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Plant Polyploidy: Origin, Evolution, and Its Influence on Crop Domestication

Horticultural Plant Journal 2019年第6期5卷 231-239页

作者： Kang Zhang xiaowu wang Feng Cheng Chinese Academy of Agricultural Sciences Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of AgricultureSino-Dutch Joint Laboratory of Horticultural GenomicsInstitute of Vegetables and FlowersBeijing 100081China

The prevalence and recurrence of polyploidization in plant species make it one of the most important evolutionary events in plants, and as a result, polyploidization is an extensively investigated research field. Due to the rapid development of sequencing technologies, there is increased evidence to support that polyploidization plays an important role in the diversification of plant species, evolution of genes, and the domestication of crops. Here, we reviewed the influence of polyploidization on various aspects of plant evolution, mainly focused on polyploid origin, characteristics, subsequent genome divergence, and its impact on gene function innovation and crop domestication. The occurrence of many independent polyploidization events in plants was found to be tightly associated with the timing of extreme climate events or natural disasters on earth, leading to mass extinction while possibly facilitating increased polyploidization. Following allo-polyploidization, a distinct phenomenon known as sub-genome dominance occurred during sub-genome evolution, which was found to be associated with the methylation of transposons. Extensive gene fractionations(lost) following polyploidization were reported in almost all paleo-polyploids, and the evolutionary fates of multi-copy genes, such as sub-/neo-functionalization, were further proposed to illustrate their underlying mechanisms. Moreover,polyploidization was found to significantly impact species diversification, with subsequent effects on crop domestication and the development of traits with agronomic importance. Based on the progress of plant polyploidization studies, we discussed several main topics that might further improve our understanding of polyploid evolution and that are likely contribute to the application of polyploidization in crop breeding in the near future.

关键词： polyploidization genome evolution sub-genome gene function innovation crop domestication

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Genome triplication drove the diversification of Brassica plants

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Horticulture Research 2014年第1期1卷 190-197页

作者： Feng Cheng Jian Wu xiaowu wang Institute of Vegetables and Flowers Chinese Academy of Agricultural SciencesBeijing 100081China

The genus Brassica belongs to the plant family Brassicaceae,which includes many important crop species that are used as oilseed,condiments,or vegetables throughout the *** plants comprise many diverse species,and each species contains rich morphotypes showing extreme *** species experienced an extra whole genome triplication(WGT)event compared with the model plant Arabidopsis *** genome sequencing of the Brassica species Brassica rapa,Brassica oleracea and others demonstrated that WGT plays an important role in the speciation and morphotype diversification of Brassica *** genomic analysis based on the genome sequences of *** and *** clearly identified the WGT event and further demonstrated that the translocated Proto-Calepine Karyotype(tPCK,n57)was the diploid ancestor of the three subgenomes in *** WGT,subsequent extensive genome fractionation,block reshuffling and chromosome reduction accompanied by paleocentromere descent from the three tPCK subgenomes during the rediploidization process produced stable diploid *** rearrangement of the diploid species and their hybridization then contributed to Brassica *** subgenome dominance effect and biased gene retention,such as the over-retention of auxin-related genes after WGT,promoted functional gene evolution and thus propelled the expansion of rich morphotypes in the Brassica *** conclusion,the WGT event initiated subsequent genomic and gene-level evolution,which further drove Brassica speciation and created rich morphotypes in each species.

关键词： subsequent retention initiated

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Wild Brassica and Its Close Relatives in Turkey,the Genetic Treasures

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Horticultural Plant Journal 2021年第2期7卷 97-107页

作者： Ali A.Donmez Zubeyde Ugurlu Aydın xiaowu wang Molecular Plant Systematic Laboratory(MOBIS) Department of BiologyFaculty of ScienceHacettepe UniversityAnkara 06800Turkey Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture Sino-Dutch Joint Laboratory of Horticultural GenomicsInstitute of Vegetables and FlowersChinese Academy of Agricultural SciencesBeijing 100081China

Brassica taxa occur naturally and are also cultivated in *** to their economic importance,several cultivars have been extensively cultivated in certain regions of the *** extensive cultivation for vegetable production of the other species of the genus,Brassica juncea has very limited *** native species of Brassica are known from restricted locations in Turkey with only a few *** them,Brassica elongata is distributed all over the Central and Eastern parts of the country and it prefers unfertile soils on *** the current data about the Brassica taxa would lead to new initiatives for Brassica research dealing with both the genetic structure and the origin of the *** characters of the genera closely related to Brassica have been discussed under the relevant ***,an overview for the Turkish Brassiceae tribe,both native and cultivated,has been presented and the relevant identification keys have been supplied for updating.

