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Baguma JK, Mukasa SB, Nuwamanya E, Alicai T, Omongo CA, Ochwo-Ssemakula M, Ozimati A, Esuma W, Kanaabi M, Wembabazi E, Baguma Y, Kawuki RS. Identification of Genomic Regions for Traits Associated with Flowering in Cassava ( Manihot esculenta Crantz). PLANTS (BASEL, SWITZERLAND) 2024; 13:796. [PMID: 38592820 PMCID: PMC10974989 DOI: 10.3390/plants13060796] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 01/25/2024] [Accepted: 01/26/2024] [Indexed: 04/11/2024]
Abstract
Flowering in cassava (Manihot esculenta Crantz) is crucial for the generation of botanical seed for breeding. However, genotypes preferred by most farmers are erect and poor at flowering or never flower. To elucidate the genetic basis of flowering, 293 diverse cassava accessions were evaluated for flowering-associated traits at two locations and seasons in Uganda. Genotyping using the Diversity Array Technology Pty Ltd. (DArTseq) platform identified 24,040 single-nucleotide polymorphisms (SNPs) distributed on the 18 cassava chromosomes. Population structure analysis using principal components (PCs) and kinships showed three clusters; the first five PCs accounted for 49.2% of the observed genetic variation. Linkage disequilibrium (LD) estimation averaged 0.32 at a distance of ~2850 kb (kilo base pairs). Polymorphism information content (PIC) and minor allele frequency (MAF) were 0.25 and 0.23, respectively. A genome-wide association study (GWAS) analysis uncovered 53 significant marker-trait associations (MTAs) with flowering-associated traits involving 27 loci. Two loci, SNPs S5_29309724 and S15_11747301, were associated with all the traits. Using five of the 27 SNPs with a Phenotype_Variance_Explained (PVE) ≥ 5%, 44 candidate genes were identified in the peak SNP sites located within 50 kb upstream or downstream, with most associated with branching traits. Eight of the genes, orthologous to Arabidopsis and other plant species, had known functional annotations related to flowering, e.g., eukaryotic translation initiation factor and myb family transcription factor. This study identified genomic regions associated with flowering-associated traits in cassava, and the identified SNPs can be useful in marker-assisted selection to overcome hybridization challenges, like unsynchronized flowering, and candidate gene validation.
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Affiliation(s)
- Julius K. Baguma
- School of Agricultural Sciences, Makerere University, Kampala P.O. Box 7062, Uganda; (S.B.M.); (E.N.); (M.O.-S.)
- National Crops Resources Research Institute, Namulonge (NaCRRI), Kampala P.O. Box 7084, Uganda; (T.A.); (C.A.O.); (A.O.); (W.E.); (M.K.); (E.W.); (R.S.K.)
| | - Settumba B. Mukasa
- School of Agricultural Sciences, Makerere University, Kampala P.O. Box 7062, Uganda; (S.B.M.); (E.N.); (M.O.-S.)
| | - Ephraim Nuwamanya
- School of Agricultural Sciences, Makerere University, Kampala P.O. Box 7062, Uganda; (S.B.M.); (E.N.); (M.O.-S.)
- National Crops Resources Research Institute, Namulonge (NaCRRI), Kampala P.O. Box 7084, Uganda; (T.A.); (C.A.O.); (A.O.); (W.E.); (M.K.); (E.W.); (R.S.K.)
| | - Titus Alicai
- National Crops Resources Research Institute, Namulonge (NaCRRI), Kampala P.O. Box 7084, Uganda; (T.A.); (C.A.O.); (A.O.); (W.E.); (M.K.); (E.W.); (R.S.K.)
| | - Christopher Abu Omongo
- National Crops Resources Research Institute, Namulonge (NaCRRI), Kampala P.O. Box 7084, Uganda; (T.A.); (C.A.O.); (A.O.); (W.E.); (M.K.); (E.W.); (R.S.K.)
- National Agricultural Research Organisation (NARO), Entebbe P.O. Box 295, Uganda;
| | - Mildred Ochwo-Ssemakula
- School of Agricultural Sciences, Makerere University, Kampala P.O. Box 7062, Uganda; (S.B.M.); (E.N.); (M.O.-S.)
| | - Alfred Ozimati
- National Crops Resources Research Institute, Namulonge (NaCRRI), Kampala P.O. Box 7084, Uganda; (T.A.); (C.A.O.); (A.O.); (W.E.); (M.K.); (E.W.); (R.S.K.)
- School of Biological Sciences, Makerere University, Kampala P.O. Box 7062, Uganda
| | - Williams Esuma
- National Crops Resources Research Institute, Namulonge (NaCRRI), Kampala P.O. Box 7084, Uganda; (T.A.); (C.A.O.); (A.O.); (W.E.); (M.K.); (E.W.); (R.S.K.)
