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Alemu A, Sundaramoorthy J, Abreha KB, Enyew M, Geleta M, Carlsson AS. Developing genomic tools to assist turnip rape [ Brassica rapa (L.) subsp. oleifera (DC.) Metzg.] breeding. Front Genet 2024; 15:1435474. [PMID: 39301528 PMCID: PMC11411567 DOI: 10.3389/fgene.2024.1435474] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2024] [Accepted: 08/14/2024] [Indexed: 09/22/2024] Open
Abstract
Introduction Turnip rape is recognized as an oilseed crop contributing to environmentally sustainable agriculture via integration into crop rotation systems. Despite its various advantages, the crop's cultivation has declined globally due to a relatively low productivity, giving way to other crops. The use of genomic tools could enhance the breeding process and accelerate genetic gains. Therefore, the present research investigated 170 turnip rape accessions representing its global gene pool to identify SNP markers associated nine phenological and agro-morphological traits and estimate the genomic breeding values (GEBVs) of the germplasm through GWAS and genomic prediction analyses, respectively. Methods Field trials were conducted at two sites in northern and southern Sweden to obtain the phenotypic data while genotyping was conducted via the genotyping-by-sequencing (GBS) method. The traits studied include days to flowering (DTF) and maturity (DTM), plant height (PH), seed yield (YLD), thousand seed weight (TSW), silique length (SL), number of siliques (NS), number of seeds per silique (SS), and pod shattering resistance (PSHR). Results and conclusion Analysis of variance revealed substantial variation among accessions, with significant genotype-by-environment interaction for most traits. A total of 25, 17, 16, 14, 7, 5, 3, and 3 MTAs were identified for TSW, DTF, PH, PSHR, SL, YLD, SS and DTM, respectively. An 80%-20% training-test set genomic prediction analysis was conducted using the ridge regression - BLUP (RR-BLUP) model. The accuracy of genomic prediction for most traits was high, indicating that these tools may assist turnip rape breeders in accelerating genetic gains. The study highlights the potential of genomic tools to significantly advance breeding programs for turnip rape by identifying pivotal SNP markers and effectively estimating genomic breeding values. Future breeding perspectives should focus on leveraging these genomic insights to enhance agronomic traits and productivity, thereby reinstating turnip rape as a competitive and sustainable crop in Sweden and broader global agriculture.
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Affiliation(s)
- Admas Alemu
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Alnarp, Sweden
| | | | - Kibrom B Abreha
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Alnarp, Sweden
| | - Muluken Enyew
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Alnarp, Sweden
- School of Biological Sciences, Washington State University, Pullman, WA, United States
- Institute of Biotechnology, Addis Ababa University, Addis Ababa, Ethiopia
| | - Mulatu Geleta
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Alnarp, Sweden
| | - Anders S Carlsson
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Alnarp, Sweden
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Wang M, Yang X. Effects of plant growth-promoting rhizobacteria on blueberry growth and rhizosphere soil microenvironment. PeerJ 2024; 12:e16992. [PMID: 38426138 PMCID: PMC10903360 DOI: 10.7717/peerj.16992] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Accepted: 01/31/2024] [Indexed: 03/02/2024] Open
Abstract
Background Plant growth-promoting rhizobacteria (PGPR) have a specific symbiotic relationship with plants and rhizosphere soil. The purpose of this study was to evaluate the effects of PGPR on blueberry plant growth, rhizospheric soil nutrients and the microbial community. Methods In this study, nine PGPR strains, belonging to the genera Pseudomonas and Buttiauxella, were selected and added into the soil in which the blueberry cuttings were planted. All the physiological indexes of the cuttings and all rhizospheric soil element contents were determined on day 6 after the quartic root irrigation experiments were completed. The microbial diversity in the soil was determined using high-throughput amplicon sequencing technology. The correlations between phosphorus solubilization, the auxin production of PGPR strains, and the physiological indexes of blueberry plants, and the correlation between rhizospheric microbial diversity and soil element contents were determined using the Pearson's correlation, Kendall's tau correlation and Spearman's rank correlation analysis methods. Results The branch number, leaf number, chlorophyllcontentand plant height of the treated blueberry group were significantly higher than those of the control group. The rhizospheric soil element contents also increased after PGPR root irrigation. The rhizospheric microbial community structure changed significantly under the PGPR of root irrigation. The dominant phyla, except Actinomycetota, in the soil samples had the greatest correlation with phosphorus solubilization and the auxin production of PGPR strains. The branch number, leaf number, and chlorophyllcontent had a positive correlation with the phosphorus solubilization and auxin production of PGPR strains and soil element contents. In conclusion, plant growth could be promoted by the root irrigation of PGPR to improve rhizospheric soil nutrients and the microenvironment, with modification of the rhizospheric soil microbial community. Discussion Plant growth could be promoted by the root irrigation of PGPR to improve rhizospheric soil nutrients and the microenvironment, with the modification of the rhizospheric soil microbial community. These data may help us to better understand the positive effects of PGPR on blueberry growth and the rhizosphere soil microenvironment, as well as provide a research basis for the subsequent development of a rhizosphere-promoting microbial fertilizer.
