Information Technology in AgricultureBeijing Research Center for Information Technology in AgricultureBeijing Academy of Agriculture and Forestry SciencesBeijingChina
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11
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Li S, Zhang C, Lu M, Yang D, Qian Y, Yue Y, Zhang Z, Jin F, Wang M, Liu X, Liu W, Li X. QTL mapping and GWAS for field kernel water content and kernel dehydration rate before physiological maturity in maize. Sci Rep 2020; 10:13114. [PMID: 32753586 PMCID: PMC7403598 DOI: 10.1038/s41598-020-69890-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Accepted: 07/20/2020] [Indexed: 11/09/2022] Open
Abstract
Kernel water content (KWC) and kernel dehydration rate (KDR) are two main factors affecting maize seed quality and have a decisive influence on the mechanical harvest. It is of great importance to map and mine candidate genes related to KWCs and KDRs before physiological maturity in maize. 120 double-haploid (DH) lines constructed from Si287 with low KWC and JiA512 with high KWC were used as the mapping population. KWCs were measured every 5 days from 10 to 40 days after pollination, and KDRs were calculated. A total of 1702 SNP markers were used to construct a linkage map, with a total length of 1,309.02 cM and an average map distance of 0.77 cM. 10 quantitative trait loci (QTLs) and 27 quantitative trait nucleotides (QTNs) were detected by genome-wide composite interval mapping (GCIM) and multi-locus random-SNP-effect mixed linear model (mrMLM), respectively. One and two QTL hotspot regions were found on Chromosome 3 and 7, respectively. Analysis of the Gene Ontology showed that 2 GO terms of biological processes (BP) were significantly enriched (P ≤ 0.05) and 6 candidate genes were obtained. This study provides theoretical support for marker-assisted breeding of mechanical harvest variety in maize.
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Affiliation(s)
- Shufang Li
- Crop Germplasm Resources Institute, Jilin Academy of Agricultural Sciences, Kemaoxi Street 303, Gongzhuling, 136100, Jilin Province, China
| | - Chunxiao Zhang
- Crop Germplasm Resources Institute, Jilin Academy of Agricultural Sciences, Kemaoxi Street 303, Gongzhuling, 136100, Jilin Province, China
| | - Ming Lu
- Maize Research Institute, Jilin Academy of Agricultural Sciences, Gongzhuling, 136100, China
| | - Deguang Yang
- College of Agronomy, Northeast Agricultural University, Harbin, 150030, China
| | - Yiliang Qian
- Maize Research Center, Anhui Academy of Agricultural Science, Hefei, 230001, China
| | - Yaohai Yue
- Maize Research Institute, Jilin Academy of Agricultural Sciences, Gongzhuling, 136100, China
| | - Zhijun Zhang
- Maize Research Institute, Jilin Academy of Agricultural Sciences, Gongzhuling, 136100, China
| | - Fengxue Jin
- Crop Germplasm Resources Institute, Jilin Academy of Agricultural Sciences, Kemaoxi Street 303, Gongzhuling, 136100, Jilin Province, China
| | - Min Wang
- Maize Research Institute, Jilin Academy of Agricultural Sciences, Gongzhuling, 136100, China
| | - Xueyan Liu
- Crop Germplasm Resources Institute, Jilin Academy of Agricultural Sciences, Kemaoxi Street 303, Gongzhuling, 136100, Jilin Province, China
| | - Wenguo Liu
- Maize Research Institute, Jilin Academy of Agricultural Sciences, Gongzhuling, 136100, China.
| | - Xiaohui Li
- Crop Germplasm Resources Institute, Jilin Academy of Agricultural Sciences, Kemaoxi Street 303, Gongzhuling, 136100, Jilin Province, China.
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12
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Zhang H, Zhang J, Xu Q, Wang D, Di H, Huang J, Yang X, Wang Z, Zhang L, Dong L, Wang Z, Zhou Y. Identification of candidate tolerance genes to low-temperature during maize germination by GWAS and RNA-seqapproaches. BMC PLANT BIOLOGY 2020; 20:333. [PMID: 32664856 PMCID: PMC7362524 DOI: 10.1186/s12870-020-02543-9] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Accepted: 07/06/2020] [Indexed: 05/19/2023]
Abstract
BACKGROUND Maize (Zea mays L.) is one of the main agricultural crops with the largest yield and acreage in the world. However, maize germplasm is very sensitive to low temperatures, mainly during germination, and low temperatures significantly affect plant growth and crop yield. Therefore, the identification of genes capable of increasing tolerance to low temperature has become necessary. RESULTS In this study, fourteen phenotypic traits related to seed germination were used to assess the genetic diversity of maize through genome-wide association study (GWAS). A total of 30 single-nucleotide polymorphisms (SNPs) linked to low-temperature tolerance were detected (-log10(P) > 4), fourteen candidate genes were found to be directly related to the SNPs, further additional 68 genes were identified when the screen was extended to include a linkage disequilibrium (LD) decay distance of r2 ≥ 0.2 from the SNPs. RNA-sequencing (RNA-seq) analysis was then used to confirm the linkage between the candidate gene and low-temperature tolerance. A total of ten differentially expressed genes (DEGs) (|log2 fold change (FC)| ≥ 0.585, P < 0.05) were found within the set distance of LD decay (r2 ≥ 0.2). Among these genes, the expression of six DEGs was verified using qRT-PCR. Zm00001d039219 and Zm00001d034319 were putatively involved in 'mitogen activated protein kinase (MAPK) signal transduction' and 'fatty acid metabolic process', respectively, based on Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses. Thus, these genes appeared to be related to low-temperature signal transduction and cell membrane fluidity. CONCLUSION Overall, by integrating the results of our GWAS and DEG analysis of low-temperature tolerance during germination in maize, we were able to identify a total of 30 SNPs and 82 related candidate genes, including 10 DEGs, two of which were involved in the response to tolerance to low temperature. Functional analysis will provide valuable information for understanding the genetic mechanism of low-temperature tolerance during germination in maize.
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Affiliation(s)
- Hong Zhang
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, College of Agronomy, Northeast Agricultural University, Harbin, 150030, Heilongjiang, China
| | - Jiayue Zhang
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, College of Agronomy, Northeast Agricultural University, Harbin, 150030, Heilongjiang, China
| | - Qingyu Xu
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, College of Agronomy, Northeast Agricultural University, Harbin, 150030, Heilongjiang, China
| | - Dandan Wang
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, College of Agronomy, Northeast Agricultural University, Harbin, 150030, Heilongjiang, China
| | - Hong Di
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, College of Agronomy, Northeast Agricultural University, Harbin, 150030, Heilongjiang, China
| | - Jun Huang
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou, 510642, Guangdong, China
| | - Xiuwei Yang
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, College of Agronomy, Northeast Agricultural University, Harbin, 150030, Heilongjiang, China
| | - Zhoufei Wang
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou, 510642, Guangdong, China
| | - Lin Zhang
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, College of Agronomy, Northeast Agricultural University, Harbin, 150030, Heilongjiang, China
| | - Ling Dong
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, College of Agronomy, Northeast Agricultural University, Harbin, 150030, Heilongjiang, China
| | - Zhenhua Wang
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, College of Agronomy, Northeast Agricultural University, Harbin, 150030, Heilongjiang, China.
| | - Yu Zhou
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, College of Agronomy, Northeast Agricultural University, Harbin, 150030, Heilongjiang, China.
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13
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Kofsky J, Zhang H, Song BH. Genetic Architecture of Early Vigor Traits in Wild Soybean. Int J Mol Sci 2020; 21:E3105. [PMID: 32354037 PMCID: PMC7247153 DOI: 10.3390/ijms21093105] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Accepted: 04/24/2020] [Indexed: 01/13/2023] Open
Abstract
A worldwide food shortage has been projected as a result of the current increase in global population and climate change. In order to provide sufficient food to feed more people, we must develop crops that can produce higher yields. Plant early vigor traits, early growth rate (EGR), early plant height (EPH), inter-node length, and node count are important traits that are related to crop yield. Glycine soja, the wild counterpart to cultivated soybean, Glycine max, harbors much higher genetic diversity and can grow in diverse environments. It can also cross easily with cultivated soybean. Thus, it holds a great potential in developing soybean cultivars with beneficial agronomic traits. In this study, we used 225 wild soybean accessions originally from diverse environments across its geographic distribution in East Asia. We quantified the natural variation of several early vigor traits, investigated the relationships among them, and dissected the genetic basis of these traits by applying a Genome-Wide Association Study (GWAS) with genome-wide single nucleotide polymorphism (SNP) data. Our results showed positive correlation between all early vigor traits studied. A total of 12 SNPs significantly associated with EPH were identified with 4 shared with EGR. We also identified two candidate genes, Glyma.07G055800.1 and Glyma.07G055900.1, playing important roles in influencing trait variation in both EGR and EPH in G. soja.
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Affiliation(s)
| | | | - Bao-Hua Song
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, NC 28223, USA; (J.K.); (H.Z.)
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14
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Li M, Liu Y, Tao Y, Xu C, Li X, Zhang X, Han Y, Yang X, Sun J, Li W, Li D, Zhao X, Zhao L. Identification of genetic loci and candidate genes related to soybean flowering through genome wide association study. BMC Genomics 2019; 20:987. [PMID: 31842754 PMCID: PMC6916438 DOI: 10.1186/s12864-019-6324-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2019] [Accepted: 11/22/2019] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND As a photoperiod-sensitive and self-pollinated species, the growth periods traits play important roles in the adaptability and yield of soybean. To examine the genetic architecture of soybean growth periods, we performed a genome-wide association study (GWAS) using a panel of 278 soybean accessions and 34,710 single nucleotide polymorphisms (SNPs) with minor allele frequencies (MAF) higher than 0.04 detected by the specific-locus amplified fragment sequencing (SLAF-seq) with a 6.14-fold average sequencing depth. GWAS was conducted by a compressed mixed linear model (CMLM) involving in both relative kinship and population structure. RESULTS GWAS revealed that 37 significant SNP peaks associated with soybean flowering time or other growth periods related traits including full bloom, beginning pod, full pod, beginning seed, and full seed in two or more environments at -log10(P) > 3.75 or -log10(P) > 4.44 were distributed on 14 chromosomes, including chromosome 1, 2, 3, 5, 6, 9, 11, 12, 13, 14, 15, 17, 18, 19. Fourteen SNPs were novel loci and 23 SNPs were located within known QTLs or 75 kb near the known SNPs. Five candidate genes (Glyma.05G101800, Glyma.11G140100, Glyma.11G142900, Glyma.19G099700, Glyma.19G100900) in a 90 kb genomic region of each side of four significant SNPs (Gm5_27111367, Gm11_10629613, Gm11_10950924, Gm19_34768458) based on the average LD decay were homologs of Arabidopsis flowering time genes of AT5G48385.1, AT3G46510.1, AT5G59780.3, AT1G28050.1, and AT3G26790.1. These genes encoding FRI (FRIGIDA), PUB13 (plant U-box 13), MYB59, CONSTANS, and FUS3 proteins respectively might play important roles in controlling soybean growth periods. CONCLUSIONS This study identified putative SNP markers associated with soybean growth period traits, which could be used for the marker-assisted selection of soybean growth period traits. Furthermore, the possible candidate genes involved in the control of soybean flowering time were predicted.
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Affiliation(s)
- Minmin Li
- Key Laboratory of Soybean Biology of Ministry of Education, China (Key Laboratory of Biology and Genetics & Breeding for Soybean in Northeast China), Northeast Agricultural University, Harbin, China
| | - Ying Liu
- Key Laboratory of Soybean Biology of Ministry of Education, China (Key Laboratory of Biology and Genetics & Breeding for Soybean in Northeast China), Northeast Agricultural University, Harbin, China
| | - Yahan Tao
- Key Laboratory of Soybean Biology of Ministry of Education, China (Key Laboratory of Biology and Genetics & Breeding for Soybean in Northeast China), Northeast Agricultural University, Harbin, China
| | - Chongjing Xu
- Key Laboratory of Soybean Biology of Ministry of Education, China (Key Laboratory of Biology and Genetics & Breeding for Soybean in Northeast China), Northeast Agricultural University, Harbin, China
| | - Xin Li
- Key Laboratory of Soybean Biology of Ministry of Education, China (Key Laboratory of Biology and Genetics & Breeding for Soybean in Northeast China), Northeast Agricultural University, Harbin, China
| | - Xiaoming Zhang
- Key Laboratory of Soybean Biology of Ministry of Education, China (Key Laboratory of Biology and Genetics & Breeding for Soybean in Northeast China), Northeast Agricultural University, Harbin, China
| | - Yingpeng Han
- Key Laboratory of Soybean Biology of Ministry of Education, China (Key Laboratory of Biology and Genetics & Breeding for Soybean in Northeast China), Northeast Agricultural University, Harbin, China
| | - Xue Yang
- Key Laboratory of Soybean Biology of Ministry of Education, China (Key Laboratory of Biology and Genetics & Breeding for Soybean in Northeast China), Northeast Agricultural University, Harbin, China
| | - Jingzhe Sun
- Key Laboratory of Soybean Biology of Ministry of Education, China (Key Laboratory of Biology and Genetics & Breeding for Soybean in Northeast China), Northeast Agricultural University, Harbin, China
| | - Wenbin Li
- Key Laboratory of Soybean Biology of Ministry of Education, China (Key Laboratory of Biology and Genetics & Breeding for Soybean in Northeast China), Northeast Agricultural University, Harbin, China
| | - Dongmei Li
- Key Laboratory of Soybean Biology of Ministry of Education, China (Key Laboratory of Biology and Genetics & Breeding for Soybean in Northeast China), Northeast Agricultural University, Harbin, China
| | - Xue Zhao
- Key Laboratory of Soybean Biology of Ministry of Education, China (Key Laboratory of Biology and Genetics & Breeding for Soybean in Northeast China), Northeast Agricultural University, Harbin, China
| | - Lin Zhao
- Key Laboratory of Soybean Biology of Ministry of Education, China (Key Laboratory of Biology and Genetics & Breeding for Soybean in Northeast China), Northeast Agricultural University, Harbin, China
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15
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Zhang Y, Wan J, He L, Lan H, Li L. Genome-Wide Association Analysis of Plant Height Using the Maize F1 Population. PLANTS 2019; 8:plants8100432. [PMID: 31640296 PMCID: PMC6843250 DOI: 10.3390/plants8100432] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/07/2019] [Revised: 10/01/2019] [Accepted: 10/17/2019] [Indexed: 12/29/2022]
Abstract
Drastic changes in plant height (PH) are observed when maize adapt to a higher plant density. Most importantly, PH is an important factor affecting maize yield. Although the genetic basis of PH has been extensively studied using different populations during the past decades, genetic basis remains unclear in the F1 population, which was a widely used population in production. In this study, a genome-wide association study (GWAS) was conducted using an F1 population consisting of 300 maize hybrids with 17,652 single nucleotide polymorphisms (SNPs) makers to identify candidate genes for controlling PH. A total of nine significant SNPs makers and two candidate genes were identified for PH. The candidate genes, Zm00001d018617 and Zm00001d023659, were the genes most probable to be involved in the development of PH. Our results provide new insights into the genetic basis of PH in maize.
