23 results on '"Zhan, Jiepeng"'
Search Results
2. A systematic dissection in oilseed rape provides insights into the genetic architecture and molecular mechanism of yield heterosis
- Author
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Ye, Jiang, primary, Liang, Huabing, additional, Zhao, Xueyang, additional, Li, Na, additional, Song, Dongji, additional, Zhan, Jiepeng, additional, Wang, Xinfa, additional, Tu, Jinxing, additional, Varshney, Rajeev Kumar, additional, Shi, Jiaqin, additional, and Wang, Hanzhong, additional
- Published
- 2023
- Full Text
- View/download PDF
3. Key genes and mechanisms underlying natural variation of silique length in oilseed rape (Brassica napus L.) germplasm
- Author
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Quaid Hussain, Xinfa Wang, Guihua Liu, Hanzhong Wang, Zhan Jiepeng, Huabing Liang, and Jiaqin Shi
- Subjects
chemistry.chemical_classification ,Genetics ,Germplasm ,Candidate gene ,Locus (genetics) ,Plant Science ,Biology ,Transcriptome ,chemistry ,Auxin ,Hormone metabolism ,Silique ,Agronomy and Crop Science ,Gene - Abstract
Silique length influences seed yield in oilseed rape. It shows extensive variation in germplasm resources, and identifying the underlying genes and regulatory mechanisms would advance breeding for the trait. In the present study, a genome-wide association study (GWAS) using 331 core accessions planted in 10 environments revealed 13 loci associated with silique length on chromosomes A01, A04, A07, A09, and C03, explaining 6.2%–19.2% of phenotypic variance. Physiological analysis showed that silique length variation was attributable to differences in silique growth rate and/or duration before four weeks after flowering, with levels of endogenous phytohormones (auxin, ethylene, and GA24, GA12, and GA44) playing an important role. Cytological analysis showed that silique length variation was due mainly to differences in cell number followed by cell size. Transcriptomic analysis of two pools of silique walls with opposite length extremes revealed 3248 differentially expressed genes (DEGs). These DEGs were enriched in several pathways (such as cell wall, cell division, and hormone metabolism) associated with cell proliferation and expansion and silique development. Integrating GWAS, RNA-seq, and functional annotation results revealed 15 candidate genes for the major associated locus qSL.A09-3. Of these, BnaA9.ARF18 and BnaA9.CYP78A9 were validated by haplotype analysis followed by candidate gene association. Sequence variation in the coding region of BnaA9.ARF18 and expression of BnaA9.CYP78A9 in silique walls were strongly associated with silique length. Our results provide an explanation for the natural variation of silique length in oilseed rape germplasm and offer useful information for its improvement.
- Published
- 2022
4. Key genes and mechanisms underlying natural variation of silique length in oilseed rape (Brassica napus L.) germplasm
- Author
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Hussain, Quaid, primary, Zhan, Jiepeng, additional, Liang, Huabing, additional, Wang, Xinfa, additional, Liu, Guihua, additional, Shi, Jiaqin, additional, and Wang, Hanzhong, additional
- Published
- 2022
- Full Text
- View/download PDF
5. Genome-wide analysis of the JAZ subfamily and functional verification of BnC8.JAZ1-1 in Brassica napus
- Author
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Wang, Ying, primary, Li, Na, additional, Zhan, Jiepeng, additional, Wang, Xinfa, additional, Shi, Jiaqin, additional, and Wang, Hanzhong, additional
- Published
- 2022
- Full Text
- View/download PDF
6. A systematic dissection of the mechanisms underlying the natural variation of silique number in rapeseed ( Brassica napus L.) germplasm
- Author
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Xiaoxiao Zheng, Jiaqin Shi, Zhu Yaoyao, Zhan Jiepeng, Guihua Liu, Li Shuyu, Rajeev K. Varshney, Xinfa Wang, and Hanzhong Wang
- Subjects
0106 biological sciences ,0301 basic medicine ,Germplasm ,Candidate gene ,leaf area ,Rapeseed ,Vegetative reproduction ,Brassica ,Brassica napus L ,Plant Science ,Biology ,Genes, Plant ,01 natural sciences ,03 medical and health sciences ,Botany ,GWAS ,Research Articles ,photosynthesis ,Bud ,Gene Expression Profiling ,Brassica napus ,fungi ,food and beverages ,Meristem ,biology.organism_classification ,030104 developmental biology ,RNA‐seq ,Silique ,silique number ,Agronomy and Crop Science ,Genome-Wide Association Study ,Research Article ,010606 plant biology & botany ,Biotechnology - Abstract