- National Agricultural Research Organisation (NARO), Entebbe P.O. Box 295, Uganda;
| | - Michael Kanaabi
- National Crops Resources Research Institute, Namulonge (NaCRRI), Kampala P.O. Box 7084, Uganda; (T.A.); (C.A.O.); (A.O.); (W.E.); (M.K.); (E.W.); (R.S.K.)
| | - Enoch Wembabazi
- National Crops Resources Research Institute, Namulonge (NaCRRI), Kampala P.O. Box 7084, Uganda; (T.A.); (C.A.O.); (A.O.); (W.E.); (M.K.); (E.W.); (R.S.K.)
| | - Yona Baguma
- National Agricultural Research Organisation (NARO), Entebbe P.O. Box 295, Uganda;
| | - Robert S. Kawuki
- National Crops Resources Research Institute, Namulonge (NaCRRI), Kampala P.O. Box 7084, Uganda; (T.A.); (C.A.O.); (A.O.); (W.E.); (M.K.); (E.W.); (R.S.K.)
- National Agricultural Research Organisation (NARO), Entebbe P.O. Box 295, Uganda;
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Zhang Y, Zhang Q, Wang H, Tao S, Cao H, Shi Y, Bakirov A, Xu A, Huang Z. Discovery of common loci and candidate genes for controlling salt-alkali tolerance and yield-related traits in Brassica napus L. PLANT CELL REPORTS 2023; 42:1039-1057. [PMID: 37076701 DOI: 10.1007/s00299-023-03011-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2022] [Accepted: 03/27/2023] [Indexed: 05/03/2023]
Abstract
KEY MESSAGE Common loci and candidate genes for controlling salt-alkali tolerance and yield-related traits were identified in Brassica napus combining QTL mapping with transcriptome under salt and alkaline stresses. The yield of rapeseed (Brassica napus L.) is determined by multiple yield-related traits, which are susceptible to environmental factors. Many yield-related quantitative trait loci (QTLs) have been reported in Brassica napus; however, no studies have been conducted to investigate both salt-alkali tolerance and yield-related traits simultaneously. Here, specific-locus amplified fragment sequencing (SLAF-seq) technologies were utilized to map the QTLs for salt-alkali tolerance and yield-related traits. A total of 65 QTLs were identified, including 30 QTLs for salt-alkali tolerance traits and 35 QTLs for yield-related traits, accounting for 7.61-27.84% of the total phenotypic variations. Among these QTLs, 18 unique QTLs controlling two to four traits were identified by meta-analysis. Six novel and unique QTLs were detected for salt-alkali tolerance traits. By comparing these unique QTLs for salt-alkali tolerance traits with those previously reported QTLs for yield-related traits, seven co-localized chromosomal regions were identified on A09 and A10. Combining QTL mapping with transcriptome of two parents under salt and alkaline stresses, thirteen genes were identified as the candidates controlling both salt-alkali tolerance and yield. These findings provide useful information for future breeding of high-yield cultivars resistant to alkaline and salt stresses.
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Affiliation(s)
- Yan Zhang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Qi Zhang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Han Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Shunxian Tao
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Hanming Cao
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Yiji Shi
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Aldiyar Bakirov
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Aixia Xu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Zhen Huang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, China.
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Revolinski SR, Maughan PJ, Coleman CE, Burke IC. Preadapted to adapt: underpinnings of adaptive plasticity revealed by the downy brome genome. Commun Biol 2023; 6:326. [PMID: 36973344 PMCID: PMC10042881 DOI: 10.1038/s42003-023-04620-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Accepted: 02/21/2023] [Indexed: 03/29/2023] Open
Abstract
Bromus tectorum L. is arguably the most successful invasive weed in the world. It has fundamentally altered arid ecosystems of the western United States, where it now found on an excess of 20 million hectares. Invasion success is related to avoidance of abiotic stress and human management. Early flowering is a heritable trait utilized by B. tectorum, enabling the species to temporally monopolize limited resources and outcompete the native plant community. Thus, understanding the genetic underpinning of flowering time is critical for the design of integrated management strategies. To study flowering time traits in B. tectorum, we assembled a chromosome scale reference genome for B. tectorum. To assess the utility of the assembled genome, 121 diverse B. tectorum accessions are phenotyped and subjected to a genome wide association study (GWAS). Candidate genes, representing homologs of genes that have been previously associated with plant height or flowering phenology traits in related species are located near QTLs we identified. This study uses a high-resolution GWAS to identify reproductive phenology genes in a weedy species and represents a considerable step forward in understanding the mechanisms underlying genetic plasticity in one of the most successful invasive weed species.
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Affiliation(s)
- Samuel R Revolinski
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA, USA
| | - Peter J Maughan
- Department of Plant & Wildlife Science, Brigham Young University, Provo, UT, USA
| | - Craig E Coleman
- Department of Plant & Wildlife Science, Brigham Young University, Provo, UT, USA
| | - Ian C Burke
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA, USA.