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Affiliation(s)
- Yong Zhang
- Maize Research Institute, Sichuan Agricultural University/Key Laboratory of Crop Genetic Resources and Improvement, Ministry of Education, Chengdu 611130, Sichuan, China.
| | - Jiyu Wan
- Maize Research Institute, Sichuan Agricultural University/Key Laboratory of Crop Genetic Resources and Improvement, Ministry of Education, Chengdu 611130, Sichuan, China.
| | - Lian He
- Maize Research Institute, Sichuan Agricultural University/Key Laboratory of Crop Genetic Resources and Improvement, Ministry of Education, Chengdu 611130, Sichuan, China.
| | - Hai Lan
- Maize Research Institute, Sichuan Agricultural University/Key Laboratory of Crop Genetic Resources and Improvement, Ministry of Education, Chengdu 611130, Sichuan, China.
| | - Lujiang Li
- Maize Research Institute, Sichuan Agricultural University/Key Laboratory of Crop Genetic Resources and Improvement, Ministry of Education, Chengdu 611130, Sichuan, China.
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16
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Gyawali A, Shrestha V, Guill KE, Flint-Garcia S, Beissinger TM. Single-plant GWAS coupled with bulk segregant analysis allows rapid identification and corroboration of plant-height candidate SNPs. BMC PLANT BIOLOGY 2019; 19:412. [PMID: 31590656 PMCID: PMC6781408 DOI: 10.1186/s12870-019-2000-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Accepted: 08/30/2019] [Indexed: 05/22/2023]
Abstract
BACKGROUND Genome wide association studies (GWAS) are a powerful tool for identifying quantitative trait loci (QTL) and causal single nucleotide polymorphisms (SNPs)/genes associated with various important traits in crop species. Typically, GWAS in crops are performed using a panel of inbred lines, where multiple replicates of the same inbred are measured and the average phenotype is taken as the response variable. Here we describe and evaluate single plant GWAS (sp-GWAS) for performing a GWAS on individual plants, which does not require an association panel of inbreds. Instead sp-GWAS relies on the phenotypes and genotypes from individual plants sampled from a randomly mating population. Importantly, we demonstrate how sp-GWAS can be efficiently combined with a bulk segregant analysis (BSA) experiment to rapidly corroborate evidence for significant SNPs. RESULTS In this study we used the Shoepeg maize landrace, collected as an open pollinating variety from a farm in Southern Missouri in the 1960's, to evaluate whether sp-GWAS coupled with BSA can efficiently and powerfully used to detect significant association of SNPs for plant height (PH). Plant were grown in 8 locations across two years and in total 768 individuals were genotyped and phenotyped for sp-GWAS. A total of 306 k polymorphic markers in 768 individuals evaluated via association analysis detected 25 significant SNPs (P ≤ 0.00001) for PH. The results from our single-plant GWAS were further validated by bulk segregant analysis (BSA) for PH. BSA sequencing was performed on the same population by selecting tall and short plants as separate bulks. This approach identified 37 genomic regions for plant height. Of the 25 significant SNPs from GWAS, the three most significant SNPs co-localize with regions identified by BSA. CONCLUSION Overall, this study demonstrates that sp-GWAS coupled with BSA can be a useful tool for detecting significant SNPs and identifying candidate genes. This result is particularly useful for species/populations where association panels are not readily available.
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Affiliation(s)
- Abiskar Gyawali
- Division of Biological Sciences, University of Missouri, Columbia, USA
| | - Vivek Shrestha
- Division of Biological Sciences, University of Missouri, Columbia, USA
| | | | - Sherry Flint-Garcia
- USDA-ARS, Columbia, MO USA
- Division of Plant Sciences, University of Missouri, Columbia, USA
| | - Timothy M. Beissinger
- Department of Crop Sciences, Georg-August Universität Göttingen, Göttingen, Germany
- Center for Integrated Breeding Research, Georg August Universität Göttingen, Göttingen, Germany
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17
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SNP-based mixed model association of growth- and yield-related traits in popcorn. PLoS One 2019; 14:e0218552. [PMID: 31237892 PMCID: PMC6592533 DOI: 10.1371/journal.pone.0218552] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Accepted: 06/04/2019] [Indexed: 12/26/2022] Open
Abstract
The identification of the genes responsible for complex traits is highly promising to accelerate crop breeding, but such information is still limited for popcorn. Thus, in the present study, a mixed linear model-based association analysis (MLMA) was applied for six important popcorn traits: plant and ear height, 100-grain weight, popping expansion, grain yield and expanded popcorn volume per hectare. To this end, 196 plants of the open-pollinated popcorn population UENF-14 were sampled, selfed (S1), and then genotyped with a panel of 10,507 single nucleotide polymorphisms (SNPs) markers distributed throughout the genome. The six traits were studied under two environments [Campos dos Goytacazes-RJ (ENV1) and Itaocara-RJ (ENV2)] in an incomplete block design. Based on the phenotypic data of the S1 progenies and on the genetic characteristics of the parents, the MLMA was performed. Thereafter, genes annotated in the MaizeGDB platform were screened for potential linkage disequilibrium with the SNPs associated to the six evaluated traits. Overall, seven and eight genes were identified as associated with the traits in ENV1 and ENV2, respectively, and proteins encoded by these genes were evaluated for their function. The results obtained here contribute to increase knowledge on the genetic architecture of the six evaluated traits and might be used for marker-assisted selection in breeding programs.
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18
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Nigro D, Gadaleta A, Mangini G, Colasuonno P, Marcotuli I, Giancaspro A, Giove SL, Simeone R, Blanco A. Candidate genes and genome-wide association study of grain protein content and protein deviation in durum wheat. PLANTA 2019; 249:1157-1175. [PMID: 30603787 DOI: 10.1007/s00425-018-03075-1] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2018] [Accepted: 12/19/2018] [Indexed: 05/26/2023]
Abstract
Stable QTL for grain protein content co-migrating with nitrogen-related genes have been identified by the candidate genes and genome-wide association mapping approaches useful for marker-assisted selection. Grain protein content (GPC) is one of the most important quality traits in wheat, defining the nutritional and end-use properties and rheological characteristics. Over the years, a number of breeding programs have been developed aimed to improving GPC, most of them having been prevented by the negative correlation with grain yield. To overcome this issue, a collection of durum wheat germplasm was evaluated for both GPC and grain protein deviation (GPD) in seven field trials. Fourteen candidate genes involved in several processes related to nitrogen metabolism were precisely located on two high-density consensus maps of common and durum wheat, and six of them were found to be highly associated with both traits. The wheat collection was genotyped using the 90 K iSelect array, and 11 stable quantitative trait loci (QTL) for GPC were detected in at least three environments and the mean across environments by the genome-wide association mapping. Interestingly, seven QTL were co-migrating with N-related candidate genes. Four QTL were found to be significantly associated to increases of GPD, indicating that selecting for GPC could not affect final grain yield per spike. The combined approaches of candidate genes and genome-wide association mapping led to a better understanding of the genetic relationships between grain storage proteins and grain yield per spike, and provided useful information for marker-assisted selection programs.
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Affiliation(s)
- D Nigro
- Department of Soil, Plant and Food Sciences, Genetics and Plant Breeding Section, University of Bari, Bari, Italy
| | - A Gadaleta
- Department of Agricultural and Environmental Science, Research Unit of "Genetics and Plant Biotechnology", University of Bari, Bari, Italy.
| | - G Mangini
- Department of Soil, Plant and Food Sciences, Genetics and Plant Breeding Section, University of Bari, Bari, Italy
| | - P Colasuonno
- Department of Agricultural and Environmental Science, Research Unit of "Genetics and Plant Biotechnology", University of Bari, Bari, Italy
| | - I Marcotuli
- Department of Agricultural and Environmental Science, Research Unit of "Genetics and Plant Biotechnology", University of Bari, Bari, Italy
| | - A Giancaspro
- Department of Agricultural and Environmental Science, Research Unit of "Genetics and Plant Biotechnology", University of Bari, Bari, Italy
| | - S L Giove
- Department of Agricultural and Environmental Science, Research Unit of "Genetics and Plant Biotechnology", University of Bari, Bari, Italy
| | - R Simeone
- Department of Soil, Plant and Food Sciences, Genetics and Plant Breeding Section, University of Bari, Bari, Italy
| | - A Blanco
- Department of Soil, Plant and Food Sciences, Genetics and Plant Breeding Section, University of Bari, Bari, Italy
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Maldonado C, Mora F, Scapim CA, Coan M. Genome-wide haplotype-based association analysis of key traits of plant lodging and architecture of maize identifies major determinants for leaf angle: hapLA4. PLoS One 2019; 14:e0212925. [PMID: 30840677 PMCID: PMC6402688 DOI: 10.1371/journal.pone.0212925] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2018] [Accepted: 02/12/2019] [Indexed: 11/18/2022] Open
Abstract
Traits related to plant lodging and architecture are important determinants of plant productivity in intensive maize cultivation systems. Motivated by the identification of genomic associations with the leaf angle, plant height (PH), ear height (EH) and the EH/PH ratio, we characterized approximately 7,800 haplotypes from a set of high-quality single nucleotide polymorphisms (SNPs), in an association panel consisting of tropical maize inbred lines. The proportion of the phenotypic variations explained by the individual SNPs varied between 7%, for the SNP S1_285330124 (located on chromosome 9 and associated with the EH/PH ratio), and 22%, for the SNP S1_317085830 (located on chromosome 6 and associated with the leaf angle). A total of 40 haplotype blocks were significantly associated with the traits of interest, explaining up to 29% of the phenotypic variation for the leaf angle, corresponding to the haplotype hapLA4.04, which was stable over two growing seasons. Overall, the associations for PH, EH and the EH/PH ratio were environment-specific, which was confirmed by performing a model comparison analysis using the information criteria of Akaike and Schwarz. In addition, five stable haplotypes (83%) and 15 SNPs (75%) were identified for the leaf angle. Finally, approximately 62% of the associated haplotypes (25/40) did not contain SNPs detected in the association study using individual SNP markers. This result confirms the advantage of haplotype-based genome-wide association studies for examining genomic regions that control the determining traits for architecture and lodging in maize plants.
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Affiliation(s)
- Carlos Maldonado
- Institute of Biological Sciences, University of Talca, Talca, Chile
| | - Freddy Mora
- Institute of Biological Sciences, University of Talca, Talca, Chile
| | - Carlos A. Scapim
- Universidade Estadual de Maringá, Departamento de Agronomia, Maringá, PR, Brazil
| | - Marlon Coan
- Universidade Estadual de Maringá, Departamento de Agronomia, Maringá, PR, Brazil
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Mazaheri M, Heckwolf M, Vaillancourt B, Gage JL, Burdo B, Heckwolf S, Barry K, Lipzen A, Ribeiro CB, Kono TJY, Kaeppler HF, Spalding EP, Hirsch CN, Robin Buell C, de Leon N, Kaeppler SM. Genome-wide association analysis of stalk biomass and anatomical traits in maize. BMC PLANT BIOLOGY 2019; 19:45. [PMID: 30704393 PMCID: PMC6357476 DOI: 10.1186/s12870-019-1653-x] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Accepted: 01/14/2019] [Indexed: 05/22/2023]
Abstract
BACKGROUND Maize stover is an important source of crop residues and a promising sustainable energy source in the United States. Stalk is the main component of stover, representing about half of stover dry weight. Characterization of genetic determinants of stalk traits provide a foundation to optimize maize stover as a biofuel feedstock. We investigated maize natural genetic variation in genome-wide association studies (GWAS) to detect candidate genes associated with traits related to stalk biomass (stalk diameter and plant height) and stalk anatomy (rind thickness, vascular bundle density and area). RESULTS Using a panel of 942 diverse inbred lines, 899,784 RNA-Seq derived single nucleotide polymorphism (SNP) markers were identified. Stalk traits were measured on 800 members of the panel in replicated field trials across years. GWAS revealed 16 candidate genes associated with four stalk traits. Most of the detected candidate genes were involved in fundamental cellular functions, such as regulation of gene expression and cell cycle progression. Two of the regulatory genes (Zmm22 and an ortholog of Fpa) that were associated with plant height were previously shown to be involved in regulating the vegetative to floral transition. The association of Zmm22 with plant height was confirmed using a transgenic approach. Transgenic lines with increased expression of Zmm22 showed a significant decrease in plant height as well as tassel branch number, indicating a pleiotropic effect of Zmm22. CONCLUSION Substantial heritable variation was observed in the association panel for stalk traits, indicating a large potential for improving useful stalk traits in breeding programs. Genome-wide association analyses detected several candidate genes associated with multiple traits, suggesting common regulatory elements underlie various stalk traits. Results of this study provide insights into the genetic control of maize stalk anatomy and biomass.