关键词： Brassica Brassiceae cultivation native Turkey

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Gene expression,transcription factor binding and histone modification predict leaf adaxial-abaxial polarity related genes

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Horticultural Plant Journal 2024年第4期10卷 971-982页

作者： Wei Sun Zhicheng Zhang Guusje Bonnema xiaowu wang Aalt Dirk Jan van Dijk State Key Laboratory of Vegetable Biobreeding Institute of Vegetables and FlowersChinese Academy of Agricultural SciencesBeijing 100081China Sino-Dutch Joint Lab of Vegetable Genomics Beijing 100081China Bioinformatics Group Wageningen University and Research6708 PB Wageningenthe Netherlands Plant Breeding Wageningen University and Research6708 PB Wageningenthe Netherlands Biosystems Data Analysis Swammerdam Institute for Life SciencesUniversity of Amsterdam1090 GE Amsterdamthe Netherlands

Leaf adaxial-abaxial(ad-abaxial)polarity is crucial for leaf morphology and function,but the genetic machinery governing this process remains *** uncover critical genes involved in leaf ad-abaxial patterning,we applied a combination of in silico prediction using machine learning(ML)and experimental analysis.A Random Forest model was trained using genes known to influence ad-abaxial polarity as ground *** expression data from various tissues and conditions as well as promoter regulation data derived from transcription factor chromatin immunoprecipitation sequencing(ChIP-seq)was used as input,enabling the prediction of novel ad-abaxial polarity-related genes and additional transcription *** to this,available and newly-obtained transcriptome data enabled us to identify genes differentially expressed across leaf ad-abaxial *** on these analyses,we obtained a set of 111 novel genes which are involved in leaf ad-abaxial *** explore implications for vegetable crop breeding,we examined the conservation of expression patterns between Arabidopsis and Brassica rapa using single-cell *** results demonstrated the utility of our computational approach for predicting candidate genes in crop *** findings expand the understanding of the genetic networks governing leaf ad-abaxial differentiation in agriculturally important vegetables,enhancing comprehension of natural variation impacting leaf morphology and development,with demonstrable breeding applications.

关键词： Machine learning Leaf polarity Arabidopsis thaliana Brassica rapa Transcription factor

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An optimized protocol for detecting guard cell specific gene expression by in situ RT-PCR in Brassica rapa

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Horticultural Plant Journal 2022年第3期8卷 311-318页

作者： Yingying Song Xinlei Guo Jian Wu Jianli Liang Runmao Lin Zifu Yan xiaowu wang College of Horticulture Henan Agricultural UniversityZhengzhou 450002China Institute of Vegetables and Flowers Chinese Academy of Agricultural SciencesBeijing 100081China

It is important to detect specific genes expressed in the guard cells,which control gas exchange and play key roles in response to drought and salt *** to the genetic transformation of Chinese cabbage(Brassica rapa)has not been well developed,in situ RT-PCR is a valuable option for detecting guard cell specific *** reported an optimized protocol of in situ RT-PCR by using an FAMA homologous gene Bra001929 in Brassica *** in Arabidopsis has been verified to be specially expressed in guard *** designed specific RT-PCR primers and optimized the protocol in terms of the(a)reverse transcription time,(b)blocking time,(c)antigen-antibody incubation time,and(d)washing *** approach provides a sensitive and effective in situ RT-PCR method for locating expression in the guard cells in Brassica ***,we proved the guard cell specific expression of Bra001929 in the epidermis indicating its’applicability as a marker gene for guard cells of Brassica rapa.