Summary Silique number is the most important component of yield in rapeseed (Brassica napus L.). To dissect the mechanism underlying the natural variation of silique number in rapeseed germplasm, a series of studies were performed. A panel of 331 core lines was employed to genome‐wide association study (GWAS), and 27 loci (including 20 novel loci) were identified. The silique number difference between the more‐ and fewer‐silique lines can be attributed to the accumulative differences in flower number and silique setting rate. Each of them accounted for 75.2% and 24.8%, respectively. The silique number was highly associated with the total photosynthesis and biomass. Microscopic analysis showed that the difference between extremely more‐ and fewer‐silique lines normally occurred at the amount of flower bud but not morphology. Transcriptome analysis of shoot apical meristem (SAM) suggested that most of enriched groups were associated with the auxin biosynthesis/metabolism, vegetative growth and nutrition/energy accumulation. By integrating GWAS and RNA‐seq results, six promising candidate genes were identified, and some of them were related to biomass accumulation. In conclusion, the natural variation of silique number is largely affected by the biomass and nutrition accumulation, which essentially reflects the positive regulatory relationship between the source and sink. Our study provides a comprehensive and systematic explanation for natural variation of silique number in rapeseed, which provides a foundation for its improvement.
- Published
- 2019
7. Maternal control of seed weight in rapeseed (Brassica napus L.): the causal link between the size of pod (mother, source) and seed (offspring, sink)
- Author
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Hanzhong Wang, Xinfa Wang, Guihua Liu, Jiaqin Shi, Song Dongji, Wei Peng, Zhan Jiepeng, and Li Na
- Subjects
0106 biological sciences ,0301 basic medicine ,Germplasm ,maternal effect ,Rapeseed ,source ,Genotype ,Quantitative Trait Loci ,Brassica ,Plant Science ,Quantitative trait locus ,01 natural sciences ,Crop ,03 medical and health sciences ,quantitative trait locus ,sink ,Research Articles ,CYP78A9 ,photosynthesis ,biology ,seed weight ,Brassica napus ,Maternal effect ,food and beverages ,biology.organism_classification ,Horticulture ,030104 developmental biology ,Point of delivery ,Phenotype ,Fruit ,Seeds ,RNA‐seq ,Sink (computing) ,Agronomy and Crop Science ,pod length ,010606 plant biology & botany ,Biotechnology ,Research Article - Abstract
Summary Seed size/weight is one of the key traits related to plant domestication and crop improvement. In rapeseed (Brassica napus L.) germplasm, seed weight shows extensive variation, but its regulatory mechanism is poorly understood. To identify the key mechanism of seed weight regulation, a systematic comparative study was performed. Genetic, morphological and cytological evidence showed that seed weight was controlled by maternal genotype, through the regulation of seed size mainly via cell number. The physiological evidence indicated that differences in the pod length might result in differences in pod wall photosynthetic area, carbohydrates and the final seed weight. We also identified two pleiotropic major quantitative trait loci that acted indirectly on seed weight via their effects on pod length. RNA‐seq results showed that genes related to pod development and hormones were significantly differentially expressed in the pod wall; genes related to development, cell division, nutrient reservoir and ribosomal proteins were all up‐regulated in the seeds of the large‐seed pool. Finally, we proposed a potential seed weight regulatory mechanism that is specific to rapeseed and novel in plants. The results demonstrate a causal link between the size of the pod (mother, source) and the seed (offspring, sink) in rapeseed, which provides novel insight into the maternal control of seed weight and will open a new research field in plants.