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Xu Y, Kong X, Guo Y, Wang R, Yao X, Chen X, Yan T, Wu D, Lu Y, Dong J, Zhu Y, Chen M, Cen H, Jiang L. Structural variations and environmental specificities of flowering time-related genes in Brassica napus. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:42. [PMID: 36897406 DOI: 10.1007/s00122-023-04326-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Accepted: 02/16/2023] [Indexed: 06/18/2023]
Abstract
We found that the flowering time order of accessions in a genetic population considerably varied across environments, and homolog copies of essential flowering time genes played different roles in different locations. Flowering time plays a critical role in determining the life cycle length, yield, and quality of a crop. However, the allelic polymorphism of flowering time-related genes (FTRGs) in Brassica napus, an important oil crop, remains unclear. Here, we provide high-resolution graphics of FTRGs in B. napus on a pangenome-wide scale based on single nucleotide polymorphism (SNP) and structural variation (SV) analyses. A total of 1337 FTRGs in B. napus were identified by aligning their coding sequences with Arabidopsis orthologs. Overall, 46.07% of FTRGs were core genes and 53.93% were variable genes. Moreover, 1.94%, 0.74%, and 4.49% FTRGs had significant presence-frequency differences (PFDs) between the spring and semi-winter, spring and winter, and winter and semi-winter ecotypes, respectively. SNPs and SVs across 1626 accessions of 39 FTRGs underlying numerous published qualitative trait loci were analyzed. Additionally, to identify FTRGs specific to an eco-condition, genome-wide association studies (GWASs) based on SNP, presence/absence variation (PAV), and SV were performed after growing and observing the flowering time order (FTO) of plants in a collection of 292 accessions at three locations in two successive years. It was discovered that the FTO of plants in a genetic population changed a lot across various environments, and homolog copies of some key FTRGs played different roles in different locations. This study revealed the molecular basis of the genotype-by-environment (G × E) effect on flowering and recommended a pool of candidate genes specific to locations for breeding selection.
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Affiliation(s)
- Ying Xu
- Institute of Crop Science, Zhejiang University, Hangzhou, 310058, China
| | - Xiangdong Kong
- Jiguang Gene Biotechnology Co., Ltd., Nanjing, 210000, China
| | - Yuan Guo
- College of Agronomy, Northwest A&F University, Yangling, 712100, China
| | - Ruisen Wang
- Jiaxing Academy of Agricultural Sciences, Jiaxing, 31400, China
| | - Xiangtan Yao
- Jiaxing Academy of Agricultural Sciences, Jiaxing, 31400, China
| | - Xiaoyang Chen
- Jinhua Academy of Agricultural Sciences, Jinhua, 321017, China
| | - Tao Yan
- College of Agronomy, Hunan Agricultural University, Changsha, 410128, China
| | - Dezhi Wu
- College of Agronomy, Hunan Agricultural University, Changsha, 410128, China
| | - Yunhai Lu
- Institute of Crop Science, Zhejiang University, Hangzhou, 310058, China
| | - Jie Dong
- Institute of Crop Science, Zhejiang University, Hangzhou, 310058, China
| | - Yang Zhu
- Institute of Crop Science, Zhejiang University, Hangzhou, 310058, China
| | - Mingxun Chen
- College of Agronomy, Northwest A&F University, Yangling, 712100, China
| | - Haiyan Cen
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou, 310058, China
| | - Lixi Jiang
- Institute of Crop Science, Zhejiang University, Hangzhou, 310058, China.
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Chen L, Lei W, He W, Wang Y, Tian J, Gong J, Hao B, Cheng X, Shu Y, Fan Z. Mapping of Two Major QTLs Controlling Flowering Time in Brassica napus Using a High-Density Genetic Map. PLANTS (BASEL, SWITZERLAND) 2022; 11:plants11192635. [PMID: 36235500 PMCID: PMC9571212 DOI: 10.3390/plants11192635] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 10/01/2022] [Accepted: 10/05/2022] [Indexed: 05/31/2023]
Abstract
Research on the flowering habit of rapeseed is important for the selection of varieties adapted to specific ecological environments. Here, quantitative trait loci (QTL) for the days-to-flowering trait were identified using a doubled haploid population of 178 lines derived from a cross between the winter type SGDH284 and the semi-winter type 158A. A linkage map encompassing 3268.01 cM was constructed using 2777 bin markers obtained from next-generation sequencing. The preliminary mapping results revealed 56 QTLs for the days to flowering in the six replicates in the three environments. Twelve consensus QTLs were identified by a QTL meta-analysis, two of which (cqDTF-C02 and cqDTF-C06) were designated as major QTLs. Based on the micro-collinearity of the target regions between B. napus and Arabidopsis, four genes possibly related to flowering time were identified in the cqDTF-C02 interval, and only one gene possibly related to flowering time was identified in the cqDTF-C06 interval. A tightly linked insertion-deletion marker for the cqFT-C02 locus was developed. These findings will aid the breeding of early maturing B. napus varieties.