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Affiliation(s)
- Mengjiao Wang
- School of Biological Science and Engineering, Shaanxi University of Technology, Hanzhong, Shaanxi, China
- Collaborative Innovation Center for Comprehensive Development of Biological Resources in Qinling-Ba Mountains, Hanzhong, Shaanxi, China
- Shaanxi Key Laboratory of Bioresources, Hanzhong, Shaanxi, China
| | - Xinlong Yang
- School of Biological Science and Engineering, Shaanxi University of Technology, Hanzhong, Shaanxi, China
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Zhang X, Li X, Li H, Wang Z, Xia R, Hu J, Wang P, Zhou X, Wan L, Hong D, Yang G. Quantitative trait locus mapping and improved resistance to sclerotinia stem rot in a backbone parent of rapeseed ( Brassica napus L.). FRONTIERS IN PLANT SCIENCE 2022; 13:1056206. [PMID: 36438142 PMCID: PMC9684713 DOI: 10.3389/fpls.2022.1056206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Accepted: 10/26/2022] [Indexed: 06/16/2023]
Abstract
There are three main challenges to improving sclerotinia stem rot (SSR) resistance in rapeseed (Brassica napus L.). First, breeding materials such as the backbone parents have not been extensively investigated, making the findings of previous studies difficult to directly implement. Second, SSR resistance and flowering time (FT) loci are typically linked; thus, use of these loci requires sacrifice of the rapeseed growth period. Third, the SSR resistance loci in susceptible materials are often neglected, thereby reducing the richness of resistant resources. This study was conducted to investigate the stem resistance, disease index, and FT of a doubled haploid population consisting of 151 lines constructed from the backbone parent 19514A and conventional rapeseed cultivar ZY50 within multiple environments. Quantitative trait locus (QTL) mapping revealed 13 stem resistance QTLs, 9 disease index QTLs, and 20 FT QTLs. QTL meta-analysis showed that uqA04, uqC03.1, and uqC03.2 were repeatable SSR resistance QTLs derived from different parents but not affected by the FT. Based on these three QTLs, we proposed a strategy for improving the SSR resistance of 19514A and ZY50. This study improves the understanding of the resistance to rapeseed SSR and genetic basis of FT and demonstrates that SSR resistance QTLs can be mined from parents with a minimal resistance level difference, thereby supporting the application of backbone parents in related research and resistance improvement.