- Published
- 2018
8. Validation and Characterization of a Seed Number Per Silique Quantitative Trait Locus qSN.A7 in Rapeseed (Brassica napus L.)
- Author
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Zhang Jiangjiang, Zhan Jiepeng, Xinfa Wang, Zhu Yaoyao, Hanzhong Wang, Guihua Liu, Jiaqin Shi, Xiaoxiao Zheng, and Jiang Ye
- Subjects
0106 biological sciences ,0301 basic medicine ,Population ,Ovary (botany) ,Brassica napus L ,Plant Science ,Quantitative trait locus ,Biology ,lcsh:Plant culture ,medicine.disease_cause ,01 natural sciences ,03 medical and health sciences ,quantitative trait locus ,Pollen ,medicine ,lcsh:SB1-1110 ,cytological mechanism ,education ,Ovule ,Original Research ,Genetics ,Molecular breeding ,education.field_of_study ,food and beverages ,seed number per silique ,030104 developmental biology ,fine-mapping ,Backcrossing ,Silique ,010606 plant biology & botany - Abstract
Seed number is a key character/trait tightly related to the plant fitness/evolution and crop domestication/improvement. The seed number per silique (SNPS) shows a huge variation from several to more than 30, however the underlying regulatory mechanisms are poorly known, which has hindered its improvement. To answer this question, several representative lines with extreme SNPS were previously subjected to systematic genetic and cytological analyses. The results showed that the natural variation of seed number per silique is mainly controlled by maternal and embryonic genotype, which are co-determined by ovule number per ovary, fertile ovule ratio, ovule fertilization rate, and fertilized ovule development rate. More importantly, we also mapped two repeatable quantitative trait loci (QTLs) for SNPS using the F2:3 population derived from Zhongshuang11 and No. 73290, of which the major QTL qSN.A6 has been fine-mapped. In the current study, the near-isogenic lines (NILs) of qSN.A7 were successfully developed by the successive backcross of F1 with Zhongshuang11. First, the effect of qSN.A7 was validated by evaluating the SNPS of two types of homozygous NILs from BC3F2 population, which showed a significant difference of 2.23 on average. Then, qSN.A7 was successfully fine-mapped from the original 4.237 to 1.389 Mb, using a BC4F2 segregating population of 2,551 individuals. To further clarify the regulatory mechanism of qSN.A7, the two types of homologous NILs were subjected to genetic and cytological analyses. The results showed that the difference in SNPS between the two homologous NILs was determined by the embryonic genotypic effect. Highly accordant with this, no significant difference was observed in ovule number per ovary, ovule fertility, fertilization rate, and pollen fertility between the two homologous NILs. Therefore, the regulatory mechanism of qSN.A7 is completely different from the cloned qSS.C9 and qSN.A6. These results will advance the understanding of SNPS and facilitate gene cloning and molecular breeding in Brassica napus.
- Published
- 2020
9. Genetic and signalling pathways of dry fruit size: targets for genome editing‐based crop improvement
- Author
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Hussain, Quaid, primary, Shi, Jiaqin, additional, Scheben, Armin, additional, Zhan, Jiepeng, additional, Wang, Xinfa, additional, Liu, Guihua, additional, Yan, Guijun, additional, King, Graham J., additional, Edwards, David, additional, and Wang, Hanzhong, additional
- Published
- 2020
- Full Text
- View/download PDF
10. Validation and Characterization of a Seed Number Per Silique Quantitative Trait Locus qSN.A7 in Rapeseed (Brassica napus L.)