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Affiliation(s)
- Lei Chen
- College of Agriculture, Anhui Science and Technology University, Fengyang 233100, China
| | - Weixia Lei
- Crop Institute, Anhui Academy of Agricultural Sciences, Hefei 230031, China
| | - Wangfei He
- College of Agriculture, Anhui Science and Technology University, Fengyang 233100, China
| | - Yifan Wang
- College of Agriculture, Anhui Science and Technology University, Fengyang 233100, China
| | - Jie Tian
- College of Agriculture, Anhui Science and Technology University, Fengyang 233100, China
| | - Jihui Gong
- College of Agriculture, Anhui Science and Technology University, Fengyang 233100, China
| | - Bing Hao
- Bengbu Ludu Crop Residue Biotechnology Co., Ltd., Bengbu 233000, China
| | - Xinxin Cheng
- College of Agriculture, Anhui Science and Technology University, Fengyang 233100, China
| | - Yingjie Shu
- College of Agriculture, Anhui Science and Technology University, Fengyang 233100, China
| | - Zhixiong Fan
- Crop Institute, Anhui Academy of Agricultural Sciences, Hefei 230031, China
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Huang X, Wu W, Su L, Lv H, Cheng Z, Yang W, Nong L, Liu T, Chen Y, Wang P, Liu Z. Development and Application of InDel Markers Linked to Fruit-Shape and Peel-Colour Genes in Wax Gourd. Genes (Basel) 2022; 13:genes13091567. [PMID: 36140735 PMCID: PMC9498789 DOI: 10.3390/genes13091567] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Revised: 08/22/2022] [Accepted: 08/29/2022] [Indexed: 12/03/2022] Open
Abstract
The wax gourd is commonly grown in many countries because of its high nutritional and economic value. While the genes for the fruit shape and peel colour of wax gourd have been reported, the InDel markers linked to these genes remain undeveloped. In this study, the InDel markers linked to fruit-shape (Bch02G016830) and peel-colour (Bch05G003950) genes were developed from resequenced data. We used 120 inbred lines, 536 isolated populations, and 4 commercial hybrids to evaluate the validity and application value of the InDel markers. The accuracy rates of nine pairs of fruit-shape InDel markers (GX1-GX9) were 84.16–91.66% in 120 inbred lines. The accuracy rates of 27 pairs of peel-colour InDel markers (PS1-PS27) within approximately 3.0 Mb upstream and 3.0 Mb downstream of the peel-colour gene were 100% and those of 6 pairs of peel-colour InDel markers (PS28-PS33) within 3.0–20 Mb upstream and downstream of the peel-colour gene were 55.83–90% in 120 inbred lines. The purity of four commercial hybrids determined using GX1, GX2, PS13, and PS14 was highly consistent with the field results for purity determination. Our results provide important information for genetic linkage map construction, molecular-marker-assisted selective breeding, and purity determination of wax gourd hybrids.
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Affiliation(s)
- Xiaochun Huang
- College of Agricultural, Guangxi University, Nanning 530004, China
| | - Wenting Wu
- College of Agricultural, Guangxi University, Nanning 530004, China
| | - Liwen Su
- College of Agricultural, Guangxi University, Nanning 530004, China
| | - Haixuan Lv
- College of Agricultural, Guangxi University, Nanning 530004, China
| | - Zhikui Cheng
- College of Agricultural, Guangxi University, Nanning 530004, China
| | - Wenrui Yang
- College of Agricultural, Guangxi University, Nanning 530004, China
| | - Lifeng Nong
- College of Agricultural, Guangxi University, Nanning 530004, China
| | - Ting Liu
- College of Agricultural, Guangxi University, Nanning 530004, China
| | - Yong Chen
- Institute for New Rural Development, Guangxi University, Nanning 530004, China
| | - Peng Wang
- Institute of Vegetable Research, Guangxi Academy of Agricultural Sciences, Nanning 530004, China
| | - Zhengguo Liu
- College of Agricultural, Guangxi University, Nanning 530004, China
- Correspondence:
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Liu Z, Dong X, Zheng G, Xu C, Wei J, Cui J, Cao X, Li H, Fang X, Wang Y, Tian H. Integrate QTL Mapping and Transcription Profiles Reveal Candidate Genes Regulating Flowering Time in Brassica napus. FRONTIERS IN PLANT SCIENCE 2022; 13:904198. [PMID: 35837459 PMCID: PMC9274139 DOI: 10.3389/fpls.2022.904198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Accepted: 05/12/2022] [Indexed: 06/15/2023]
Abstract
Flowering at the proper time is an important part of acclimation to the ambient environment and season and maximizes the plant yield. To reveal the genetic architecture and molecular regulation of flowering time in oilseed rape (Brassica napus), we performed an RNA-seq analysis of the two parents after vernalization at low temperature and combined this with quantitative trait loci (QTL) mapping in an F2 population. A genetic linkage map that included 1,017 markers merged into 268 bins and covered 793.53 cM was constructed. Two QTLs associated with flowering time were detected in the F2 population. qFTA06 was the major QTL in the 7.06 Mb interval on chromosome A06 and accounted for 19.3% of the phenotypic variation. qFTC08 was located on chromosome C06 and accounted for 8.6% of the phenotypic variation. RNA-seq analysis revealed 4,626 differentially expressed genes (DEGs) between two parents during vernalization. Integration between QTL mapping and RNA-seq analysis revealed six candidate genes involved in the regulation of flowering time through the circadian clock/photoperiod, auxin and ABA hormone signal, and cold signal transduction and vernalization pathways. These results provide insights into the molecular genetic architecture of flowering time in B. napus.