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Affiliation(s)
- Mona Mazaheri
- Department of Agronomy, University of Wisconsin, Madison, WI 53706 USA
- Department of Energy, Great Lakes Bioenergy Research Center, University of Wisconsin, Madison, WI 53706 USA
| | - Marlies Heckwolf
- Department of Agronomy, University of Wisconsin, Madison, WI 53706 USA
- Department of Energy, Great Lakes Bioenergy Research Center, University of Wisconsin, Madison, WI 53706 USA
| | - Brieanne Vaillancourt
- Department of Plant Biology, Michigan State University, East Lansing, MI 48824 USA
- Department of Energy, Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, MI 48824 USA
| | - Joseph L. Gage
- Department of Agronomy, University of Wisconsin, Madison, WI 53706 USA
| | - Brett Burdo
- Department of Agronomy, University of Wisconsin, Madison, WI 53706 USA
| | - Sven Heckwolf
- Department of Botany, University of Wisconsin, Madison, WI 53706 USA
| | - Kerrie Barry
- Department of Energy, Joint Genome Institute, Walnut Creek, California, 94598 USA
| | - Anna Lipzen
- Department of Energy, Joint Genome Institute, Walnut Creek, California, 94598 USA
| | - Camila Bastos Ribeiro
- Genótika Super Sementes. Colonizador Ênio Pipino - St. Industrial Sul, Sinop, MT 78550-098 Brazil
| | - Thomas J. Y. Kono
- Department of Agronomy and Plant Genetics, University of Minnesota, 1991 Upper Buford Circle, St Paul, MN 55108 USA
- Present address: Minnesota Supercomputing Institute, 117 Pleasant Street SE, Minneapolis, MN 55455 USA
| | - Heidi F. Kaeppler
- Department of Agronomy, University of Wisconsin, Madison, WI 53706 USA
- Department of Energy, Great Lakes Bioenergy Research Center, University of Wisconsin, Madison, WI 53706 USA
| | - Edgar P. Spalding
- Department of Botany, University of Wisconsin, Madison, WI 53706 USA
| | - Candice N. Hirsch
- Department of Agronomy and Plant Genetics, University of Minnesota, 1991 Upper Buford Circle, St Paul, MN 55108 USA
| | - C. Robin Buell
- Department of Plant Biology, Michigan State University, East Lansing, MI 48824 USA
- Department of Energy, Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, MI 48824 USA
- Plant Resilience Institute, Michigan State University, East Lansing, MI 48824 USA
| | - Natalia de Leon
- Department of Agronomy, University of Wisconsin, Madison, WI 53706 USA
- Department of Energy, Great Lakes Bioenergy Research Center, University of Wisconsin, Madison, WI 53706 USA
| | - Shawn M. Kaeppler
- Department of Agronomy, University of Wisconsin, Madison, WI 53706 USA
- Department of Energy, Great Lakes Bioenergy Research Center, University of Wisconsin, Madison, WI 53706 USA
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Wu X, Wang A, Guo X, Liu P, Zhu Y, Li X, Chen Z. Genetic characterization of maize germplasm derived from Suwan population and temperate resources. Hereditas 2019; 156:2. [PMID: 30655731 PMCID: PMC6329131 DOI: 10.1186/s41065-018-0077-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2018] [Accepted: 12/14/2018] [Indexed: 11/17/2022] Open
Abstract
Background The Suwan population is a well-known maize germplasm that has greatly contributed to the development of maize breeding in tropical and subtropical regions, especially in southern China. Inbred lines derived from the Suwan population always contain stronger resistance and extensive adaptability in different environments. To evaluate the genetic character of inbred lines derived from the Suwan population, a panel including 226 inbred line derived from the Suwan population and temperate resources was assembled and genotyped by using MaizeSNP50 BeadChip, which contained 56,110 genome-wide single nucleotide polymorphism (SNP) markers. This panel contained 98 temperate inbred line and 128 lines derived from the Suwan population. Results The results showed that high genetic diversity was found, with PIC and GD to be 0.67 and 0.60, respectively. In addition, two novel subgroups were identified, with representative inbred lines as HCL645 and Ki32, respectively. One acknowledged heterotic group of Iowa Stiff Stalk Synthetic (SS) was also identified in this study. This study can provide some additional scientific evidence for heterotic group division and use in maize. Additionally, lower linkage disequilibrium (LD) levels and weaker genetic relationships were found, with an average LD level of 41.15 kb that varied from 3.5 to 96 kb. A total of 82.8% of paired relative kinships ranged from 0.05 to 0.28. Conclusions These results would not only facilitate maize breeding practices in tropical and subtropical regions, but also revealed that this panel can be used in dissecting the genetic basis of complex quantitative traits’ variations by using genome-wide association studies (GWAS). Electronic supplementary material The online version of this article (10.1186/s41065-018-0077-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Xun Wu
- Institute of Upland Food Crops, Guizhou Academy of Agricultural Sciences, Guiyang, 550000 Guizhou China
| | - Angui Wang
- Institute of Upland Food Crops, Guizhou Academy of Agricultural Sciences, Guiyang, 550000 Guizhou China
| | - Xiangyang Guo
- Institute of Upland Food Crops, Guizhou Academy of Agricultural Sciences, Guiyang, 550000 Guizhou China
| | - Pengfei Liu
- Institute of Upland Food Crops, Guizhou Academy of Agricultural Sciences, Guiyang, 550000 Guizhou China
| | - Yunfang Zhu
- Institute of Upland Food Crops, Guizhou Academy of Agricultural Sciences, Guiyang, 550000 Guizhou China
| | - Xiushi Li
- Institute of Upland Food Crops, Guizhou Academy of Agricultural Sciences, Guiyang, 550000 Guizhou China
| | - Zehui Chen
- Institute of Upland Food Crops, Guizhou Academy of Agricultural Sciences, Guiyang, 550000 Guizhou China
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Zhao J, Yang W, Zhang S, Yang T, Liu Q, Dong J, Fu H, Mao X, Liu B. Genome-wide association study and candidate gene analysis of rice cadmium accumulation in grain in a diverse rice collection. RICE (NEW YORK, N.Y.) 2018; 11:61. [PMID: 30465288 PMCID: PMC6249348 DOI: 10.1186/s12284-018-0254-x] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Accepted: 11/14/2018] [Indexed: 05/05/2023]
Abstract
BACKGROUND Cadmium (Cd) accumulation in rice followed by transfer to the food chain causes severe health problems in humans. Breeding of low Cd accumulation varieties is one of the most economical ways to solve the problem. However, information on the identity of rice germplasm with low Cd accumulation is limited, particularly in indica, and the genetic basis of Cd accumulation in rice is not well understood. RESULTS Screening of 312 diverse rice accessions revealed that the grain Cd concentrations of these rice accessions ranged from 0.12 to 1.23 mg/kg, with 24 accessions less than 0.20 mg/kg. Three of the 24 accessions belong to indica. Japonica accumulated significantly less Cd than indica (p < 0.001), while tropical japonica accumulated significantly less Cd than temperate japonica (p < 0.01). GWAS in all accessions identified 14 QTLs for Cd accumulation, with 7 identified in indica and 7 identified in japonica subpopulations. No common QTL was identified between indica and japonica. The previously identified genes (OsHMA3, OsNRAMP1, and OsNRAMP5) from japonica were colocalized with QTLs identified in japonica instead of indica. Expression analysis of OsNRAMP2, the candidate gene of the novel QTL (qCd3-2) identified in the present study, demonstrated that OsNRAMP2 was mainly induced in the shoots of high Cd accumulation accessions after Cd treatment. Four amino acid differences were found in the open reading frame of OsNRAMP2 between high and low Cd accumulation accessions. The allele from low Cd accumulation accessions significantly increased the Cd sensitivity and accumulation in yeast. Subcellular localization analysis demonstrated OsNRAMP2 expressed in the tonoplast of rice protoplast. CONCLUSION The results suggest that grain Cd concentrations are significantly different among subgroups, with Cd concentrations decreasing from indica to temperate japonica to tropical japonica. However, considerable variations exist within subgroups. The fact that no common QTL was identified between indica and japonica implies that there is a different genetic basis for determining Cd accumulation between indica and japonica, or that some QTLs for Cd accumulation in rice are subspecies-specific. Through further integrated analysis, it is speculated that OsNRAMP2 could be a novel functional gene associated with Cd accumulation in rice.
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Affiliation(s)
- Junliang Zhao
- Guangdong Key Laboratory of New Technology in Rice Breeding, Guangzhou, 510640 China
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640 China
| | - Wu Yang
- Guangdong Key Laboratory of New Technology in Rice Breeding, Guangzhou, 510640 China
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640 China
| | - Shaohong Zhang
- Guangdong Key Laboratory of New Technology in Rice Breeding, Guangzhou, 510640 China
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640 China
| | - Tifeng Yang
- Guangdong Key Laboratory of New Technology in Rice Breeding, Guangzhou, 510640 China
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640 China
| | - Qin Liu
- Guangdong Key Laboratory of New Technology in Rice Breeding, Guangzhou, 510640 China
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640 China
| | - Jingfang Dong
- Guangdong Key Laboratory of New Technology in Rice Breeding, Guangzhou, 510640 China
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640 China
| | - Hua Fu
- Guangdong Key Laboratory of New Technology in Rice Breeding, Guangzhou, 510640 China
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640 China
| | - Xingxue Mao
- Guangdong Key Laboratory of New Technology in Rice Breeding, Guangzhou, 510640 China
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640 China
| | - Bin Liu
- Guangdong Key Laboratory of New Technology in Rice Breeding, Guangzhou, 510640 China
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640 China
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Jing Y, Zhao X, Wang J, Teng W, Qiu L, Han Y, Li W. Identification of the Genomic Region Underlying Seed Weight per Plant in Soybean ( Glycine max L. Merr.) via High-Throughput Single-Nucleotide Polymorphisms and a Genome-Wide Association Study. FRONTIERS IN PLANT SCIENCE 2018; 9:1392. [PMID: 30369935 PMCID: PMC6194254 DOI: 10.3389/fpls.2018.01392] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Accepted: 09/03/2018] [Indexed: 05/30/2023]
Abstract
Seed weight per plant (SWPP) of soybean (Glycine max (L.) Merr.), a complicated quantitative trait controlled by multiple genes, was positively associated with soybean seed yields. In the present study, a natural soybean population containing 185 diverse accessions primarily from China was used to analyze the genetic basis of SWPP via genome-wide association analysis (GWAS) based on high-throughput single-nucleotide polymorphisms (SNPs) generated by the Specific Locus Amplified Fragment Sequencing (SLAF-seq) method. A total of 33,149 SNPs were finally identified with minor allele frequencies (MAF) > 5% which were present in 97% of all the genotypes. Twenty association signals associated with SWPP were detected via GWAS. Among these signals, eight SNPs were novel loci, and the other twelve SNPs were overlapped or located in the linked genomic regions of the reported QTL from SoyBase database. Several genes belonging to the categories of hormone pathways, RNA regulation of transcription in plant development, ubiquitin, transporting systems, and other metabolisms were considered as candidate genes associated with SWPP. Furthermore, nine genes from the flanking region of Gm07:19488264, Gm08:15768591, Gm08:15768603, or Gm18:23052511 were significantly associated with SWPP and were stable among multiple environments. Nine out of 18 haplotypes from nine genes showed the effect of increasing SWPP. The identified loci along with the beneficial alleles and candidate genes could be of great value for studying the molecular mechanisms underlying SWPP and for improving the potential seed yield of soybean in the future.
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Affiliation(s)
- Yan Jing
- Key Laboratory of Soybean Biology in Chinese Ministry of Education (Key Laboratory of Soybean Biology and Breeding/Genetics of Chinese Agriculture Ministry), Northeast Agricultural University, Harbin, China
| | - Xue Zhao
- Key Laboratory of Soybean Biology in Chinese Ministry of Education (Key Laboratory of Soybean Biology and Breeding/Genetics of Chinese Agriculture Ministry), Northeast Agricultural University, Harbin, China
| | - Jinyang Wang
- Key Laboratory of Soybean Biology in Chinese Ministry of Education (Key Laboratory of Soybean Biology and Breeding/Genetics of Chinese Agriculture Ministry), Northeast Agricultural University, Harbin, China
| | - Weili Teng
- Key Laboratory of Soybean Biology in Chinese Ministry of Education (Key Laboratory of Soybean Biology and Breeding/Genetics of Chinese Agriculture Ministry), Northeast Agricultural University, Harbin, China
| | - Lijuan Qiu
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yingpeng Han
- Key Laboratory of Soybean Biology in Chinese Ministry of Education (Key Laboratory of Soybean Biology and Breeding/Genetics of Chinese Agriculture Ministry), Northeast Agricultural University, Harbin, China
| | - Wenbin Li
- Key Laboratory of Soybean Biology in Chinese Ministry of Education (Key Laboratory of Soybean Biology and Breeding/Genetics of Chinese Agriculture Ministry), Northeast Agricultural University, Harbin, China
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Zhou Z, Zhang C, Lu X, Wang L, Hao Z, Li M, Zhang D, Yong H, Zhu H, Weng J, Li X. Dissecting the Genetic Basis Underlying Combining Ability of Plant Height Related Traits in Maize. FRONTIERS IN PLANT SCIENCE 2018; 9:1117. [PMID: 30116252 PMCID: PMC6083371 DOI: 10.3389/fpls.2018.01117] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2018] [Accepted: 07/11/2018] [Indexed: 05/27/2023]
Abstract
Maize plant height related traits including plant height, ear height, and internode number are tightly linked with biomass, planting density, and grain yield in the field. Previous studies have focused on understanding the genetic basis of plant architecture traits per se, but the genetic basis of combining ability remains poorly understood. In this study, 328 recombinant inbred lines were inter-group crossed with two testers to produce 656 hybrids using the North Carolina II mating design. Both of the parental lines and hybrids were evaluated in two summer maize-growing regions of China in 2015 and 2016. QTL mapping highlighted that 7 out of 16 QTL detected for RILs per se could be simultaneously detected for general combining ability (GCA) effects, suggesting that GCA effects and the traits were genetically controlled by different sets of loci. Among the 35 QTL identified for hybrid performance, 57.1% and 28.5% QTL overlapped with additive/GCA and non-additive/SCA effects, suggesting that the small percentage of hybrid variance due to SCA effects in our design. Two QTL hotspots, located on chromosomes 5 and 10 and including the qPH5-1 and qPH10 loci, were validated for plant height related traits by Ye478 derivatives. Notably, the qPH5-1 locus could simultaneously affect the RILs per se and GCA effects while the qPH10, a major QTL (PVE > 10%) with pleiotropic effects, only affected the GCA effects. These results provide evidence that more attention should be focused on loci that influence combining ability directly in maize hybrid breeding.