- Author
-
Zhu, Yaoyao, primary, Ye, Jiang, additional, Zhan, Jiepeng, additional, Zheng, Xiaoxiao, additional, Zhang, Jiangjiang, additional, Shi, Jiaqin, additional, Wang, Xinfa, additional, Liu, Guihua, additional, and Wang, Hanzhong, additional
- Published
- 2020
- Full Text
- View/download PDF
11. Key genes and mechanisms underlying natural variation of silique length in oilseed rape (Brassica napusL.) germplasm
- Author
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Hussain, Quaid, Zhan, Jiepeng, Liang, Huabing, Wang, Xinfa, Liu, Guihua, Shi, Jiaqin, and Wang, Hanzhong
- Abstract
Silique length influences seed yield in oilseed rape. It shows extensive variation in germplasm resources, and identifying the underlying genes and regulatory mechanisms would advance breeding for the trait. In the present study, a genome-wide association study (GWAS) using 331 core accessions planted in 10 environments revealed 13 loci associated with silique length on chromosomes A01, A04, A07, A09, and C03, explaining 6.2%–19.2% of phenotypic variance. Physiological analysis showed that silique length variation was attributable to differences in silique growth rate and/or duration before four weeks after flowering, with levels of endogenous phytohormones (auxin, ethylene, and GA24, GA12, and GA44) playing an important role. Cytological analysis showed that silique length variation was due mainly to differences in cell number followed by cell size. Transcriptomic analysis of two pools of silique walls with opposite length extremes revealed 3248 differentially expressed genes (DEGs). These DEGs were enriched in several pathways (such as cell wall, cell division, and hormone metabolism) associated with cell proliferation and expansion and silique development. Integrating GWAS, RNA-seq, and functional annotation results revealed 15 candidate genes for the major associated locus qSL.A09-3. Of these, BnaA9.ARF18and BnaA9.CYP78A9were validated by haplotype analysis followed by candidate gene association. Sequence variation in the coding region of BnaA9.ARF18and expression of BnaA9.CYP78A9in silique walls were strongly associated with silique length. Our results provide an explanation for the natural variation of silique length in oilseed rape germplasm and offer useful information for its improvement.
- Published
- 2022
- Full Text
- View/download PDF
12. A systematic dissection of the mechanisms underlying the natural variation of silique number in rapeseed ( Brassica napus L.) germplasm
- Author
-
Li, Shuyu, primary, Zhu, Yaoyao, additional, Varshney, Rajeev Kumar, additional, Zhan, Jiepeng, additional, Zheng, Xiaoxiao, additional, Shi, Jiaqin, additional, Wang, Xinfa, additional, Liu, Guihua, additional, and Wang, Hanzhong, additional
- Published
- 2019
- Full Text
- View/download PDF
13. Genetic and Cytological Analyses of the Natural Variation of Seed Number per Pod in Rapeseed (Brassica napus L.)
- Author
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Zhan Jiepeng, Hanzhong Wang, Xinfa Wang, Jiaqin Shi, Yuhua Yang, Guihua Liu, and Wang Ying
- Subjects
0106 biological sciences ,0301 basic medicine ,Germplasm ,maternal effect ,ovule number ,Rapeseed ,embryo effect ,Plant Science ,Biology ,lcsh:Plant culture ,01 natural sciences ,03 medical and health sciences ,seed number per pod ,Genetic variation ,Botany ,lcsh:SB1-1110 ,Cultivar ,cytoplasm effect ,Ovule ,Brassica napus ,Maternal effect ,Horticulture ,030104 developmental biology ,Point of delivery ,Ploidy ,010606 plant biology & botany - Abstract
Seed number is one of the key traits related to plant evolution/domestication and crop improvement/breeding. In rapeseed germplasm, the seed number per pod (SNPP) shows a very wide variation from several to nearly 30; however, the underlying causations/mechanisms for this variation are poorly known. In the current study, the genetic and cytological bases for the natural variation of SNPP in rapeseed was firstly and systematically investigated using the representative four high-SNPP and five low-SNPP lines. The results of self- or cross-pollination experiment between the high- and low-SNPP lines showed that the natural variation of SNPP was mainly controlled by maternal effect (mean = 0.79), followed by paternal effect (mean = 0.21). Analysis of the data using diploid seed embryo-cytoplasmic-maternal model further showed that the maternal genotype, embryo, and cytoplasm effects, respectively, explained 47.6, 35.2, and 7.5% of the genetic variance. In addition, the analysis of combining ability showed that for the SNPP of hybrid F1 was mainly determined by the general combining ability of parents (63.0%), followed by special combining ability of parental combination (37.0%). More importantly, the cytological observation showed that the SNPP difference between the high- and low-SNPP lines was attributable to the accumulative differences in its components. Of which, the number of ovules, the proportion of fertile ovules, the proportion of fertile ovules to be fertilized, and the proportion of fertilized ovules to develop into seeds accounted for 30.7, 18.2, 7.1, and 43.9%, respectively. The accordant results of both genetic and cytological analyses provide solid evidences and systematic insights to further understand the mechanisms underlying the natural variation of SNPP, which will facilitate the development of high-yield cultivars in rapeseed.