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Affiliation(s)
- Xiaohui Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
- Sanya Nanfan Research Institute of Hainan University, Hainan Yazhou Bay Seed Laboratory, Sanya, China
- College of Tropical Crops, Hainan University, Haikou, China
| | - Xiang Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Huining Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Zhuanrong Wang
- Institute of Crops, Wuhan Academy of Agricultural Sciences, Wuhan, China
| | - Rui Xia
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Jin Hu
- Sanya Nanfan Research Institute of Hainan University, Hainan Yazhou Bay Seed Laboratory, Sanya, China
- College of Tropical Crops, Hainan University, Haikou, China
| | - Pengfei Wang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Xianming Zhou
- Sanya Nanfan Research Institute of Hainan University, Hainan Yazhou Bay Seed Laboratory, Sanya, China
- College of Tropical Crops, Hainan University, Haikou, China
| | - Lili Wan
- Institute of Crops, Wuhan Academy of Agricultural Sciences, Wuhan, China
| | - Dengfeng Hong
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Guangsheng Yang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
- Sanya Nanfan Research Institute of Hainan University, Hainan Yazhou Bay Seed Laboratory, Sanya, China
- College of Tropical Crops, Hainan University, Haikou, China
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Rushworth CA, Wagner MR, Mitchell-Olds T, Anderson JT. The Boechera model system for evolutionary ecology. AMERICAN JOURNAL OF BOTANY 2022; 109:1939-1961. [PMID: 36371714 DOI: 10.1002/ajb2.16090] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 08/27/2022] [Accepted: 08/30/2022] [Indexed: 06/16/2023]
Abstract
Model systems in biology expand the research capacity of individuals and the community. Closely related to Arabidopsis, the genus Boechera has emerged as an important ecological model owing to the ability to integrate across molecular, functional, and eco-evolutionary approaches. Boechera species are broadly distributed in relatively undisturbed habitats predominantly in western North America and provide one of the few experimental systems for identification of ecologically important genes through genome-wide association studies and investigations of selection with plants in their native habitats. The ecologically, evolutionarily, and agriculturally important trait of apomixis (asexual reproduction via seeds) is common in the genus, and field experiments suggest that abiotic and biotic environments shape the evolution of sex. To date, population genetic studies have focused on the widespread species B. stricta, detailing population divergence and demographic history. Molecular and ecological studies show that balancing selection maintains genetic variation in ~10% of the genome, and ecological trade-offs contribute to complex trait variation for herbivore resistance, flowering phenology, and drought tolerance. Microbiome analyses have shown that host genotypes influence leaf and root microbiome composition, and the soil microbiome influences flowering phenology and natural selection. Furthermore, Boechera offers numerous opportunities for investigating biological responses to global change. In B. stricta, climate change has induced a shift of >2 weeks in the timing of first flowering since the 1970s, altered patterns of natural selection, generated maladaptation in previously locally-adapted populations, and disrupted life history trade-offs. Here we review resources and results for this eco-evolutionary model system and discuss future research directions.
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Affiliation(s)
| | - Maggie R Wagner
- Department of Ecology and Evolutionary Biology, Kansas Biological Survey and Center for Ecological Research, University of Kansas, Lawrence, KS, 66045, USA
| | | | - Jill T Anderson
- Department of Genetics and Odum School of Ecology, University of Georgia, Athens, GA, 30602, USA
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Qu G, Gao Y, Wang X, Fu W, Sun Y, Gao X, Wang W, Hao C, Feng H, Wang Y. Fine mapping and analysis of candidate genes for qFT7.1, a major quantitative trait locus controlling flowering time in Brassica rapa L. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:2233-2246. [PMID: 35532733 DOI: 10.1007/s00122-022-04108-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Accepted: 04/13/2022] [Indexed: 06/14/2023]
Abstract
qFT7.1, a major QTL for flowering time in Brassica rapa was fine-mapped to chromosome A07 in a 56.4-kb interval, in which the most likely candidate gene is BraA07g018240.3C. In Brassica rapa, flowering time (FT) is an important agronomic trait that affects the yield, quality, and adaption. FT is a complicated trait that is regulated by many genes and is affected greatly by the environment. In this study, a chromosome segment substitution line (CSSL), CSSL16, was selected that showed later flowering than the recurrent parent, a rapid-cycling inbred line of B. rapa (RcBr). Using Bulked Segregant RNA sequencing, we identified a late flowering quantitative trait locus (QTL), designated as qFT7.1, on chromosome A07, based on a secondary-F2 population derived from the cross between CSSL16 and RcBr. qFT7.1 was further validated by conventional QTL mapping. This QTL explained 39.9% (logarithm of odds = 32.2) of the phenotypic variations and was fine mapped to a 56.4-kb interval using recombinant analysis. Expression analysis suggested that BraA07g018240.3C, which is homologous to ATC (encoding Arabidopsis thaliana CENTRORADIALIS homologue), a gene for delayed flowering in Arabidopsis, as the most promising candidate gene. Sequence analysis demonstrated that two synonymous mutations existed in the coding region and numerous bases replacements existed in promoter region between BraA07g018240.3C from CSSL16 and RcBr. The results will increase our knowledge related to the molecular mechanism of late flowering in B. rapa and lays a solid foundation for the breeding of late bolting B. rapa.