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Affiliation(s)
- Zhiqiang Zhou
- National Engineering Laboratory for Crop Molecular Breeding, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Chaoshu Zhang
- National Engineering Laboratory for Crop Molecular Breeding, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xiaohuan Lu
- National Engineering Laboratory for Crop Molecular Breeding, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Liwei Wang
- National Engineering Laboratory for Crop Molecular Breeding, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
- Institute of Cereal and Oil Crops, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, China
| | - Zhuanfang Hao
- National Engineering Laboratory for Crop Molecular Breeding, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Mingshun Li
- National Engineering Laboratory for Crop Molecular Breeding, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Degui Zhang
- National Engineering Laboratory for Crop Molecular Breeding, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Hongjun Yong
- National Engineering Laboratory for Crop Molecular Breeding, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Hanyong Zhu
- National Engineering Laboratory for Crop Molecular Breeding, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
- Yunnan Wenshanzhou Academy of Agricultural Sciences, Wenshan, China
| | - Jianfeng Weng
- National Engineering Laboratory for Crop Molecular Breeding, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xinhai Li
- National Engineering Laboratory for Crop Molecular Breeding, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
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Chen Q, Song J, Du WP, Xu LY, Jiang Y, Zhang J, Xiang XL, Yu GR. Identification and genetic mapping for rht-DM, a dominant dwarfing gene in mutant semi-dwarf maize using QTL-seq approach. Genes Genomics 2018; 40:1091-1099. [PMID: 29951965 DOI: 10.1007/s13258-018-0716-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2018] [Accepted: 06/13/2018] [Indexed: 12/11/2022]
Abstract
Semi-dwarfism is an agronomically important trait in breeding for stable high yields and for resistance to damage by wind and rain (lodging resistance). Many QTLs and genes causing dwarf phenotype have been found in maize. However, because of the yield loss associated with these QTLs and genes, they have been difficult to use in breeding for dwarf stature in maize. Therefore, it is important to find the new dwarfing genes or materials without undesirable characters. The objectives of this study were: (1) to figure out the inheritance of semi-dwarfism in mutants; (2) mapping dwarfing gene or QTL. Maize inbred lines '18599' and 'DM173', which is the dwarf mutant derived from the maize inbred line '173' through 60Co-γ ray irradiation. F2 and BC1F1 population were used for genetic analysis. Whole genome resequencing-based technology (QTL-seq) were performed to map dwarfing gene and figured out the SNP markers in predicted region using dwarf bulk and tall bulk from F2 population. Based on the polymorphic SNP markers from QTL-seq, we were fine-mapping the dwarfing gene using F2 population. In F2 population, 398 were dwarf plants and 135 were tall plants. Results of χ2 tests indicated that the ratio of dwarf plants to tall plants was fitted to 3:1 ratio. Furthermore, the χ2 tests of BC1F1 population showed that the ratio was fitted to 1:1 ratio. Based on QTL-seq, the dwarfing gene was located at the region from 111.07 to 124.56 Mb of chromosome 9, and we named it rht-DM. Using traditional QTL mapping with SNP markers, the rht-DM was narrowed down to 400 kb region between SNP-21 and SNP-24. The two SNPs were located at 0.43 and 0.11 cM. Segregation analysis of F2 and BC1F1 indicated that the dwarfing gene was likely a dominant gene. This dwarfing gene was located in the region between 115.02 and 115.42 Mb on chromosome 9.
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Affiliation(s)
- Qian Chen
- Institute of Biotechnology and Nuclear Technology, Sichuan Academy of Agricultural Sciences, Chengdu, 610061, Sichuan, China
| | - Jun Song
- Institute of Biotechnology and Nuclear Technology, Sichuan Academy of Agricultural Sciences, Chengdu, 610061, Sichuan, China
| | - Wen-Ping Du
- Institute of Biotechnology and Nuclear Technology, Sichuan Academy of Agricultural Sciences, Chengdu, 610061, Sichuan, China
| | - Li-Yuan Xu
- Institute of Biotechnology and Nuclear Technology, Sichuan Academy of Agricultural Sciences, Chengdu, 610061, Sichuan, China
| | - Yun Jiang
- Institute of Biotechnology and Nuclear Technology, Sichuan Academy of Agricultural Sciences, Chengdu, 610061, Sichuan, China
| | - Jie Zhang
- Institute of Biotechnology and Nuclear Technology, Sichuan Academy of Agricultural Sciences, Chengdu, 610061, Sichuan, China
| | - Xiao-Li Xiang
- Institute of Biotechnology and Nuclear Technology, Sichuan Academy of Agricultural Sciences, Chengdu, 610061, Sichuan, China
| | - Gui-Rong Yu
- Institute of Biotechnology and Nuclear Technology, Sichuan Academy of Agricultural Sciences, Chengdu, 610061, Sichuan, China.
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Zhang Y, Liu P, Zhang X, Zheng Q, Chen M, Ge F, Li Z, Sun W, Guan Z, Liang T, Zheng Y, Tan X, Zou C, Peng H, Pan G, Shen Y. Multi-Locus Genome-Wide Association Study Reveals the Genetic Architecture of Stalk Lodging Resistance-Related Traits in Maize. FRONTIERS IN PLANT SCIENCE 2018; 9:611. [PMID: 29868068 PMCID: PMC5949362 DOI: 10.3389/fpls.2018.00611] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Accepted: 04/18/2018] [Indexed: 05/21/2023]
Abstract
Stalk lodging resistance, which is mainly measured by stem diameter (SD), stalk bending strength (SBS), and rind penetrometer resistance (RPR) in maize, seriously affects the yield and quality of maize (Zea mays L.). To dissect its genetic architecture, in this study multi-locus genome-wide association studies for stalk lodging resistance-related traits were conducted in a population of 257 inbred lines, with tropical, subtropical, and temperate backgrounds, genotyped with 48,193 high-quality single nucleotide polymorphisms. The analyses of phenotypic variations for the above traits in three environments showed high broad-sense heritability (0.679, 0.720, and 0.854, respectively). In total, 423 significant Quantitative Trait Nucleotides (QTNs) were identified by mrMLM, FASTmrEMMA, ISIS EM-BLASSO, and pLARmEB methods to be associated with the above traits. Among these QTNs, 29, 34, and 48 were commonly detected by multiple methods or across multiple environments to be related to SD, SBS, and RPR, respectively. The superior allele analyses in 30 elite lines showed that only eight lines contained more than 50% of the superior alleles, indicating that stalk lodging resistance can be improved by the integration of more superior alleles. Among sixty-three candidate genes of the consistently expressed QTNs, GRMZM5G856734 and GRMZM2G116885, encoding membrane steroid-binding protein 1 and cyclin-dependent kinase inhibitor 1, respectively, possibly inhibit cell elongation and division, which regulates lodging resistance. Our results provide the further understanding of the genetic foundation of maize lodging resistance.
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Affiliation(s)
- Yanling Zhang
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Maize Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Peng Liu
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Maize Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Xiaoxiang Zhang
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Maize Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Qi Zheng
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Maize Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Min Chen
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Maize Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Fei Ge
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Maize Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Zhaoling Li
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Maize Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Wenting Sun
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Maize Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Zhongrong Guan
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Maize Research Institute, Sichuan Agricultural University, Chengdu, China
- Research Center of Tumofous Stem Mustard, Chongqing Yudongnan Academy of Agricultural Sciences, Chongqing, China
| | - Tianhu Liang
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Maize Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Yan Zheng
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Maize Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Xiaolong Tan
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Maize Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Chaoying Zou
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Maize Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Huanwei Peng
- Institute of Animal Nutrition, Sichuan Agricultural University, Chengdu, China
| | - Guangtang Pan
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Maize Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Yaou Shen
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Maize Research Institute, Sichuan Agricultural University, Chengdu, China
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Wang B, Liu H, Liu Z, Dong X, Guo J, Li W, Chen J, Gao C, Zhu Y, Zheng X, Chen Z, Chen J, Song W, Hauck A, Lai J. Identification of minor effect QTLs for plant architecture related traits using super high density genotyping and large recombinant inbred population in maize (Zea mays). BMC PLANT BIOLOGY 2018; 18:17. [PMID: 29347909 PMCID: PMC5774087 DOI: 10.1186/s12870-018-1233-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Accepted: 01/14/2018] [Indexed: 05/29/2023]
Abstract
BACKGROUND Plant Architecture Related Traits (PATs) are of great importance for maize breeding, and mainly controlled by minor effect quantitative trait loci (QTLs). However, cloning or even fine-mapping of minor effect QTLs is very difficult in maize. Theoretically, large population and high density genetic map can be helpful for increasing QTL mapping resolution and accuracy, but such a possibility have not been actually tested. RESULTS Here, we employed a genotyping-by-sequencing (GBS) strategy to construct a linkage map with 16,769 marker bins for 1021 recombinant inbred lines (RILs). Accurately mapping of well studied genes P1, pl1 and r1 underlying silk color demonstrated the map quality. After QTL analysis, a total of 51 loci were mapped for six PATs. Although all of them belong to minor effect alleles, the lengths of the QTL intervals, with a minimum and median of 1.03 and 3.40 Mb respectively, were remarkably reduced as compared with previous reports using smaller size of population or small number of markers. Several genes with known function in maize were shown to be overlapping with or close neighboring to these QTL peaks, including na1, td1, d3 for plant height, ra1 for tassel branch number, and zfl2 for tassel length. To further confirm our mapping results, a plant height QTL, qPH1a, was verified by an introgression lines (ILs). CONCLUSIONS We demonstrated a method for high resolution mapping of minor effect QTLs in maize, and the resulted comprehensive QTLs for PATs are valuable for maize molecular breeding in the future.
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Affiliation(s)
- Baobao Wang
- State Key Laboratory of Agrobiotechnology and National Maize Improvement Center, Department of Plant Genetics and Breeding, China Agricultural University, Beijing, China
| | - Han Liu
- State Key Laboratory of Agrobiotechnology and National Maize Improvement Center, Department of Plant Genetics and Breeding, China Agricultural University, Beijing, China
| | - Zhipeng Liu
- State Key Laboratory of Agrobiotechnology and National Maize Improvement Center, Department of Plant Genetics and Breeding, China Agricultural University, Beijing, China
| | - Xiaomei Dong
- State Key Laboratory of Agrobiotechnology and National Maize Improvement Center, Department of Plant Genetics and Breeding, China Agricultural University, Beijing, China
| | - Jinjie Guo
- State Key Laboratory of Agrobiotechnology and National Maize Improvement Center, Department of Plant Genetics and Breeding, China Agricultural University, Beijing, China
| | - Wei Li
- State Key Laboratory of Agrobiotechnology and National Maize Improvement Center, Department of Plant Genetics and Breeding, China Agricultural University, Beijing, China
| | - Jing Chen
- State Key Laboratory of Agrobiotechnology and National Maize Improvement Center, Department of Plant Genetics and Breeding, China Agricultural University, Beijing, China
| | - Chi Gao
- State Key Laboratory of Agrobiotechnology and National Maize Improvement Center, Department of Plant Genetics and Breeding, China Agricultural University, Beijing, China
| | - Yanbin Zhu
- State Key Laboratory of Agrobiotechnology and National Maize Improvement Center, Department of Plant Genetics and Breeding, China Agricultural University, Beijing, China
| | - Xinmei Zheng
- State Key Laboratory of Agrobiotechnology and National Maize Improvement Center, Department of Plant Genetics and Breeding, China Agricultural University, Beijing, China
| | - Zongliang Chen
- State Key Laboratory of Agrobiotechnology and National Maize Improvement Center, Department of Plant Genetics and Breeding, China Agricultural University, Beijing, China
| | - Jian Chen
- State Key Laboratory of Agrobiotechnology and National Maize Improvement Center, Department of Plant Genetics and Breeding, China Agricultural University, Beijing, China
| | - Weibin Song
- State Key Laboratory of Agrobiotechnology and National Maize Improvement Center, Department of Plant Genetics and Breeding, China Agricultural University, Beijing, China
| | - Andrew Hauck
- State Key Laboratory of Agrobiotechnology and National Maize Improvement Center, Department of Plant Genetics and Breeding, China Agricultural University, Beijing, China
| | - Jinsheng Lai
- State Key Laboratory of Agrobiotechnology and National Maize Improvement Center, Department of Plant Genetics and Breeding, China Agricultural University, Beijing, China
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Li T, Ma X, Li N, Zhou L, Liu Z, Han H, Gui Y, Bao Y, Chen J, Dai X. Genome-wide association study discovered candidate genes of Verticillium wilt resistance in upland cotton (Gossypium hirsutum L.). PLANT BIOTECHNOLOGY JOURNAL 2017; 15:1520-1532. [PMID: 28371164 PMCID: PMC5698051 DOI: 10.1111/pbi.12734] [Citation(s) in RCA: 68] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2017] [Revised: 03/16/2017] [Accepted: 03/21/2017] [Indexed: 05/03/2023]
Abstract
Verticillium wilt (VW), caused by infection by Verticillium dahliae, is considered one of the most yield-limiting diseases in cotton. To examine the genetic architecture of cotton VW resistance, we performed a genome-wide association study (GWAS) using a panel of 299 accessions and 85 630 single nucleotide polymorphisms (SNPs) detected using the specific-locus amplified fragment sequencing (SLAF-seq) approach. Trait-SNP association analysis detected a total of 17 significant SNPs at P < 1.17 × 10-5 (P = 1/85 630, -log10 P = 4.93); the peaks of SNPs associated with VW resistance on A10 were continuous and common in three environments (RDIG2015, RDIF2015 and RDIF2016). Haplotype block structure analysis predicted 22 candidate genes for VW resistance based on A10_99672586 with a minimum P-value (-log10 P = 6.21). One of these genes (CG02) was near the significant SNP A10_99672586 (0.26 Mb), located in a 372-kb haplotype block, and its Arabidopsis AT3G25510 homologues contain TIR-NBS-LRR domains that may be involved in disease resistance response. Real-time quantitative PCR and virus-induced gene silencing (VIGS) analysis showed that CG02 was specific to up-regulation in the resistant (R) genotype Zhongzhimian2 (ZZM2) and that silenced plants were more susceptible to V. dahliae. These results indicate that CG02 is likely the candidate gene for resistance against V. dahliae in cotton. The identified locus or gene may serve as a promising target for genetic engineering and selection for improving resistance to VW in cotton.