- Published
- 2017
14. Maternal control of seed weight in rapeseed (Brassica napus L.): the causal link between the size of pod (mother, source) and seed (offspring, sink)
- Author
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Li, Na, primary, Song, Dongji, additional, Peng, Wei, additional, Zhan, Jiepeng, additional, Shi, Jiaqin, additional, Wang, Xinfa, additional, Liu, Guihua, additional, and Wang, Hanzhong, additional
- Published
- 2018
- Full Text
- View/download PDF
15. Genome-Wide Microsatellite Characterization and Marker Development in the Sequenced Brassica Crop Species
- Author
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Zhan Jiepeng, Hanzhong Wang, Wei Hua, Shunmou Huang, Guihua Liu, Shengyi Liu, Jiaqin Shi, Jingyin Yu, and Xinfa Wang
- Subjects
Crops, Agricultural ,Genetic Markers ,Transposable element ,microsatellite ,brassica ,Gene Dosage ,Brassica ,Biology ,Genome ,Species Specificity ,Databases, Genetic ,Brassica rapa ,distribution ,Genetics ,Molecular Biology ,Gene ,database ,marker ,fungi ,food and beverages ,Molecular Sequence Annotation ,General Medicine ,Full Papers ,biology.organism_classification ,Genetic marker ,Microsatellite ,Brassica oleracea ,Corrigendum ,Genome, Plant ,Microsatellite Repeats - Abstract
Although much research has been conducted, the pattern of microsatellite distribution has remained ambiguous, and the development/utilization of microsatellite markers has still been limited/inefficient in Brassica, due to the lack of genome sequences. In view of this, we conducted genome-wide microsatellite characterization and marker development in three recently sequenced Brassica crops: Brassica rapa, Brassica oleracea and Brassica napus. The analysed microsatellite characteristics of these Brassica species were highly similar or almost identical, which suggests that the pattern of microsatellite distribution is likely conservative in Brassica. The genomic distribution of microsatellites was highly non-uniform and positively or negatively correlated with genes or transposable elements, respectively. Of the total of 115 869, 185 662 and 356 522 simple sequence repeat (SSR) markers developed with high frequencies (408.2, 343.8 and 356.2 per Mb or one every 2.45, 2.91 and 2.81 kb, respectively), most represented new SSR markers, the majority had determined physical positions, and a large number were genic or putative single-locus SSR markers. We also constructed a comprehensive database for the newly developed SSR markers, which was integrated with public Brassica SSR markers and annotated genome components. The genome-wide SSR markers developed in this study provide a useful tool to extend the annotated genome resources of sequenced Brassica species to genetic study/breeding in different Brassica species.
- Published
- 2013
16. A systematic dissection of the mechanisms underlying the natural variation of silique number in rapeseed (Brassica napus L.) germplasm.