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Meng Q, Liu Z, Feng C, Zhang H, Xu Z, Wang X, Wu J, She H, Qian W. Quantitative Trait Locus Mapping and Identification of Candidate Genes Controlling Bolting in Spinach ( Spinacia oleracea L.). FRONTIERS IN PLANT SCIENCE 2022; 13:850810. [PMID: 35432424 PMCID: PMC9006512 DOI: 10.3389/fpls.2022.850810] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 02/28/2022] [Indexed: 06/14/2023]
Abstract
Spinach is a typical light-sensitive plant. Long days can induce early bolting, thereby influencing the regional adaptation, quality, and vegetative yield of spinach. However, the genes and genetic mechanisms underlying this trait in spinach remain unclear. In this study, a major quantitative trait locus (QTL) qBT1.1, was mapped on chromosome 1 using a BC1 population (BC1a) derived from 12S3 (late-bolting recurrent lines) and 12S4 (early bolting lines) with specific-locus amplified fragment (SLAF) markers and Kompetitive Allele Specific PCR (KASP) markers. The qBT1.1 locus was further confirmed and narrowed down to 0.56 Mb by using a large BC1 (BC1b) population and an F2 population using the above KASP markers and the other 20 KASP markers. Within this region, two putative genes, namely, SpFLC and SpCOL14, were of interest due to their relationship with flower regulatory pathways. For SpCOL14, we found multiple variations in the promoter, and the expression pattern was consistent with bolting stages. SpCOL14 was therefore assumed to the best candidate gene for bolting. Overall, our results provide a basis for understanding the molecular mechanisms of bolting in spinach and contribute to the breeding of diverse spinach germplasms for adaptation to different regions.
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Affiliation(s)
- Qing Meng
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Zhiyuan Liu
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Chunda Feng
- Ilera Healthcare LLC, Waterfall, PA, United States
| | - Helong Zhang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Zhaosheng Xu
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xiaowu Wang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jian Wu
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Hongbing She
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Wei Qian
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
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Zhao X, Yu K, Pang C, Wu X, Shi R, Sun C, Zhang W, Chen F, Zhang J, Wang X. QTL Analysis of Five Silique-Related Traits in Brassica napus L. Across Multiple Environments. FRONTIERS IN PLANT SCIENCE 2021; 12:766271. [PMID: 34887891 PMCID: PMC8650614 DOI: 10.3389/fpls.2021.766271] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2021] [Accepted: 10/06/2021] [Indexed: 06/12/2023]
Abstract
As an important physiological and reproductive organ, the silique is a determining factor of seed yield and a breeding target trait in rapeseed (Brassica napus L.). Genetic studies of silique-related traits are helpful for rapeseed marker-assisted high-yield breeding. In this study, a recombinant inbred population containing 189 lines was used to perform a quantitative trait loci (QTLs) analysis for five silique-related traits in seven different environments. As a result, 120 consensus QTLs related to five silique-related traits were identified, including 23 for silique length, 25 for silique breadth, 29 for silique thickness, 22 for seed number per silique and 21 for silique volume, which covered all the chromosomes, except C5. Among them, 13 consensus QTLs, one, five, two, four and one for silique length, silique breadth, silique thickness, seed number per silique and silique volume, respectively, were repeatedly detected in multiple environments and explained 4.38-13.0% of the phenotypic variation. On the basis of the functional annotations of Arabidopsis homologous genes and previously reported silique-related genes, 12 potential candidate genes underlying these 13 QTLs were screened and found to be stable in multiple environments by analyzing the re-sequencing results of the two parental lines. These findings provide new insights into the gene networks affecting silique-related traits at the QTL level in rapeseed.