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Affiliation(s)
- Tinggang Li
- Laboratory of Cotton DiseaseInstitute of Food Science and TechnologyChinese Academy of Agricultural SciencesBeijingChina
| | - Xuefeng Ma
- Laboratory of Cotton DiseaseInstitute of Food Science and TechnologyChinese Academy of Agricultural SciencesBeijingChina
| | - Nanyang Li
- Laboratory of Cotton DiseaseInstitute of Food Science and TechnologyChinese Academy of Agricultural SciencesBeijingChina
| | - Lei Zhou
- Laboratory of Cotton DiseaseInstitute of Food Science and TechnologyChinese Academy of Agricultural SciencesBeijingChina
| | - Zheng Liu
- Xinjiang Academy of Agricultural and Reclamation ScienceXinjiangChina
| | - Huanyong Han
- Xinjiang Academy of Agricultural and Reclamation ScienceXinjiangChina
| | - Yuejing Gui
- Laboratory of Cotton DiseaseInstitute of Food Science and TechnologyChinese Academy of Agricultural SciencesBeijingChina
| | - Yuming Bao
- Laboratory of Cotton DiseaseInstitute of Food Science and TechnologyChinese Academy of Agricultural SciencesBeijingChina
| | - Jieyin Chen
- Laboratory of Cotton DiseaseInstitute of Food Science and TechnologyChinese Academy of Agricultural SciencesBeijingChina
| | - Xiaofeng Dai
- Laboratory of Cotton DiseaseInstitute of Food Science and TechnologyChinese Academy of Agricultural SciencesBeijingChina
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Hu S, Sanchez DL, Wang C, Lipka AE, Yin Y, Gardner CAC, Lübberstedt T. Brassinosteroid and gibberellin control of seedling traits in maize (Zea mays L.). PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2017; 263:132-141. [PMID: 28818369 DOI: 10.1016/j.plantsci.2017.07.011] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2017] [Revised: 07/09/2017] [Accepted: 07/11/2017] [Indexed: 05/24/2023]
Abstract
In this study, we established two doubled haploid (DH) libraries with a total of 207 DH lines. We applied BR and GA inhibitors to all DH lines at seedling stage and measured seedling BR and GA inhibitor responses. Moreover, we evaluated field traits for each DH line (untreated). We conducted genome-wide association studies (GWAS) with 62,049 genome wide SNPs to explore the genetic control of seedling traits by BR and GA. In addition, we correlate seedling stage hormone inhibitor response with field traits. Large variation for BR and GA inhibitor response and field traits was observed across these DH lines. Seedling stage BR and GA inhibitor response was significantly correlate with yield and flowering time. Using three different GWAS approaches to balance false positive/negatives, multiple SNPs were discovered to be significantly associated with BR/GA inhibitor responses with some localized within gene models. SNPs from gene model GRMZM2G013391 were associated with GA inhibitor response across all three GWAS models. This gene is expressed in roots and shoots and was shown to regulate GA signaling. These results show that BRs and GAs have a great impact for controlling seedling growth. Gene models from GWAS results could be targets for seeding traits improvement.
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Affiliation(s)
- Songlin Hu
- Department of Agronomy, Iowa State University, 100 Osborn Drive, Ames, IA 50011, USA.
| | - Darlene L Sanchez
- Department of Agronomy, Iowa State University, 100 Osborn Drive, Ames, IA 50011, USA
| | - Cuiling Wang
- Department of Agronomy, Henan University of Science and Technology, 263 Kaiyuan Avenue, Luoyang, Henan 471023, China
| | - Alexander E Lipka
- Department of Crop Sciences, University of Illinois, Champaign, IL 61801, USA
| | - Yanhai Yin
- Department of Genetics, Development and Cell Biology, Iowa State University, 100 Osborn Drive, Ames, IA 50011, USA
| | - Candice A C Gardner
- Department of Agronomy, Iowa State University, 100 Osborn Drive, Ames, IA 50011, USA; U.S. Department of Agriculture-Agricultural Research Service (USDA-ARS), 100 Osborn Drive, Ames, IA 50011, USA
| | - Thomas Lübberstedt
- Department of Agronomy, Iowa State University, 100 Osborn Drive, Ames, IA 50011, USA
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Ren J, Wu P, Tian X, Lübberstedt T, Chen S. QTL mapping for haploid male fertility by a segregation distortion method and fine mapping of a key QTL qhmf4 in maize. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2017; 130:1349-1359. [PMID: 28389771 DOI: 10.1007/s00122-017-2892-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2016] [Accepted: 03/10/2017] [Indexed: 05/18/2023]
Abstract
Four QTL related to haploid male fertility were detected by a segregation distortion method and the key QTL qhmf4 was fine mapped to an interval of ~800 kb. Doubled haploid (DH) technology enables rapid development of homozygous lines in maize breeding programs. However, haploid genome doubling is a bottleneck for the commercialization of DH technology and is limited by haploid male fertility (HMF). This is the first study reporting the quantitative trait locus (QTL) analysis of HMF in maize. Four QTL, qhmf1, qhmf2, qhmf3, and qhmf4, controlling HMF have been identified by segregation distortion (SD) loci detection in the selected haploid population derived from 'Yu87-1/Zheng58'. Three loci, qhmf1, qhmf2, and qhmf4, were also detected in the selected haploid population derived from '4F1/Zheng58'. The QTL qhmf4 showed the strongest SD in both haploid populations. Based on the sequence information of 'Yu87-1' and 'Zheng58', thirteen markers being polymorphic between the two lines were developed to saturate the qhmf4 region. A total of 8168 H1BC2 (haploid backcross generation) plants produced from 'Yu87-1' and 'Zheng58' were screened for recombinants. All the 48 recombinants were backcrossed to 'Zheng58' to develop H1BC3 progeny. The heterozygous H1BC3 individuals were crossed with CAU5 to induce haploids. In each H1BC3 progeny, haploids were genotyped and evaluated for anther emergence score (AES). Significant (or no significant) difference (P < 0.05) between haploids with or without 'Yu87-1' donor segment indicated presence or absence of qhmf4 in the donor segment. The analysis of the 48 recombinants narrowed the qhmf4 locus down to an ~800 kb interval flanked by markers IND166 and IND1668.
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Affiliation(s)
- Jiaojiao Ren
- College of Agriculture and Biotechnology, China Agricultural University, No. 2 Yuan Ming Yuan West Road, 100193, Beijing, China
| | - Penghao Wu
- College of Agronomy, Xinjiang Agriculture University, 830052, Urumqi, China
| | - Xiaolong Tian
- College of Agriculture and Biotechnology, China Agricultural University, No. 2 Yuan Ming Yuan West Road, 100193, Beijing, China
| | | | - Shaojiang Chen
- College of Agriculture and Biotechnology, China Agricultural University, No. 2 Yuan Ming Yuan West Road, 100193, Beijing, China.
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31
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Zhang C, Zhou Z, Yong H, Zhang X, Hao Z, Zhang F, Li M, Zhang D, Li X, Wang Z, Weng J. Analysis of the genetic architecture of maize ear and grain morphological traits by combined linkage and association mapping. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2017; 130:1011-1029. [PMID: 28215025 DOI: 10.1007/s00122-017-2867-7] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Accepted: 01/24/2017] [Indexed: 05/05/2023]
Abstract
Using combined linkage and association mapping, 26 stable QTL and six stable SNPs were detected across multiple environments for eight ear and grain morphological traits in maize. One QTL, PKS2, might play an important role in maize yield improvement. In the present study, one bi-parental population and an association panel were used to identify quantitative trait loci (QTL) for eight ear and grain morphological traits. A total of 108 QTL related to these traits were detected across four environments using an ultra-high density bin map constructed using recombinant inbred lines (RILs) derived from a cross between Ye478 and Qi319, and 26 QTL were identified in more than two environments. Furthermore, 64 single nucleotide polymorphisms (SNPs) were found to be significantly associated with the eight ear and grain morphological traits (-log10(P) > 4) in an association panel of 240 maize inbred lines. Combining the two mapping populations, a total of 17 pleiotropic QTL/SNPs (pQTL/SNPs) were associated with various traits across multiple environments. PKS2, a stable locus influencing kernel shape identified on chromosome 2 in a genome-wide association study (GWAS), was within the QTL confidence interval defined by the RILs. The candidate region harbored a short 13-Kb LD block encompassing four SNPs (SYN11386, PHM14783.16, SYN11392, and SYN11378). In the association panel, 13 lines derived from the hybrid PI78599 possessed the same allele as Qi319 at the PHM14783.16 (GG) locus, with an average value of 0.21 for KS, significantly lower than that of the 34 lines derived from Ye478 that carried a different allele (0.25, P < 0.05). Therefore, further fine mapping of PKS2 will provide valuable information for understanding the genetic components of grain yield and improving molecular marker-assisted selection (MAS) in maize.
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Affiliation(s)
- Chaoshu Zhang
- College of Agronomy, Northeast Agricultural University, Mucai Street, XiangFang District, Harbin, 150030, Heilongjiang, China
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Zhongguancun South Street, Haidian District, Beijing, 100081, China
| | - Zhiqiang Zhou
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Zhongguancun South Street, Haidian District, Beijing, 100081, China
| | - Hongjun Yong
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Zhongguancun South Street, Haidian District, Beijing, 100081, China
| | - Xiaochong Zhang
- College of Agronomy, Northeast Agricultural University, Mucai Street, XiangFang District, Harbin, 150030, Heilongjiang, China
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Zhongguancun South Street, Haidian District, Beijing, 100081, China
| | - Zhuanfang Hao
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Zhongguancun South Street, Haidian District, Beijing, 100081, China
| | - Fangjun Zhang
- College of Agronomy, Northeast Agricultural University, Mucai Street, XiangFang District, Harbin, 150030, Heilongjiang, China
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Zhongguancun South Street, Haidian District, Beijing, 100081, China
| | - Mingshun Li
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Zhongguancun South Street, Haidian District, Beijing, 100081, China
| | - Degui Zhang
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Zhongguancun South Street, Haidian District, Beijing, 100081, China
| | - Xinhai Li
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Zhongguancun South Street, Haidian District, Beijing, 100081, China
| | - Zhenhua Wang
- College of Agronomy, Northeast Agricultural University, Mucai Street, XiangFang District, Harbin, 150030, Heilongjiang, China.
| | - Jianfeng Weng
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Zhongguancun South Street, Haidian District, Beijing, 100081, China.