关键词： Brassica rapa In situ RT-PCR Gene expression Bra001929 Protocol

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Development of InDel Markers for Brassica rapa Based on a High-resolution Melting Curve

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Horticultural Plant Journal 2021年第1期7卷 31-37页

作者： Rong Chen Lichun Chang Xu Cai JianWu Jianli Liang Runmao Lin Yong Song xiaowu wang College of Horticulture Hunan Agricultural UniversityChangsha 410128China Institute of Vegetables and Flowers Chinese Academy of Agricultural SciencesBeijing 100081China

Brassica rapa is one of the most important leafy vegetable crops with large cultivated area in *** increase the availability of DNA markers in ***,we developed insertion-deletion(InDel)markers utilizing high-resolution melting(HRM)curve *** designed primers for 252 InDels(≥3 bp)evenly distributed in the genome and tested gene polymorphisms with eight *** total,208 markers were specifically amplified,and 148 InDels with polymorphism were genotyped successfully using *** further analyzed the correlation with InDel size,GC number,and predicted the difference in Tm values(Tm)using 208 markers with specific *** found that the success rate of InDel markers was correlated with the GC number of InDel and the predicted-Tm,but not clearly correlated with the length of *** the GC number within InDel was≥8,the successful rate exceeded 90.0%.When the predicted-Tm reached 0.5°C,the success rate was greater than 90.0%,and when it was≥0.6°C,the rate climbed to 100.0%,indicating their role as the optimal parameter for successful development of an applicable InDel *** polymorphic InDel markers can be easily genotyped using *** are of great value in genetic analysis,construction of linkage map,and molecular marker-assisted selection in ***.

关键词： Brassica rapa InDel marker HRM genotyping

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Variation in Plant Morphology and Sinigrin Content in Ethiopian Mustard(Brassica carinata L.)

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Horticultural Plant Journal 2019年第5期5卷 205-212页

作者： Tesfay Teklehaymanot Haijing wang Jianli Liang Jian Wu Runmao Lin Zhen Zhou Xu Cai xiaowu wang Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture Sino-Dutch Joint Laboratory of Horticultural GenomicsInstitute of Vegetables and FlowersChinese Academy of Agricultural SciencesBeijing100081China Tigray Agricultural Research Institute MekelleTigrayEthiopia

Ethiopian mustard(Brassica carinata) is mainly grown as a leafy vegetable and oilseed crop. Sinigrin is predominant glucosinolate in the leaves of Ethiopian mustard. It is hydrolyzed by enzyme myrosinase to produce bioactive product specifically allyl-isothiocyanates. Due to sinigrin content, Ethiopian mustard has a mild flavor and it is a healthy addition to human diet. However, sinigrin concentration depends on *** variations of plant morphology and sinigrin content may be the first step for crop improvement. According to the analyses of various plant characteristics among ninety nine Ethiopian mustard accessions, we found significant differences in plant height, chlorophyll content, and petiole length. In addition, sinigrin content was determined using ultra-performance liquid chromatography tandem quadrupole mass spectrometers/tunable ultraviolet detector(UPLC-TQS/TUV). We found a significant difference in sinigrin content among leaves of 94 Ethiopian mustard accessions. Except for petiole length, the sinigrin content was negatively correlated with leaf area, leaf width, number of primary branches, and plant height. This information will help Ethiopian mustard breeders in screening breeding lines for new accessions.

关键词： Brassicaceae mustard sinigrin leafy vegetable glucosinolate metabolite

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A naturally occurring variation in the BrMAM-3 gene is associated with aliphatic glucosinolate accumulation in Brassica rapa leaves

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Horticulture Research 2018年第1期5卷 32-42页

作者： Jifang Zhang Hui wang Zhiyuan Liu Jianli Liang Jian Wu Feng Cheng Shiyong Mei xiaowu wang Institute of Vegetables and Flowers Chinese Academy of Agricultural Sciences100081BeijingChina Institute of Southern Economic Crops Institute of Bast Fiber CropsChinese Academy of Agricultural Sciences410205ChangshaChina College of Horticulture Qingdao Agricultural University266109QingdaoChina