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Affiliation(s)
- Gaoyang Qu
- College of Horticulture, Shenyang Agricultural University, 120 Dongling Road, Shenhe District, Shenyang, 110866, People's Republic of China
- Key Laboratory of Protected Horticulture, Ministry of Education, Shenyang Agricultural University, Shenyang, 110866, People's Republic of China
| | - Yue Gao
- College of Horticulture, Shenyang Agricultural University, 120 Dongling Road, Shenhe District, Shenyang, 110866, People's Republic of China
- Key Laboratory of Protected Horticulture, Ministry of Education, Shenyang Agricultural University, Shenyang, 110866, People's Republic of China
| | - Xian Wang
- College of Horticulture, Shenyang Agricultural University, 120 Dongling Road, Shenhe District, Shenyang, 110866, People's Republic of China
- Key Laboratory of Protected Horticulture, Ministry of Education, Shenyang Agricultural University, Shenyang, 110866, People's Republic of China
| | - Wei Fu
- College of Horticulture, Shenyang Agricultural University, 120 Dongling Road, Shenhe District, Shenyang, 110866, People's Republic of China
- Key Laboratory of Protected Horticulture, Ministry of Education, Shenyang Agricultural University, Shenyang, 110866, People's Republic of China
| | - Yunxia Sun
- College of Horticulture, Shenyang Agricultural University, 120 Dongling Road, Shenhe District, Shenyang, 110866, People's Republic of China
- Key Laboratory of Protected Horticulture, Ministry of Education, Shenyang Agricultural University, Shenyang, 110866, People's Republic of China
| | - Xu Gao
- College of Horticulture, Shenyang Agricultural University, 120 Dongling Road, Shenhe District, Shenyang, 110866, People's Republic of China
- Key Laboratory of Protected Horticulture, Ministry of Education, Shenyang Agricultural University, Shenyang, 110866, People's Republic of China
| | - Wei Wang
- College of Horticulture, Shenyang Agricultural University, 120 Dongling Road, Shenhe District, Shenyang, 110866, People's Republic of China
- Key Laboratory of Protected Horticulture, Ministry of Education, Shenyang Agricultural University, Shenyang, 110866, People's Republic of China
| | - Chunming Hao
- College of Horticulture, Shenyang Agricultural University, 120 Dongling Road, Shenhe District, Shenyang, 110866, People's Republic of China
- Key Laboratory of Protected Horticulture, Ministry of Education, Shenyang Agricultural University, Shenyang, 110866, People's Republic of China
| | - Hui Feng
- College of Horticulture, Shenyang Agricultural University, 120 Dongling Road, Shenhe District, Shenyang, 110866, People's Republic of China
- Key Laboratory of Protected Horticulture, Ministry of Education, Shenyang Agricultural University, Shenyang, 110866, People's Republic of China
| | - Yugang Wang
- College of Horticulture, Shenyang Agricultural University, 120 Dongling Road, Shenhe District, Shenyang, 110866, People's Republic of China.
- Key Laboratory of Protected Horticulture, Ministry of Education, Shenyang Agricultural University, Shenyang, 110866, People's Republic of China.
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Fang C, Wang Z, Wang P, Song Y, Ahmad A, Dong F, Hong D, Yang G. Heterosis Derived From Nonadditive Effects of the BnFLC Homologs Coordinates Early Flowering and High Yield in Rapeseed ( Brassica napus L.). FRONTIERS IN PLANT SCIENCE 2022; 12:798371. [PMID: 35251061 PMCID: PMC8893081 DOI: 10.3389/fpls.2021.798371] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Accepted: 12/22/2021] [Indexed: 05/31/2023]
Abstract
Early flowering facilitates crops to adapt multiple cropping systems or growing regions with a short frost-free season; however, it usually brings an obvious yield loss. In this study, we identified that the three genes, namely, BnFLC.A2, BnFLC.C2, and BnFLC.A3b, are the major determinants for the flowering time (FT) variation of two elite rapeseed (Brassica napus L.) accessions, i.e., 616A and R11. The early-flowering alleles (i.e., Bnflc.a2 and Bnflc.c2) and late-flowering allele (i.e., BnFLC.A3b) from R11 were introgressed into the recipient parent 616A through a breeding strategy of marker-assisted backcross, giving rise to eight homozygous near-isogenic lines (NILs) associated with these three loci and 19 NIL hybrids produced by the mutual crossing of these NILs. Phenotypic investigations showed that NILs displayed significant variations in both FT and plant yield (PY). Notably, genetic analysis indicated that BnFLC.A2, BnFLC.C2, and BnFLC.A3b have additive effects of 1.446, 1.365, and 1.361 g on PY, respectively, while their dominant effects reached 3.504, 2.991, and 3.284 g, respectively, indicating that the yield loss caused by early flowering can be successfully compensated by exploring the heterosis of FT genes in the hybrid NILs. Moreover, we further validated that the heterosis of FT genes in PY was also effective in non-NIL hybrids. The results demonstrate that the exploration of the potential heterosis underlying the FT genes can coordinate early flowering (maturation) and high yield in rapeseed (B. napus L.), providing an effective strategy for early flowering breeding in crops.