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32
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Li H, Yang Q, Fan N, Zhang M, Zhai H, Ni Z, Zhang Y. Quantitative trait locus analysis of heterosis for plant height and ear height in an elite maize hybrid zhengdan 958 by design III. BMC Genet 2017; 18:36. [PMID: 28415964 PMCID: PMC5392948 DOI: 10.1186/s12863-017-0503-9] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2017] [Accepted: 04/06/2017] [Indexed: 11/23/2022] Open
Abstract
Background Plant height (PH) and ear height (EH) are two important agronomic traits in maize selection breeding. F1 hybrid exhibit significant heterosis for PH and EH as compared to their parental inbred lines. To understand the genetic basis of heterosis controlling PH and EH, we conducted quantitative trait locus (QTL) analysis using a recombinant inbreed line (RIL) based design III population derived from the elite maize hybrid Zhengdan 958 in five environments. Results A total of 14 environmentally stable QTLs were identified, and the number of QTLs for Z1 and Z2 populations was six and eight, respectively. Notably, all the eight environmentally stable QTLs for Z2 were characterized by overdominance effect (OD), suggesting that overdominant QTLs were the most important contributors to heterosis for PH and EH. Furthermore, 14 environmentally stable QTLs were anchored on six genomic regions, among which four are trait-specific QTLs, suggesting that the genetic basis for PH and EH is partially different. Additionally, qPH.A-1.3, modifying about 10 centimeters of PH, was further validated in backcross populations. Conclusions The genetic basis for PH and EH is partially different, and overdominant QTLs are important factors for heterosis of PH and EH. A major QTL qPH.A-1.3 may be a desired target for genetic improvement of maize plant height. Electronic supplementary material The online version of this article (doi:10.1186/s12863-017-0503-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Hongjian Li
- State Key Laboratory for Agrobiotechnology and Key Laboratory of Crop Heterosis Utilization (MOE), China Agricultural University, Beijing, 100193, China
| | - Qingsong Yang
- State Key Laboratory for Agrobiotechnology and Key Laboratory of Crop Heterosis Utilization (MOE), China Agricultural University, Beijing, 100193, China.,National Maize Improvement Center of China, China Agricultural University, Beijing, 100193, China
| | - Nannan Fan
- State Key Laboratory for Agrobiotechnology and Key Laboratory of Crop Heterosis Utilization (MOE), China Agricultural University, Beijing, 100193, China.,National Maize Improvement Center of China, China Agricultural University, Beijing, 100193, China
| | - Ming Zhang
- State Key Laboratory for Agrobiotechnology and Key Laboratory of Crop Heterosis Utilization (MOE), China Agricultural University, Beijing, 100193, China
| | - Huijie Zhai
- State Key Laboratory for Agrobiotechnology and Key Laboratory of Crop Heterosis Utilization (MOE), China Agricultural University, Beijing, 100193, China
| | - Zhongfu Ni
- State Key Laboratory for Agrobiotechnology and Key Laboratory of Crop Heterosis Utilization (MOE), China Agricultural University, Beijing, 100193, China
| | - Yirong Zhang
- State Key Laboratory for Agrobiotechnology and Key Laboratory of Crop Heterosis Utilization (MOE), China Agricultural University, Beijing, 100193, China. .,National Maize Improvement Center of China, China Agricultural University, Beijing, 100193, China.
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Xiao Y, Liu H, Wu L, Warburton M, Yan J. Genome-wide Association Studies in Maize: Praise and Stargaze. MOLECULAR PLANT 2017; 10:359-374. [PMID: 28039028 DOI: 10.1016/j.molp.2016.12.008] [Citation(s) in RCA: 208] [Impact Index Per Article: 29.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2016] [Revised: 12/02/2016] [Accepted: 12/20/2016] [Indexed: 05/18/2023]
Abstract
Genome-wide association study (GWAS) has become a widely accepted strategy for decoding genotype-phenotype associations in many species thanks to advances in next-generation sequencing (NGS) technologies. Maize is an ideal crop for GWAS and significant progress has been made in the last decade. This review summarizes current GWAS efforts in maize functional genomics research and discusses future prospects in the omics era. The general goal of GWAS is to link genotypic variations to corresponding differences in phenotype using the most appropriate statistical model in a given population. The current review also presents perspectives for optimizing GWAS design and analysis. GWAS analysis of data from RNA, protein, and metabolite-based omics studies is discussed, along with new models and new population designs that will identify causes of phenotypic variation that have been hidden to date. The joint and continuous efforts of the whole community will enhance our understanding of maize quantitative traits and boost crop molecular breeding designs.
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Affiliation(s)
- Yingjie Xiao
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Haijun Liu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Liuji Wu
- Synergetic Innovation Center of Henan Grain Crops, Henan Agricultural University, Zhengzhou 450002, China
| | - Marilyn Warburton
- United States of Department of Agriculture, Agricultural Research Service, Corn Host Plant Resistance Research Unit, Box 9555, MS 39762, Mississippi, USA
| | - Jianbing Yan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China.
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34
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Wang Y, Zhao J, Lu W, Deng D. Gibberellin in plant height control: old player, new story. PLANT CELL REPORTS 2017; 36:391-398. [PMID: 28160061 DOI: 10.1007/s00299-017-2104-5] [Citation(s) in RCA: 76] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2016] [Accepted: 01/05/2017] [Indexed: 05/24/2023]
Abstract
Height relates to plant architecture, lodging resistance, and yield performance. Growth-promoting phytohormones gibberellins (GAs) play a pivotal role in plant height control. Mutations in GA biosynthesis, metabolism, and signaling cascades influence plant height. Moreover, GA interacts with other phytohormones in the modulation of plant height. Here, we first briefly describe the regulation of plant height by altered GA pathway. Then, we depict effects of the crosstalk between GA and other phytohormones on plant height. We also dissect the co-localization of GA pathway genes and established quantitative genetic loci for plant height. Finally, we suggest ways forward for the application of hormone GA knowledge in breeding of crops with plant height ideotypes.
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Affiliation(s)
- Yijun Wang
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Co-Innovation Center for Modern Production Technology of Grain Crops, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou University, Yangzhou, 225009, China.
| | - Jia Zhao
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Co-Innovation Center for Modern Production Technology of Grain Crops, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou University, Yangzhou, 225009, China
| | - Wenjie Lu
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Co-Innovation Center for Modern Production Technology of Grain Crops, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou University, Yangzhou, 225009, China
| | - Dexiang Deng
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Co-Innovation Center for Modern Production Technology of Grain Crops, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou University, Yangzhou, 225009, China
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35
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Hu S, Wang C, Sanchez DL, Lipka AE, Liu P, Yin Y, Blanco M, Lübberstedt T. Gibberellins Promote Brassinosteroids Action and Both Increase Heterosis for Plant Height in Maize ( Zea mays L.). FRONTIERS IN PLANT SCIENCE 2017; 8:1039. [PMID: 28676808 PMCID: PMC5477294 DOI: 10.3389/fpls.2017.01039] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2017] [Accepted: 05/30/2017] [Indexed: 05/20/2023]
Abstract
Brassinosteroids (BRs) and Gibberellins (GAs) are two classes of plant hormones affecting plant height (PHT). Thus, manipulation of BR and GA levels or signaling enables optimization of crop grain and biomass yields. We established backcross (BC) families, selected for increased PHT, in two elite maize inbred backgrounds. Various exotic accessions used in the germplasm enhancement in maize project served as donors. BC1-derived doubled haploid lines in the same two elite maize inbred backgrounds established without selection for plant height were included for comparison. We conducted genome-wide association studies to explore the genetic control of PHT by BR and GA. In addition, we used BR and GA inhibitors to compare the relationship between PHT, BR, and GA in inbred lines and heterozygotes from a physiological and biological perspective. A total of 73 genomic loci were discovered to be associated with PHT, with seven co-localized with GA, and two co-localized with BR candidate genes. PHT determined in field trials was significantly correlated with seedling stage BR and GA inhibitor responses. However, this observation was only true for maize heterozygotes, not for inbred lines. Path analysis results suggest that heterozygosity increases GA levels, which in turn promote BR levels. Thus, at least part of heterosis for PHT in maize can be explained by increased GA and BR levels, and seedling stage hormone inhibitor response is promising to predict heterosis for PHT.
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Affiliation(s)
- Songlin Hu
- Department of Agronomy, Iowa State University, AmesIA, United States
- *Correspondence: Songlin Hu,
| | - Cuiling Wang
- Department of Agronomy, Henan University of Science and TechnologyLuoyang, China
| | | | - Alexander E. Lipka
- Department of Crop Sciences, University of Illinois at Urbana–Champaign, ChampaignIL, United States
| | - Peng Liu
- Department of Statistics, Iowa State University, AmesIA, United States
| | - Yanhai Yin
- Department of Genetics, Development and Cell biology, Iowa State University, AmesIA, United States
| | - Michael Blanco
- Plant Introduction Research Unit, Department of Agronomy, United States Department of Agriculture – Agricultural Research Service, Iowa State University, AmesIA, United States
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36
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Guan H, Ali F, Pan Q. Dissection of Recombination Attributes for Multiple Maize Populations Using a Common SNP Assay. FRONTIERS IN PLANT SCIENCE 2017; 8:2063. [PMID: 29250099 PMCID: PMC5714861 DOI: 10.3389/fpls.2017.02063] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2017] [Accepted: 11/17/2017] [Indexed: 05/16/2023]
Abstract
Recombination is a vital characteristic for quantitative trait loci mapping and breeding to enhance the yield potential of maize. However, recombination characteristics in globally used segregating populations have never been evaluated at similar genetic marker densities. This study aimed to divulge the characteristics of recombination events, recombinant chromosomal segments, and recombination frequency for four dissimilar populations. These populations were doubled haploid (DH), recombination inbred line (RIL), intermated B73xMo17 (IBM), and multi-parent advanced generation inter-cross (MAGIC), using the Illumina MaizeSNP50 BeadChip to provide markers. Our results revealed that the average number of recombination events was 16, 41, 72, and 86 per line in DH, RIL, IBM, and MAGIC populations, respectively. Accordingly, the average length of recombinant chromosomal segments was 84.8, 47.3, 29.2, and 20.4 Mb in DH, RIL, IBM, and MAGIC populations, respectively. Furtherly, the recombination frequency varied in different genomic regions and population types [DH (0-12.7 cM/Mb), RIL (0-15.5 cM/Mb), IBM (0-24.1 cM/Mb), MAGIC (0-42.3 cM/Mb)]. Utilizing different sub-sets of lines, the recombination bin number and size were analyzed in each population. Additionally, different sub-sets of markers and lines were employed to estimate the recombination bin number and size via formulas for relationship in these populations. The relationship between recombination events and recombination bin length was also examined. Our results contribute to determining the most suitable number of genetic markers, lines in each population, and population type for successful mapping and breeding.
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Affiliation(s)
- Haiying Guan
- Maize Research Institute, Shandong Academy of Agricultural Sciences, Jinan, China
- National Engineering Laboratory of Wheat and Maize, Jinan, China
- Key Laboratory of Biology and Genetic Improvement of Maize in Northern Yellow-Huai River Plain, Ministry of Agriculture, Jinan, China
| | - Farhan Ali
- Cereal Crops Research Institute, Nowshera, Pakistan
| | - Qingchun Pan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
- *Correspondence: Qingchun Pan,
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Chen J, Shrestha R, Ding J, Zheng H, Mu C, Wu J, Mahuku G. Genome-Wide Association Study and QTL Mapping Reveal Genomic Loci Associated with Fusarium Ear Rot Resistance in Tropical Maize Germplasm. G3 (BETHESDA, MD.) 2016; 6:3803-3815. [PMID: 27742723 PMCID: PMC5144952 DOI: 10.1534/g3.116.034561] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Accepted: 08/25/2016] [Indexed: 11/18/2022]
Abstract
Fusarium ear rot (FER) incited by Fusarium verticillioides is a major disease of maize that reduces grain quality globally. Host resistance is the most suitable strategy for managing the disease. We report the results of genome-wide association study (GWAS) to detect alleles associated with increased resistance to FER in a set of 818 tropical maize inbred lines evaluated in three environments. Association tests performed using 43,424 single-nucleotide polymorphic (SNPs) markers identified 45 SNPs and 15 haplotypes that were significantly associated with FER resistance. Each associated SNP locus had relatively small additive effects on disease resistance and accounted for 1-4% of trait variation. These SNPs and haplotypes were located within or adjacent to 38 candidate genes, 21 of which were candidate genes associated with plant tolerance to stresses, including disease resistance. Linkage mapping in four biparental populations to validate GWAS results identified 15 quantitative trait loci (QTL) associated with F. verticillioides resistance. Integration of GWAS and QTL to the maize physical map showed eight colocated loci on chromosomes 2, 3, 4, 5, 9, and 10. QTL on chromosomes 2 and 9 are new. These results reveal that FER resistance is a complex trait that is conditioned by multiple genes with minor effects. The value of selection on identified markers for improving FER resistance is limited; rather, selection to combine small effect resistance alleles combined with genomic selection for polygenic background for both the target and general adaptation traits might be fruitful for increasing FER resistance in maize.
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Affiliation(s)
- Jiafa Chen
- College of Agronomy, Synergetic Innovation Center of Henan Grain Crops and National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou 450002, China
- International Maize and Wheat Improvement Center, 06600 Mexico Distrito Federal, Mexico
| | - Rosemary Shrestha
- International Maize and Wheat Improvement Center, 06600 Mexico Distrito Federal, Mexico
| | - Junqiang Ding
- College of Agronomy, Synergetic Innovation Center of Henan Grain Crops and National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou 450002, China
| | - Hongjian Zheng
- International Maize and Wheat Improvement Center, 06600 Mexico Distrito Federal, Mexico
- Crop Breeding and Cultivation Research Institute, Shanghai Academy of Agricultural Sciences, Shangai 201403 China
| | - Chunhua Mu
- International Maize and Wheat Improvement Center, 06600 Mexico Distrito Federal, Mexico
- Maize Research Institute, Shandong Academy of Agricultural Sciences, Jinan 250100, China
| | - Jianyu Wu
- College of Agronomy, Synergetic Innovation Center of Henan Grain Crops and National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou 450002, China
- College of Life Sciences, Henan Agricultural University, Zhengzhou 450002, China
| | - George Mahuku
- International Maize and Wheat Improvement Center, 06600 Mexico Distrito Federal, Mexico
- International Institute of Tropical Agriculture, 34441 Dar es Salaam, Tanzania
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Bernardo R. Bandwagons I, too, have known. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2016; 129:2323-2332. [PMID: 27681088 DOI: 10.1007/s00122-016-2772-5] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2016] [Accepted: 08/12/2016] [Indexed: 05/19/2023]
Abstract
Bandwagons come in waves. A plant breeder, just like a surfer, needs to carefully choose which waves to be on. A bandwagon is an idea, activity, or cause that becomes increasingly fashionable as more and more people adopt it. In a 1991 article entitled Bandwagons I Have Known, Professor N. W. Simmonds described several bandwagons that he encountered in his career, beginning with induced polyploidy and mutation breeding and ending with the then-new field of biotechnology. This article reviews and speculates about post-1990 bandwagons in plant improvement, including transgenic cultivars, quantitative trait locus (QTL) mapping, association mapping, genomewide (or genomic) selection, phenomics, envirotyping, and genome editing. The life cycle of a bandwagon includes an excitement phase of hype and funding; a realization phase when the initial hype is either tempered or the initial expectations are found to have been too low; and a reality phase when the useful aspects of a bandwagon become part of mainstream thinking and practice, or when an unsuccessful bandwagon is largely abandoned. During the realization phase, a new bandwagon that draws our attention and gives us renewed optimism typically arises. The most popular bandwagons, such as QTL mapping, are those for which the needed experimental resources are accessible, the required technical knowledge and skills can be easily learned, and the outputs can almost always be reported. The favorite bandwagon of any plant breeder has, in one way or another, resulted from Mendel's seminal discoveries 150 years ago. Our community of plant breeders needs to be continually diligent in welcoming new bandwagons, but also in hopping off from those that do not prove useful.