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Affiliation(s)
- Xiaozhen Zhao
- Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Cotton and Rapeseed, Ministry of Agriculture and Rural Affairs, Nanjing, China
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
| | - Kunjiang Yu
- College of Agriculture, Guizhou University, Guiyang, China
| | - Chengke Pang
- Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Cotton and Rapeseed, Ministry of Agriculture and Rural Affairs, Nanjing, China
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
| | - Xu Wu
- Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Cotton and Rapeseed, Ministry of Agriculture and Rural Affairs, Nanjing, China
| | - Rui Shi
- Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Cotton and Rapeseed, Ministry of Agriculture and Rural Affairs, Nanjing, China
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
| | - Chengming Sun
- Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Cotton and Rapeseed, Ministry of Agriculture and Rural Affairs, Nanjing, China
| | - Wei Zhang
- Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Cotton and Rapeseed, Ministry of Agriculture and Rural Affairs, Nanjing, China
| | - Feng Chen
- Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Cotton and Rapeseed, Ministry of Agriculture and Rural Affairs, Nanjing, China
| | - Jiefu Zhang
- Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Cotton and Rapeseed, Ministry of Agriculture and Rural Affairs, Nanjing, China
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
| | - Xiaodong Wang
- Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Cotton and Rapeseed, Ministry of Agriculture and Rural Affairs, Nanjing, China
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Helal MMU, Gill RA, Tang M, Yang L, Hu M, Yang L, Xie M, Zhao C, Cheng X, Zhang Y, Zhang X, Liu S. SNP- and Haplotype-Based GWAS of Flowering-Related Traits in Brassica napus. PLANTS (BASEL, SWITZERLAND) 2021; 10:plants10112475. [PMID: 34834840 PMCID: PMC8619824 DOI: 10.3390/plants10112475] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2021] [Revised: 11/09/2021] [Accepted: 11/09/2021] [Indexed: 05/05/2023]
Abstract
Traits related to flowering time are the most promising agronomic traits that directly impact the seed yield and oil quality of rapeseed (Brassica napus L.). Developing early flowering and maturity rapeseed varieties is an important breeding objective in B. napus. Many studies have reported on days to flowering, but few have reported on budding, bolting, and the interval between bolting and DTF. Therefore, elucidating the genetic architecture of QTLs and genes regulating flowering time, we presented an integrated investigation on SNP and haplotype-based genome-wide association study of 373 diverse B. napus germplasm, which were genotyped by the 60K SNP array and were phenotyped in the four environments. The results showed that a total of 15 and 37 QTLs were detected from SNP and haplotype-based GWAS, respectively. Among them, seven QTL clusters were identified by haplotype-based GWAS. Moreover, three and eight environmentally stable QTLs were detected by SNP-GWAS and haplotype-based GWAS, respectively. By integrating the above two approaches and by co-localizing the four traits, ten (10) genomic regions were under selection on chromosomes A03, A07, A08, A10, C06, C07, and C08. Interestingly, the genomic regions FT.A07.1, FT.A08, FT.C06, and FT.C07 were identified as novel. In these ten regions, a total of 197 genes controlling FT were detected, of which 14 highly expressed DEGs were orthologous to 13 Arabidopsis thaliana genes after integration with transcriptome results. In a nutshell, the above results uncovered the genetic architecture of important agronomic traits related to flowering time and provided a basis for multiple molecular marker-trait associations in B. napus.
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Affiliation(s)
- MMU Helal
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Wuhan 430062, China; (M.M.U.H.); (R.A.G.); (M.T.); (L.Y.); (M.H.); (L.Y.); (M.X.); (C.Z.); (X.C.); (S.L.)
| | - Rafaqat Ali Gill
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Wuhan 430062, China; (M.M.U.H.); (R.A.G.); (M.T.); (L.Y.); (M.H.); (L.Y.); (M.X.); (C.Z.); (X.C.); (S.L.)
| | - Minqiang Tang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Wuhan 430062, China; (M.M.U.H.); (R.A.G.); (M.T.); (L.Y.); (M.H.); (L.Y.); (M.X.); (C.Z.); (X.C.); (S.L.)
- Key Laboratory of Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants (Ministry of Education), College of Forestry, Hainan University, Haikou 570228, China
| | - Li Yang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Wuhan 430062, China; (M.M.U.H.); (R.A.G.); (M.T.); (L.Y.); (M.H.); (L.Y.); (M.X.); (C.Z.); (X.C.); (S.L.)
| | - Ming Hu
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Wuhan 430062, China; (M.M.U.H.); (R.A.G.); (M.T.); (L.Y.); (M.H.); (L.Y.); (M.X.); (C.Z.); (X.C.); (S.L.)
| | - Lingli Yang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Wuhan 430062, China; (M.M.U.H.); (R.A.G.); (M.T.); (L.Y.); (M.H.); (L.Y.); (M.X.); (C.Z.); (X.C.); (S.L.)
| | - Meili Xie
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Wuhan 430062, China; (M.M.U.H.); (R.A.G.); (M.T.); (L.Y.); (M.H.); (L.Y.); (M.X.); (C.Z.); (X.C.); (S.L.)
| | - Chuanji Zhao
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Wuhan 430062, China; (M.M.U.H.); (R.A.G.); (M.T.); (L.Y.); (M.H.); (L.Y.); (M.X.); (C.Z.); (X.C.); (S.L.)
| | - Xiaohui Cheng
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Wuhan 430062, China; (M.M.U.H.); (R.A.G.); (M.T.); (L.Y.); (M.H.); (L.Y.); (M.X.); (C.Z.); (X.C.); (S.L.)
| | - Yuanyuan Zhang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Wuhan 430062, China; (M.M.U.H.); (R.A.G.); (M.T.); (L.Y.); (M.H.); (L.Y.); (M.X.); (C.Z.); (X.C.); (S.L.)