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Affiliation(s)
- Caochuang Fang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Zhaoyang Wang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Pengfei Wang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Yixian Song
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Ali Ahmad
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Faming Dong
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Dengfeng Hong
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
| | - Guangsheng Yang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
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Zheng Y, Gao Z, Luo L, Wang Y, Chen Q, Yang Y, Kong X, Yang Y. Divergence of the genetic contribution of FRIGIDA homologues in regulating the flowering time in Brassica rapa ssp. rapa. Gene 2021; 796-797:145790. [PMID: 34175395 DOI: 10.1016/j.gene.2021.145790] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Revised: 06/04/2021] [Accepted: 06/22/2021] [Indexed: 10/21/2022]
Affiliation(s)
- Yan Zheng
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; Plant Germplasm and Genomics Center, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zean Gao
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; Plant Germplasm and Genomics Center, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Landi Luo
- School of Ecology and Environmental Science, Yunnan University, Kunming 650504, China
| | - Yonggang Wang
- Agricultural Technology Extension Center of Zhaoyang District, Zhaotong 657000, China
| | - Qian Chen
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; Plant Germplasm and Genomics Center, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
| | - Ya Yang
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; Plant Germplasm and Genomics Center, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
| | - Xiangxiang Kong
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; Plant Germplasm and Genomics Center, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China.
| | - Yongping Yang
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; Plant Germplasm and Genomics Center, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China.
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Han X, Xu ZR, Zhou L, Han CY, Zhang YM. Identification of QTNs and their candidate genes for flowering time and plant height in soybean using multi-locus genome-wide association studies. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2021; 41:39. [PMID: 37309439 PMCID: PMC10236079 DOI: 10.1007/s11032-021-01230-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Accepted: 05/06/2021] [Indexed: 06/14/2023]
Abstract
Flowering time (FT) and plant height (PH) are important agronomic traits in soybean. However, their genetic foundations are not fully understood. Thus, in this study, a total of 106,013 single nucleotide polymorphisms in 286 soybean accessions were used to associate with the first and full FT (FT1 and FT2) and PH in 4 environments and their BLUP values using 6 multi-locus genome-wide association study methods. As a result, 38, 43, and 27 stable quantitative trait nucleotides (QTNs) were identified, respectively, for FT1, FT2, and PH across at least 3 methods and/or environments. Among these QTNs for FT1, FT2, and PH, 31, 36, and 21 were found to have significant phenotype differences across 2 alleles; 22, 18, and 13 were consistent with the corresponding loci in previous studies; 13 and 8 genes, with more than average expression level, around 64 FT and 27 PH QTNs were predicted as their corresponding candidate genes. Among these candidate genes, GmPRR3b, and GmGIa for FT, and GmTFL1b for PH were known, while some were new, e.g., GmPHYA4, GmVRN5, GmFPA, and GmSPA1 for FT, and Glyma.02g300200, GmFPA, and Glyma.13g339800 for PH. All the validated QTNs were used to design the best cross-combinations in 2 FT directions. In each FT direction, the best 5 cross-combinations were predicted, such as Heihe 54 × Qincha 1 for early FT, and Yingdejiadou × Wuhuabayuehuang for late FT. This study provides solid foundations for genetic basis, molecular biology, and breeding by design of soybean FT and PH. Supplementary Information The online version contains supplementary material available at 10.1007/s11032-021-01230-3.
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Affiliation(s)
- Xu Han
- Crop Information Center, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070 China
| | - Zhuo-Ran Xu
- Crop Information Center, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070 China
| | - Ling Zhou
- Institute of Crop Germplasm and Biotechnology, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014 China
| | - Chun-Yu Han
- Crop Information Center, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070 China
| | - Yuan-Ming Zhang
- Crop Information Center, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070 China
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