- Author
-
Li, Shuyu, Zhu, Yaoyao, Varshney, Rajeev Kumar, Zhan, Jiepeng, Zheng, Xiaoxiao, Shi, Jiaqin, Wang, Xinfa, Liu, Guihua, and Wang, Hanzhong
- Subjects
RAPESEED ,BRASSICA ,MICROSCOPY ,MERISTEMS ,RATE setting - Abstract
Summary: Silique number is the most important component of yield in rapeseed (Brassica napus L.). To dissect the mechanism underlying the natural variation of silique number in rapeseed germplasm, a series of studies were performed. A panel of 331 core lines was employed to genome‐wide association study (GWAS), and 27 loci (including 20 novel loci) were identified. The silique number difference between the more‐ and fewer‐silique lines can be attributed to the accumulative differences in flower number and silique setting rate. Each of them accounted for 75.2% and 24.8%, respectively. The silique number was highly associated with the total photosynthesis and biomass. Microscopic analysis showed that the difference between extremely more‐ and fewer‐silique lines normally occurred at the amount of flower bud but not morphology. Transcriptome analysis of shoot apical meristem (SAM) suggested that most of enriched groups were associated with the auxin biosynthesis/metabolism, vegetative growth and nutrition/energy accumulation. By integrating GWAS and RNA‐seq results, six promising candidate genes were identified, and some of them were related to biomass accumulation. In conclusion, the natural variation of silique number is largely affected by the biomass and nutrition accumulation, which essentially reflects the positive regulatory relationship between the source and sink. Our study provides a comprehensive and systematic explanation for natural variation of silique number in rapeseed, which provides a foundation for its improvement. [ABSTRACT FROM AUTHOR]
- Published
- 2020
- Full Text
- View/download PDF
17. Genetic and Cytological Analyses of the Natural Variation of Seed Number per Pod in Rapeseed (Brassica napus L.)
- Author
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Yang, Yuhua, primary, Wang, Ying, additional, Zhan, Jiepeng, additional, Shi, Jiaqin, additional, Wang, Xinfa, additional, Liu, Guihua, additional, and Wang, Hanzhong, additional
- Published
- 2017
- Full Text
- View/download PDF
18. Linkage and regional association analysis reveal two new tightly-linked major-QTLs for pod number and seed number per pod in rapeseed (Brassica napus L.)
- Author
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Ruiyuan Li, Shunmou Huang, Zhan Jiepeng, Yuhua Yang, Hanzhong Wang, Xinfa Wang, Jiang Ye, Jiaqin Shi, and Guihua Liu
- Subjects
Genetics ,Linkage disequilibrium ,Multidisciplinary ,Rapeseed ,Brassica napus ,Brassica rapa ,Quantitative Trait Loci ,Plant genetics ,Chromosome Mapping ,Molecular Sequence Annotation ,Sequence Analysis, DNA ,Biology ,Quantitative trait locus ,Article ,Chromosomes, Plant ,Linkage Disequilibrium ,Phenotype ,Point of delivery ,Pleiotropy ,Seeds ,Genetic Association Studies ,Genome, Plant ,Microsatellite Repeats ,Genetic association - Abstract
To facilitate the pseudochromosomes assembly and gene cloning in rapeseed, we developed a reference genetic population/map (named BnaZNF2) from two sequenced cultivars, Zhongshuang11 and No.73290, those exhibit significant differences in many traits, particularly yield components. The BnaZNF2 genetic map exhibited perfect collinearity with the physical map of B. napus, indicating its high quality. Comparative mapping revealed several genomic rearrangements between B. napus and B. rapa or B. oleracea. A total of eight and 16 QTLs were identified for pod number and seed number per pod, respectively and of which three and five QTLs are identical to previously identified ones, whereas the other five and 11 are novel. Two new major QTL respectively for pod number and seed number per pod, qPN.A06-1 and qSN.A06-1 (R2 = 22.8% and 32.1%), were colocalised with opposite effects and only qPN.A06-1 was confirmed and narrowed by regional association analysis to 180 kb including only 33 annotated genes. Conditional QTL analysis and subsequent NILs test indicated that tight linkage, rather than pleiotropy, was the genetic causation of their colocalisation. Our study demonstrates potential of this reference genetic population/map for precise QTL mapping and as a base for positional gene cloning in rapeseed.