- Correspondence: (Y.Z.); (X.Z.)
| | - Xiong Zhang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Wuhan 430062, China; (M.M.U.H.); (R.A.G.); (M.T.); (L.Y.); (M.H.); (L.Y.); (M.X.); (C.Z.); (X.C.); (S.L.)
- Correspondence: (Y.Z.); (X.Z.)
| | - Shengyi Liu
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Wuhan 430062, China; (M.M.U.H.); (R.A.G.); (M.T.); (L.Y.); (M.H.); (L.Y.); (M.X.); (C.Z.); (X.C.); (S.L.)
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11
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Wang H, Yang Y, Zhang Y, Zhao T, Jiang J, Li J, Xu X, Yang H. Transcriptome Analysis of Flower Development and Mining of Genes Related to Flowering Time in Tomato ( Solanum lycopersicum). Int J Mol Sci 2021; 22:ijms22158128. [PMID: 34360893 PMCID: PMC8347202 DOI: 10.3390/ijms22158128] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Revised: 07/25/2021] [Accepted: 07/26/2021] [Indexed: 11/29/2022] Open
Abstract
Flowering is a morphogenetic process in which angiosperms shift from vegetative growth to reproductive growth. Flowering time has a strong influence on fruit growth, which is closely related to productivity. Therefore, research on crop flowering time is particularly important. To better understand the flowering period of the tomato, we performed transcriptome sequencing of early flower buds and flowers during the extension period in the later-flowering “Moneymaker” material and the earlier-flowering “20965” homozygous inbred line, and we analyzed the obtained data. At least 43.92 million clean reads were obtained from 12 datasets, and the similarity with the tomato internal reference genome was 92.86–94.57%. Based on gene expression and background annotations, 49 candidate genes related to flowering time and flower development were initially screened, among which the greatest number belong to the photoperiod pathway. According to the expression pattern of candidate genes, the cause of early flowering of “20965” is predicted. The modes of action of the differentially expressed genes were classified, and the results show that they are closely related to hormone regulation and participated in a variety of life activities in crops. The candidate genes we screened and the analysis of their expression patterns provide a basis for future functional verification, helping to explore the molecular mechanism of tomato flowering time more comprehensively.
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Song J, Li B, Cui Y, Zhuo C, Gu Y, Hu K, Wen J, Yi B, Shen J, Ma C, Fu T, Tu J. QTL Mapping and Diurnal Transcriptome Analysis Identify Candidate Genes Regulating Brassica napus Flowering Time. Int J Mol Sci 2021; 22:ijms22147559. [PMID: 34299178 PMCID: PMC8305928 DOI: 10.3390/ijms22147559] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 07/04/2021] [Accepted: 07/07/2021] [Indexed: 12/16/2022] Open
Abstract
Timely flowering is important for seed formation and maximization of rapeseed (Brassica napus) yield. Here, we performed flowering-time quantitative trait loci (QTL) mapping using a double haploid (DH) population grown in three environments to study the genetic architecture. Brassica 60 K Illumina Infinium™ single nucleotide polymorphism (SNP) array and simple sequence repeat (SSR) markers were used for genotyping of the DH population, and a high-density genetic linkage map was constructed. QTL analysis of flowering time from the three environments revealed five consensus QTLs, including two major QTLs. A major QTL located on chromosome A03 was detected specifically in the semi-winter rapeseed growing region, and the one on chromosome C08 was detected in all environments. Ribonucleic acid sequencing (RNA-seq) was performed on the parents’ leaves at seven time-points in a day to determine differentially expressed genes (DEGs). The biological processes and pathways with significant enrichment of DEGs were obtained. The DEGs in the QTL intervals were analyzed, and four flowering time-related candidate genes were found. These results lay a foundation for the genetic regulation of rapeseed flowering time and create a rapeseed gene expression library for seven time-points in a day.