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Affiliation(s)
- Rex Bernardo
- Department of Agronomy and Plant Genetics, University of Minnesota, 411 Borlaug Hall, 1991 Upper Buford Circle, Saint Paul, MN, 55108, USA.
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A major QTL and a candidate gene for heading date in an early maturing rice mutant induced by gamma ray irradiation. Genes Genomics 2016. [DOI: 10.1007/s13258-016-0419-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Mahuku G, Chen J, Shrestha R, Narro LA, Guerrero KVO, Arcos AL, Xu Y. Combined linkage and association mapping identifies a major QTL (qRtsc8-1), conferring tar spot complex resistance in maize. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2016; 129:1217-29. [PMID: 26971113 DOI: 10.1007/s00122-016-2698-y] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2015] [Accepted: 02/18/2016] [Indexed: 05/22/2023]
Abstract
A major QTL ( qRtsc8 - 1 ) conditioning resistance to tar spot complex of maize and occurring at a frequency of 3.5 % across 890 maize inbred lines. Tar spot complex (TSC) is a highly destructive disease of maize found in some countries in America. Identification of TSC resistant germplasm and elucidating the genetic mechanism of resistance is crucial for the use of host resistance to manage this disease. We evaluated 890 elite maize inbred lines in multiple environments and used genome wide association analysis (GWAS) with genotypic data from Illumina MaizeSNP50 BeadChip containing 56 K SNPs to dissect the genetics of TSC resistance. GWAS results were validated through linkage analysis in three bi-parental populations derived from different resistant and susceptible parents. Through GWAS, three TSC resistance loci were identified on chromosome 2, 7 and 8 (-log10 (p) > 5.99). A major quantitative resistance locus (QTL) designated qRtsc8-1, was detected on maize chromosome bin 8.03. qRtsc8-1, was confirmed in three independent bi-parental populations and it accounted for 18-43 % of the observed phenotypic variation for TSC. A rare haplotype within the qRtsc8-1 region, occurring at a frequency of 3.5 % increased TSC resistance by 14 %. Candidate gene analysis revealed that a leucine-rich repeat receptor-like protein (LRR-RLKs) gene family maybe the candidate gene for qRtsc8-1. Identification and localization of a major locus conditioning TSC resistance provides the foundation for fine mapping qRtsc8-1 and developing functional markers for improving TSC resistance in maize breeding programs. To the best of our knowledge, this is the first report of a major QTL for TSC resistance.
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Affiliation(s)
- George Mahuku
- International Maize and Wheat Improvement Center (CIMMYT), ICRAF Campus, UN Avenue, Gigiri, PO Box 1041-00621, Nairobi, Kenya.
- International Institute of Tropical Agriculture (IITA), P.O.Box, 34443, Dar es Salaam, Tanzania.
| | - Jiafa Chen
- International Maize and Wheat Improvement Center (CIMMYT), Apdo. Postal 6-641, 06600, Mexico, DF, Mexico
- College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China
| | - Rosemary Shrestha
- International Maize and Wheat Improvement Center (CIMMYT), Apdo. Postal 6-641, 06600, Mexico, DF, Mexico
| | - Luis A Narro
- International Maize and Wheat Improvement Center (CIMMYT), Apdo. Aereo 67-13, Cali, Colombia
| | | | - Alba Lucia Arcos
- International Maize and Wheat Improvement Center (CIMMYT), Apdo. Aereo 67-13, Cali, Colombia
| | - Yunbi Xu
- International Maize and Wheat Improvement Center (CIMMYT) and Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
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Zhou Z, Zhang C, Zhou Y, Hao Z, Wang Z, Zeng X, Di H, Li M, Zhang D, Yong H, Zhang S, Weng J, Li X. Genetic dissection of maize plant architecture with an ultra-high density bin map based on recombinant inbred lines. BMC Genomics 2016; 17:178. [PMID: 26940065 PMCID: PMC4778306 DOI: 10.1186/s12864-016-2555-z] [Citation(s) in RCA: 71] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2015] [Accepted: 02/29/2016] [Indexed: 11/21/2022] Open
Abstract
Background Plant architecture attributes, such as plant height, ear height, and internode number, have played an important role in the historical increases in grain yield, lodging resistance, and biomass in maize (Zea mays L.). Analyzing the genetic basis of variation in plant architecture using high density QTL mapping will be of benefit for the breeding of maize for many traits. However, the low density of molecular markers in existing genetic maps has limited the efficiency and accuracy of QTL mapping. Genotyping by sequencing (GBS) is an improved strategy for addressing a complex genome via next-generation sequencing technology. GBS has been a powerful tool for SNP discovery and high-density genetic map construction. The creation of ultra-high density genetic maps using large populations of advanced recombinant inbred lines (RILs) is an efficient way to identify QTL for complex agronomic traits. Results A set of 314 RILs derived from inbreds Ye478 and Qi319 were generated and subjected to GBS. A total of 137,699,000 reads with an average of 357,376 reads per individual RIL were generated, which is equivalent to approximately 0.07-fold coverage of the maize B73 RefGen_V3 genome for each individual RIL. A high-density genetic map was constructed using 4183 bin markers (100-Kb intervals with no recombination events). The total genetic distance covered by the linkage map was 1545.65 cM and the average distance between adjacent markers was 0.37 cM with a physical distance of about 0.51 Mb. Our results demonstrated a relatively high degree of collinearity between the genetic map and the B73 reference genome. The quality and accuracy of the bin map for QTL detection was verified by the mapping of a known gene, pericarp color 1 (P1), which controls the color of the cob, with a high LOD value of 80.78 on chromosome 1. Using this high-density bin map, 35 QTL affecting plant architecture, including 14 for plant height, 14 for ear height, and seven for internode number were detected across three environments. Interestingly, pQTL10, which influences all three of these traits, was stably detected in three environments on chromosome 10 within an interval of 14.6 Mb. Two MYB transcription factor genes, GRMZM2G325907 and GRMZM2G108892, which might regulate plant cell wall metabolism are the candidate genes for qPH10. Conclusions Here, an ultra-high density accurate linkage map for a set of maize RILs was constructed using a GBS strategy. This map will facilitate identification of genes and exploration of QTL for plant architecture in maize. It will also be helpful for further research into the mechanisms that control plant architecture while also providing a basis for marker-assisted selection. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2555-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Zhiqiang Zhou
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Zhongguancun South Street, Haidian District, Beijing, 100081, China.
| | - Chaoshu Zhang
- College of Agronomy, Northeast Agricultural University, Mucai Street, XiangFang District, Harbin, Heilongjiang, 150030, China.
| | - Yu Zhou
- College of Agronomy, Northeast Agricultural University, Mucai Street, XiangFang District, Harbin, Heilongjiang, 150030, China.
| | - Zhuanfang Hao
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Zhongguancun South Street, Haidian District, Beijing, 100081, China.
| | - Zhenhua Wang
- College of Agronomy, Northeast Agricultural University, Mucai Street, XiangFang District, Harbin, Heilongjiang, 150030, China.
| | - Xing Zeng
- College of Agronomy, Northeast Agricultural University, Mucai Street, XiangFang District, Harbin, Heilongjiang, 150030, China.
| | - Hong Di
- College of Agronomy, Northeast Agricultural University, Mucai Street, XiangFang District, Harbin, Heilongjiang, 150030, China.
| | - Mingshun Li
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Zhongguancun South Street, Haidian District, Beijing, 100081, China.
| | - Degui Zhang
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Zhongguancun South Street, Haidian District, Beijing, 100081, China.
| | - Hongjun Yong
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Zhongguancun South Street, Haidian District, Beijing, 100081, China.
| | - Shihuang Zhang
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Zhongguancun South Street, Haidian District, Beijing, 100081, China.
| | - Jianfeng Weng
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Zhongguancun South Street, Haidian District, Beijing, 100081, China.
| | - Xinhai Li
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Zhongguancun South Street, Haidian District, Beijing, 100081, China.
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Wang Y, Xu J, Deng D, Ding H, Bian Y, Yin Z, Wu Y, Zhou B, Zhao Y. A comprehensive meta-analysis of plant morphology, yield, stay-green, and virus disease resistance QTL in maize (Zea mays L.). PLANTA 2016; 243:459-71. [PMID: 26474992 DOI: 10.1007/s00425-015-2419-9] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2014] [Accepted: 10/07/2015] [Indexed: 05/09/2023]
Abstract
The meta-QTL and candidate genes will facilitate the elucidation of molecular bases underlying agriculturally important traits and open new avenues for functional markers development and elite alleles introgression in maize breeding program. A large number of QTLs attributed to grain productivity and other agriculturally important traits have been identified and deposited in public repositories. The integration of fruitful QTL becomes a major issue in current plant genomics. To this end, we first collected QTL for six agriculturally important traits in maize, including yield, plant height, ear height, leaf angle, stay-green, and maize rough dwarf disease resistance. The meta-analysis method was then employed to retrieve 113 meta-QTL. Additionally, we also isolated candidate genes for target traits by the bioinformatic technique. Several candidates, including some well-characterized genes, GA3ox2 for plant height, lg1 and lg4 for leaf angle, zfl1 and zfl2 for flowering time, were co-localized with established meta-QTL intervals. Intriguingly, in a relatively narrow meta-QTL region, the maize ortholog of rice yield-related gene GW8/OsSPL16 was believed to be a candidate for yield. Leveraging results presented in this study will provide further insights into the genetic architecture of maize agronomic traits. Moreover, the meta-QTL and candidate genes reported here could be harnessed for the enhancement of stress tolerance and yield performance in maize and translation to other crops.
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Li X, Zhou Z, Ding J, Wu Y, Zhou B, Wang R, Ma J, Wang S, Zhang X, Xia Z, Chen J, Wu J. Combined Linkage and Association Mapping Reveals QTL and Candidate Genes for Plant and Ear Height in Maize. FRONTIERS IN PLANT SCIENCE 2016; 7:833. [PMID: 27379126 PMCID: PMC4908132 DOI: 10.3389/fpls.2016.00833] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2016] [Accepted: 05/27/2016] [Indexed: 05/19/2023]
Abstract
Plant height (PH) and ear height (EH) are two very important agronomic traits related to the population density and lodging in maize. In order to better understand of the genetic basis of nature variation in PH and EH, two bi-parental populations and one genome-wide association study (GWAS) population were used to map quantitative trait loci (QTL) for both traits. Phenotypic data analysis revealed a wide normal distribution and high heritability for PH and EH in the three populations, which indicated that maize height is a highly polygenic trait. A total of 21 QTL for PH and EH in three common genomic regions (bin 1.05, 5.04/05, and 6.04/05) were identified by QTL mapping in the two bi-parental populations under multiple environments. Additionally, 41 single nucleotide polymorphisms (SNPs) were identified for PH and EH by GWAS, of which 29 SNPs were located in 19 unique candidate gene regions. Most of the candidate genes were related to plant growth and development. One QTL on Chromosome 1 was further verified in a near-isogenic line (NIL) population, and GWAS identified a C2H2 zinc finger family protein that maybe the candidate gene for this QTL. These results revealed that nature variation of PH and EH are strongly controlled by multiple genes with low effect and facilitated a better understanding of the underlying mechanism of height in maize.
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Sehgal D, Singh R, Rajpal VR. Quantitative Trait Loci Mapping in Plants: Concepts and Approaches. MOLECULAR BREEDING FOR SUSTAINABLE CROP IMPROVEMENT 2016. [DOI: 10.1007/978-3-319-27090-6_2] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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Li F, Chen B, Xu K, Gao G, Yan G, Qiao J, Li J, Li H, Li L, Xiao X, Zhang T, Nishio T, Wu X. A genome-wide association study of plant height and primary branch number in rapeseed (Brassica napus). PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2016; 242:169-177. [PMID: 26566834 DOI: 10.1016/j.plantsci.2015.05.012] [Citation(s) in RCA: 69] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2015] [Revised: 05/14/2015] [Accepted: 05/17/2015] [Indexed: 05/18/2023]
Abstract
Crop plant architecture plays a highly important role in its agronomic performance. Plant height (PH) and primary branch number (PB) are two major factors that affect the plant architecture of rapeseed (Brassica napus). Previous studies have shown that these two traits are controlled by multiple quantitative trait loci (QTL); however, QTLs have not been delimited to regions less than 10cM. Genome-wide association study (GWAS) is a highly efficient approach for identifying genetic loci controlling traits at relatively high resolution. In this study, variations in PH and PB of a panel of 472 rapeseed accessions that had previously been analyzed by a 60k SNP array were investigated for three consecutive years and studied by GWAS. Eight QTLs on chromosome A03, A05, A07 and C07 were identified for PH, and five QTLs on A01, A03, A07 and C07 were identified for PB. Although most QTLs have been detected in previous studies based on linkage analyses, the two QTLs of PH on A05 and the QTL of PB on C07 were novel. In the genomic regions close to the GWAS peaks, orthologs of the genes involved in flower development, phytohormone biosynthesis, metabolism and signaling in Arabidopsis were identified.