- Published
- 2015
- Full Text
- View/download PDF
19. An integrated analysis of QTL mapping and RNA sequencing provides further insights and promising candidates for pod number variation in rapeseed (Brassica napus L.)
- Author
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Ye, Jiang, primary, Yang, Yuhua, additional, Chen, Bo, additional, Shi, Jiaqin, additional, Luo, Meizhong, additional, Zhan, Jiepeng, additional, Wang, Xinfa, additional, Liu, Guihua, additional, and Wang, Hanzhong, additional
- Published
- 2017
- Full Text
- View/download PDF
20. Maternal control of seed weight in rapeseed (Brassica napus L.): the causal link between the size of pod (mother, source) and seed (offspring, sink).
- Author
-
Li, Na, Song, Dongji, Peng, Wei, Zhan, Jiepeng, Shi, Jiaqin, Wang, Xinfa, Liu, Guihua, and Wang, Hanzhong
- Subjects
SEED pods ,WEIGHT of seeds ,WEIGHT loss - Abstract
Summary: Seed size/weight is one of the key traits related to plant domestication and crop improvement. In rapeseed (Brassica napus L.) germplasm, seed weight shows extensive variation, but its regulatory mechanism is poorly understood. To identify the key mechanism of seed weight regulation, a systematic comparative study was performed. Genetic, morphological and cytological evidence showed that seed weight was controlled by maternal genotype, through the regulation of seed size mainly via cell number. The physiological evidence indicated that differences in the pod length might result in differences in pod wall photosynthetic area, carbohydrates and the final seed weight. We also identified two pleiotropic major quantitative trait loci that acted indirectly on seed weight via their effects on pod length. RNA‐seq results showed that genes related to pod development and hormones were significantly differentially expressed in the pod wall; genes related to development, cell division, nutrient reservoir and ribosomal proteins were all up‐regulated in the seeds of the large‐seed pool. Finally, we proposed a potential seed weight regulatory mechanism that is specific to rapeseed and novel in plants. The results demonstrate a causal link between the size of the pod (mother, source) and the seed (offspring, sink) in rapeseed, which provides novel insight into the maternal control of seed weight and will open a new research field in plants. [ABSTRACT FROM AUTHOR]
- Published
- 2019
- Full Text
- View/download PDF
21. Linkage and regional association analysis reveal two new tightly-linked major-QTLs for pod number and seed number per pod in rapeseed (Brassica napus L.)
- Author
-
Shi, Jiaqin, primary, Zhan, Jiepeng, additional, Yang, Yuhua, additional, Ye, Jiang, additional, Huang, Shunmou, additional, Li, Ruiyuan, additional, Wang, Xinfa, additional, Liu, Guihua, additional, and Wang, Hanzhong, additional