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Affiliation(s)
- Jurong Song
- National Key Laboratory of Crop Genetic Improvement, Hongshan Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (J.S.); (B.L.); (Y.C.); (C.Z.); (K.H.); (J.W.); (B.Y.); (J.S.); (C.M.); (T.F.)
| | - Bao Li
- National Key Laboratory of Crop Genetic Improvement, Hongshan Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (J.S.); (B.L.); (Y.C.); (C.Z.); (K.H.); (J.W.); (B.Y.); (J.S.); (C.M.); (T.F.)
| | - Yanke Cui
- National Key Laboratory of Crop Genetic Improvement, Hongshan Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (J.S.); (B.L.); (Y.C.); (C.Z.); (K.H.); (J.W.); (B.Y.); (J.S.); (C.M.); (T.F.)
| | - Chenjian Zhuo
- National Key Laboratory of Crop Genetic Improvement, Hongshan Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (J.S.); (B.L.); (Y.C.); (C.Z.); (K.H.); (J.W.); (B.Y.); (J.S.); (C.M.); (T.F.)
| | - Yuanguo Gu
- Institute of Economic Crops, Xinjiang Academy of Agricultural Sciences, Urumqi 830091, China;
| | - Kaining Hu
- National Key Laboratory of Crop Genetic Improvement, Hongshan Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (J.S.); (B.L.); (Y.C.); (C.Z.); (K.H.); (J.W.); (B.Y.); (J.S.); (C.M.); (T.F.)
| | - Jing Wen
- National Key Laboratory of Crop Genetic Improvement, Hongshan Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (J.S.); (B.L.); (Y.C.); (C.Z.); (K.H.); (J.W.); (B.Y.); (J.S.); (C.M.); (T.F.)
| | - Bin Yi
- National Key Laboratory of Crop Genetic Improvement, Hongshan Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (J.S.); (B.L.); (Y.C.); (C.Z.); (K.H.); (J.W.); (B.Y.); (J.S.); (C.M.); (T.F.)
| | - Jinxiong Shen
- National Key Laboratory of Crop Genetic Improvement, Hongshan Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (J.S.); (B.L.); (Y.C.); (C.Z.); (K.H.); (J.W.); (B.Y.); (J.S.); (C.M.); (T.F.)
| | - Chaozhi Ma
- National Key Laboratory of Crop Genetic Improvement, Hongshan Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (J.S.); (B.L.); (Y.C.); (C.Z.); (K.H.); (J.W.); (B.Y.); (J.S.); (C.M.); (T.F.)
| | - Tingdong Fu
- National Key Laboratory of Crop Genetic Improvement, Hongshan Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (J.S.); (B.L.); (Y.C.); (C.Z.); (K.H.); (J.W.); (B.Y.); (J.S.); (C.M.); (T.F.)
| | - Jinxing Tu
- National Key Laboratory of Crop Genetic Improvement, Hongshan Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (J.S.); (B.L.); (Y.C.); (C.Z.); (K.H.); (J.W.); (B.Y.); (J.S.); (C.M.); (T.F.)
- Correspondence:
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13
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Hong S, Lim YP, Kwon SY, Shin AY, Kim YM. Genome-Wide Comparative Analysis of Flowering-Time Genes; Insights on the Gene Family Expansion and Evolutionary Perspective. FRONTIERS IN PLANT SCIENCE 2021; 12:702243. [PMID: 34290729 PMCID: PMC8288248 DOI: 10.3389/fpls.2021.702243] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 06/14/2021] [Indexed: 05/03/2023]
Abstract
In polyploids, whole genome duplication (WGD) played a significant role in genome expansion, evolution and diversification. Many gene families are expanded following polyploidization, with the duplicated genes functionally diversified by neofunctionalization or subfunctionalization. These mechanisms may support adaptation and have likely contributed plant survival during evolution. Flowering time is an important trait in plants, which affects critical features, such as crop yields. The flowering-time gene family is one of the largest expanded gene families in plants, with its members playing various roles in plant development. Here, we performed genome-wide identification and comparative analysis of flowering-time genes in three palnt families i.e., Malvaceae, Brassicaceae, and Solanaceae, which indicate these genes were expanded following the event/s of polyploidization. Duplicated genes have been retained during evolution, although genome reorganization occurred in their flanking regions. Further investigation of sequence conservation and similarity network analyses provide evidence for functional diversification of duplicated genes during evolution. These functionally diversified genes play important roles in plant development and provide advantages to plants for adaptation and survival in response to environmental changes encountered during evolution. Collectively, we show that flowering-time genes were expanded following polyploidization and retained as large gene family by providing advantages from functional diversification during evolution.
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Affiliation(s)
- Seongmin Hong
- Genome Editing Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, South Korea
- Molecular Genetics and Genomics Laboratory, Department of Horticulture, College of Agriculture and Life Sciences, Chungnam National University, Daejeon, South Korea
| | - Yong Pyo Lim
- Molecular Genetics and Genomics Laboratory, Department of Horticulture, College of Agriculture and Life Sciences, Chungnam National University, Daejeon, South Korea
| | - Suk-Yoon Kwon
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, South Korea
| | - Ah-Young Shin
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, South Korea
| | - Yong-Min Kim
- Genome Editing Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, South Korea
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