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Affiliation(s)
- Feng Li
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crop Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China; Graduate School of Agricultural Science, Tohoku University, 1-1 Tsutsumidori Amamiyamachi, Aoba-ku, Sendai, Miyagi 981-8555, Japan
| | - Biyun Chen
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crop Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China
| | - Kun Xu
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crop Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China
| | - Guizhen Gao
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crop Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China
| | - Guixin Yan
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crop Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China
| | - Jiangwei Qiao
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crop Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China
| | - Jun Li
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crop Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China
| | - Hao Li
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crop Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China
| | - Lixia Li
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crop Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China
| | - Xin Xiao
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crop Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China
| | - Tianyao Zhang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crop Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China
| | - Takeshi Nishio
- Graduate School of Agricultural Science, Tohoku University, 1-1 Tsutsumidori Amamiyamachi, Aoba-ku, Sendai, Miyagi 981-8555, Japan
| | - Xiaoming Wu
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crop Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China.
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Liu Y, Hou X, Xiao Q, Yi Q, Bian S, Hu Y, Liu H, Zhang J, Hao X, Cheng W, Li Y, Huang Y. Genetic Analysis in Maize Foundation Parents with Mapping Population and Testcross Population: Ye478 Carried More Favorable Alleles and Using QTL Information Could Improve Foundation Parents. FRONTIERS IN PLANT SCIENCE 2016; 7:1417. [PMID: 27721817 PMCID: PMC5034680 DOI: 10.3389/fpls.2016.01417] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2016] [Accepted: 09/06/2016] [Indexed: 05/17/2023]
Abstract
The development of maize foundation parents is an important part of genetics and breeding research, and applying new genetic information to produce foundation parents has been challenging. In this study, we focused on quantitative trait loci (QTLs) and general combining ability (GCA) of Ye478, a widely used foundation parent in China. We developed three sets of populations for QTL mapping and to analyze the GCA for some agronomic traits. The assessment of 15 traits resulted in the detection of 251 QTLs in six tested environments, with 119 QTLs identified through a joint analysis across all environments. Further, analyses revealed that most favorable alleles for plant type-related traits were from Ye478, and more than half of the favorable alleles for yield-related traits were from R08, another foundation parent used in southwestern China, suggesting that different types of foundation parents carried different favorable alleles. We observed that the GCA for most traits (e.g., plant height and 100-kernel weight) was maintained in the inbred lines descended from the foundation parents. Additionally, the continuous improvement in the GCA of the descendants of the foundation parents was consistent with the main trend in maize breeding programs. We identified three significant genomic regions that were highly conserved in three Ye478 descendants, including the stable QTL for plant height. The GCA for the traits in the F7 generation revealed that the QTLs for the given traits per se were affected by additive effects in the same way in different populations.
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Affiliation(s)
- Yinghong Liu
- Maize Research Institute, Sichuan Agricultural UniversityChengdu, China
| | - Xianbin Hou
- College of Agronomy, Sichuan Agricultural UniversityChengdu, China
| | - Qianlin Xiao
- College of Agronomy, Sichuan Agricultural UniversityChengdu, China
| | - Qiang Yi
- College of Agronomy, Sichuan Agricultural UniversityChengdu, China
| | - Shaowei Bian
- College of Agronomy, Sichuan Agricultural UniversityChengdu, China
| | - Yufeng Hu
- College of Agronomy, Sichuan Agricultural UniversityChengdu, China
| | - Hanmei Liu
- College of Life Science, Sichuan Agricultural UniversityYa'an, China
| | - Junjie Zhang
- College of Life Science, Sichuan Agricultural UniversityYa'an, China
| | - Xiaoqin Hao
- College of Agronomy, Guangxi UniversityNanning, China
| | - Weidong Cheng
- Maize Research Institute, Guangxi Academy of Agricultural SciencesNanning, China
| | - Yu Li
- Institute of Crop Science, Chinese Academy of Agricultural SciencesBeijing, China
- *Correspondence: Yu Li
| | - Yubi Huang
- College of Agronomy, Sichuan Agricultural UniversityChengdu, China
- Yubi Huang
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Kang Y, Sakiroglu M, Krom N, Stanton-Geddes J, Wang M, Lee YC, Young ND, Udvardi M. Genome-wide association of drought-related and biomass traits with HapMap SNPs in Medicago truncatula. PLANT, CELL & ENVIRONMENT 2015; 38:1997-2011. [PMID: 25707512 DOI: 10.1111/pce.12520] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2014] [Revised: 02/09/2015] [Accepted: 02/10/2015] [Indexed: 05/21/2023]
Abstract
Improving drought tolerance of crop plants is a major goal of plant breeders. In this study, we characterized biomass and drought-related traits of 220 Medicago truncatula HapMap accessions. Characterized traits included shoot biomass, maximum leaf size, specific leaf weight, stomatal density, trichome density and shoot carbon-13 isotope discrimination (δ(13) C) of well-watered M. truncatula plants, and leaf performance in vitro under dehydration stress. Genome-wide association analyses were carried out using the general linear model (GLM), the standard mixed linear model (MLM) and compressed MLM (CMLM) in TASSEL, which revealed significant overestimation of P-values by CMLM. For each trait, candidate genes and chromosome regions containing SNP markers were found that are in significant association with the trait. For plant biomass, a 0.5 Mbp region on chromosome 2 harbouring a plasma membrane intrinsic protein, PIP2, was discovered that could potentially be targeted to increase dry matter yield. A protein disulfide isomerase-like protein was found to be tightly associated with both shoot biomass and leaf size. A glutamate-cysteine ligase and an aldehyde dehydrogenase family protein with Arabidopsis homologs strongly expressed in the guard cells were two of the top genes identified by stomata density genome-wide association studies analysis.
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Affiliation(s)
- Yun Kang
- Plant Biology Division, The Samuel Roberts Noble Foundation, Ardmore, OK, 73401, USA
| | | | - Nicholas Krom
- Plant Biology Division, The Samuel Roberts Noble Foundation, Ardmore, OK, 73401, USA
| | | | - Mingyi Wang
- Plant Biology Division, The Samuel Roberts Noble Foundation, Ardmore, OK, 73401, USA
| | - Yi-Ching Lee
- Plant Biology Division, The Samuel Roberts Noble Foundation, Ardmore, OK, 73401, USA
| | - Nevin D Young
- Department of Plant Biology, University of Minnesota, St. Paul, MN, 55108, USA
| | - Michael Udvardi
- Plant Biology Division, The Samuel Roberts Noble Foundation, Ardmore, OK, 73401, USA
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48
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Nambeesan SU, Mandel JR, Bowers JE, Marek LF, Ebert D, Corbi J, Rieseberg LH, Knapp SJ, Burke JM. Association mapping in sunflower (Helianthus annuus L.) reveals independent control of apical vs. basal branching. BMC PLANT BIOLOGY 2015; 15:84. [PMID: 25887675 PMCID: PMC4407831 DOI: 10.1186/s12870-015-0458-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2014] [Accepted: 02/13/2015] [Indexed: 05/20/2023]
Abstract
BACKGROUND Shoot branching is an important determinant of plant architecture and influences various aspects of growth and development. Selection on branching has also played an important role in the domestication of crop plants, including sunflower (Helianthus annuus L.). Here, we describe an investigation of the genetic basis of variation in branching in sunflower via association mapping in a diverse collection of cultivated sunflower lines. RESULTS Detailed phenotypic analyses revealed extensive variation in the extent and type of branching within the focal population. After correcting for population structure and kinship, association analyses were performed using a genome-wide collection of SNPs to identify genomic regions that influence a variety of branching-related traits. This work resulted in the identification of multiple previously unidentified genomic regions that contribute to variation in branching. Genomic regions that were associated with apical and mid-apical branching were generally distinct from those associated with basal and mid-basal branching. Homologs of known branching genes from other study systems (i.e., Arabidopsis, rice, pea, and petunia) were also identified from the draft assembly of the sunflower genome and their map positions were compared to those of associations identified herein. Numerous candidate branching genes were found to map in close proximity to significant branching associations. CONCLUSIONS In sunflower, variation in branching is genetically complex and overall branching patterns (i.e., apical vs. basal) were found to be influenced by distinct genomic regions. Moreover, numerous candidate branching genes mapped in close proximity to significant branching associations. Although the sunflower genome exhibits localized islands of elevated linkage disequilibrium (LD), these non-random associations are known to decay rapidly elsewhere. The subset of candidate genes that co-localized with significant associations in regions of low LD represents the most promising target for future functional analyses.
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Affiliation(s)
- Savithri U Nambeesan
- Department of Plant Biology, Miller Plant Sciences, University of Georgia, Athens, GA, 30602, USA.
- Present address: Department of Horticulture, University of Georgia, Athens, GA, 30602, USA.
| | - Jennifer R Mandel
- Department of Plant Biology, Miller Plant Sciences, University of Georgia, Athens, GA, 30602, USA.
- Present address: Department of Biological Sciences, University of Memphis, Memphis, TN, 38152, USA.
| | - John E Bowers
- Department of Plant Biology, Miller Plant Sciences, University of Georgia, Athens, GA, 30602, USA.
| | - Laura F Marek
- North Central Regional Plant Introduction Station, Iowa State University/USDA-ARS, Ames, IA, 50014, USA.
| | - Daniel Ebert
- Department of Botany, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada.
| | - Jonathan Corbi
- Department of Plant Biology, Miller Plant Sciences, University of Georgia, Athens, GA, 30602, USA.
- Present address: Department of Crop and Soil Sciences, University of Georgia, Athens, GA, 30602, USA.
| | - Loren H Rieseberg
- Department of Botany, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada.
| | - Steven J Knapp
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA.
| | - John M Burke
- Department of Plant Biology, Miller Plant Sciences, University of Georgia, Athens, GA, 30602, USA.
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49
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Pace J, Gardner C, Romay C, Ganapathysubramanian B, Lübberstedt T. Genome-wide association analysis of seedling root development in maize (Zea mays L.). BMC Genomics 2015; 16:47. [PMID: 25652714 PMCID: PMC4326187 DOI: 10.1186/s12864-015-1226-9] [Citation(s) in RCA: 101] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2014] [Accepted: 01/08/2015] [Indexed: 12/21/2022] Open
Abstract
Background Plants rely on the root system for anchorage to the ground and the acquisition and absorption of nutrients critical to sustaining productivity. A genome wide association analysis enables one to analyze allelic diversity of complex traits and identify superior alleles. 384 inbred lines from the Ames panel were genotyped with 681,257 single nucleotide polymorphism markers using Genotyping-by-Sequencing technology and 22 seedling root architecture traits were phenotyped. Results Utilizing both a general linear model and mixed linear model, a GWAS study was conducted identifying 268 marker trait associations (p ≤ 5.3×10-7). Analysis of significant SNP markers for multiple traits showed that several were located within gene models with some SNP markers localized within regions of previously identified root quantitative trait loci. Gene model GRMZM2G153722 located on chromosome 4 contained nine significant markers. This predicted gene is expressed in roots and shoots. Conclusion This study identifies putatively associated SNP markers associated with root traits at the seedling stage. Some SNPs were located within or near (<1 kb) gene models. These gene models identify possible candidate genes involved in root development at the seedling stage. These and respective linked or functional markers could be targets for breeders for marker assisted selection of seedling root traits. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1226-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jordon Pace
- Department of Agronomy, Iowa State University, Ames, Iowa, 50013, USA.
| | - Candice Gardner
- Department of Agronomy, Iowa State University, Ames, Iowa, 50013, USA.
| | - Cinta Romay
- Institute for Genomic Diversity, Cornell University, Ithaca, NY, 14853, USA.
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50
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Pace J, Gardner C, Romay C, Ganapathysubramanian B, Lübberstedt T. Genome-wide association analysis of seedling root development in maize (Zea mays L.). BMC Genomics 2015. [PMID: 25652714 DOI: 10.1186/s12864-015-1226-1229] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/28/2023] Open
Abstract
BACKGROUND Plants rely on the root system for anchorage to the ground and the acquisition and absorption of nutrients critical to sustaining productivity. A genome wide association analysis enables one to analyze allelic diversity of complex traits and identify superior alleles. 384 inbred lines from the Ames panel were genotyped with 681,257 single nucleotide polymorphism markers using Genotyping-by-Sequencing technology and 22 seedling root architecture traits were phenotyped. RESULTS Utilizing both a general linear model and mixed linear model, a GWAS study was conducted identifying 268 marker trait associations (p ≤ 5.3×10(-7)). Analysis of significant SNP markers for multiple traits showed that several were located within gene models with some SNP markers localized within regions of previously identified root quantitative trait loci. Gene model GRMZM2G153722 located on chromosome 4 contained nine significant markers. This predicted gene is expressed in roots and shoots. CONCLUSION This study identifies putatively associated SNP markers associated with root traits at the seedling stage. Some SNPs were located within or near (<1 kb) gene models. These gene models identify possible candidate genes involved in root development at the seedling stage. These and respective linked or functional markers could be targets for breeders for marker assisted selection of seedling root traits.
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Affiliation(s)
- Jordon Pace
- Department of Agronomy, Iowa State University, Ames, Iowa, 50013, USA.
| | - Candice Gardner
- Department of Agronomy, Iowa State University, Ames, Iowa, 50013, USA.
| | - Cinta Romay
- Institute for Genomic Diversity, Cornell University, Ithaca, NY, 14853, USA.
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