- Published
- 2015
- Full Text
- View/download PDF
22. Genome-Wide Microsatellite Characterization and Marker Development in the Sequenced Brassica Crop Species.
- Author
-
Shi, Jiaqin, Huang, Shunmou, Zhan, Jiepeng, Yu, Jingyin, Wang, Xinfa, Hua, Wei, Liu, Shengyi, Liu, Guihua, and Wang, Hanzhong
- Abstract
Although much research has been conducted, the pattern of microsatellite distribution has remained ambiguous, and the development/utilization of microsatellite markers has still been limited/inefficient in Brassica, due to the lack of genome sequences. In view of this, we conducted genome-wide microsatellite characterization and marker development in three recently sequenced Brassica crops: Brassica rapa, Brassica oleracea and Brassica napus. The analysed microsatellite characteristics of these Brassica species were highly similar or almost identical, which suggests that the pattern of microsatellite distribution is likely conservative in Brassica. The genomic distribution of microsatellites was highly non-uniform and positively or negatively correlated with genes or transposable elements, respectively. Of the total of 115 869, 185 662 and 356 522 simple sequence repeat (SSR) markers developed with high frequencies (408.2, 343.8 and 356.2 per Mb or one every 2.45, 2.91 and 2.81 kb, respectively), most represented new SSR markers, the majority had determined physical positions, and a large number were genic or putative single-locus SSR markers. We also constructed a comprehensive database for the newly developed SSR markers, which was integrated with public Brassica SSR markers and annotated genome components. The genome-wide SSR markers developed in this study provide a useful tool to extend the annotated genome resources of sequenced Brassica species to genetic study/breeding in different Brassica species. [ABSTRACT FROM PUBLISHER]
- Published
- 2014
- Full Text
- View/download PDF
23. An integrated analysis of QTL mapping and RNA sequencing provides further insights and promising candidates for pod number variation in rapeseed (Brassica napus L.)
- Author
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Yuhua Yang, Jiang Ye, Zhan Jiepeng, Xinfa Wang, Guihua Liu, Bo Chen, Jiaqin Shi, Hanzhong Wang, and Meizhong Luo
- Subjects
0301 basic medicine ,QTL mapping ,Candidate gene ,Transcription, Genetic ,In silico ,Population ,Quantitative Trait Loci ,Meristem growth ,Quantitative trait locus ,Biology ,03 medical and health sciences ,Genetic linkage ,Genetics ,DEG ,KEGG ,education ,Gene ,Pod number ,education.field_of_study ,Sequence Analysis, RNA ,Gene Expression Profiling ,Brassica napus ,fungi ,Chromosome Mapping ,food and beverages ,RNA sequencing ,Molecular Sequence Annotation ,030104 developmental biology ,Research Article ,Biotechnology - Abstract
Background As the most important yield component in rapeseed (Brassica napus L.), pod number is determined by a series of successive growth and development processes. Pod number shows extensive variation in rapeseed natural germplasm, which is valuable for genetic improvement. However, the genetic and especially the molecular mechanism for this kind of variation are poorly understood. In this study, we conducted QTL mapping and RNA sequencing, respectively, using the BnaZNRIL population and its two parental cultivars Zhongshuang11 and No.73290 which showed significant difference in pod number, primarily due to the difference in floral organ number. Result A total of eight QTLs for pod number were identified using BnaZNRIL population with a high-density SNP linkage map, each was distributed on seven linkage groups and explained 5.8–11.9% of phenotypic variance. Then, they were integrated with those previously detected in BnaZNF2 population (deriving from same parents) and resulted in 15 consensus-QTLs. Of which, seven QTLs were identical to other studies, whereas the other eight should be novel. RNA sequencing of the shoot apical meristem (SAM) at the formation stage of floral bud primordia identified 9135 genes that were differentially expressed between the two parents. Gene ontology (GO) analysis showed that the top two enriched groups were S-assimilation, providing an essential nutrient for the synthesis of diverse metabolites, and polyamine metabolism, serving as second messengers that play an essential role in flowering genes initiation. KEGG analysis showed that the top three overrepresented pathways were carbohydrate (707 genes), amino acid (390 genes) and lipid metabolisms (322 genes). In silico mapping showed that 647 DEGs were located within the confidence intervals of 15 consensus QTLs. Based on annotations of Arabidopsis homologs corresponding to DEGs, nine genes related to meristem growth and development were considered as promising candidates for six QTLs. Conclusion In this study, we discovered the first repeatable major QTL for pod number in rapeseed. In addition, RNA sequencing was performed for SAM in rapeseed, which provides new insights into the determination of floral organ number. Furthermore, the integration of DEGs and QTLs identified promising candidates for further gene cloning and mechanism study. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-3402-y) contains supplementary material, which is available to authorized users.
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