Glucosinolate profiles significantly vary among Brassica rapa ***,the molecular basis of these variations is largely *** this study,we investigated a major quantitative trait locus(QTL)controlling aliphatic glucosinolate accumulation in *** *** QTL,which encompasses three tandem MAM genes and two MYB genes,was detected in two BC2DH *** the five-candidate genes,only the expression level of BrMAM-3(Bra013007)was significantly correlated with the accumulation of aliphatic glucosinolates in *** *** identified a naturally occurring insertion within exon 1 of BrMAM-3,which is predicted to be a loss-of-function mutation,as confirmed by *** determined that the loss of function was associated with the low glucosinolate content in *** ***,overexpressing the BrMAM-3 gene resulted in an increase in total aliphatic glucosinolates in Arabidopsis transgenic *** study provides insights into the molecular mechanism underlying the accumulation of aliphatic glucosinolates in *** leaves,thereby facilitating in the manipulation of total aliphatic glucosinolate content in Brassica crops.

关键词： thereby insertion insight

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The APETALA2 homolog CaFFN regulates flowering time in pepper

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Horticulture Research 2021年第1期8卷 3158-3171页

作者： Xinjie Yuan Rong Fang Kunhua Zhou Yueqin Huang Gang Lei xiaowu wang Xuejun Chen Institute of Vegetables and Flowers Jiangxi Academy of Agricultural Sciences330200 NanchangChina Institute of Vegetables and Flowers Chinese Academy of Agricultural Sciences100081 BeijingChina

Flowering time is an important agronomic trait that contributes to fitness in ***,the genetic basis of flowering time has not been extensively studied in *** understand the genetics underlying flowering time,we constructed an F 2 population by crossing a spontaneous early flowering mutant and a late-flowering pepper *** bulked segregant RNA-seq,a major locus controlling flowering time in this population was mapped to the end of chromosome *** APETALA2(AP2)homolog(CaFFN)cosegregated with flowering time in 297 individuals of the F 2 population.A comparison between the parents revealed a naturally occurring rare SNP(SNP2T>C)that resulted in the loss of a start codon in CaFFN in the early flowering *** Nicotiana benthamiana plants with high CaFFN expression exhibited a delay in flowering time and floral patterning *** the other hand,pepper plants with CaFFN silencing flowered ***,the CaFFN gene acts as a flowering repressor in *** may function as a transcriptional activator to activate the expression of CaAGL15 and miR156e and as a transcriptional repressor to repress the expression of CaAG,CaAP1,CaSEP3,CaSOC1,and miR172b based on a qRT-PCR *** activation of CaAGL15 by CaFFN was detected using yeast one-hybrid and dual-luciferase reporter assays,consistent with the hypothesis that CaFFN regulates flowering ***,the CaFFN gene association analysis revealed a significant association with flowering time in a natural pepper population,indicating that the CaFFN gene has a broad effect on flowering time in ***,the phylogeny,evolutionary expansion and expression patterns of CaFFN/AP2 homologs were analyzed to provide valuable insight into *** study increases our understanding of the involvement of CaFFN in controlling flowering time in pepper,thus making CaFFN a target gene for breeding early maturing pepper.

关键词： homolog pepper breeding

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Brassica rapa Genome 2.0： A Reference Upgrade through Sequence Re-assembly and Gene Re-annotation

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Molecular Plant 2017年第4期10卷 649-651页

作者： Chengcheng Cai Xiaobo wang Bo Liu Jian Wu Jianli Liang Yinan Cui Feng Cheng xiaowu wang Institute of Vegetables and Flowers Chinese Academy of AgriculturalSciences Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture Sino-Dutch Joint Laboratory of Horticultural Genomics Beijing 100081 P.R. China

Brassica rapa includes many important crops that are cultivated as vegetables, condiments, and oilseeds. Recently, the Brassica genomes have been sequenced extensively： a B. rapa draft reference genome in 2011 （wang et al., 2011）, a Brassica oleracea in 2014 （Liu et al., 2014）, a Brassica napus in 2014 （Chalhoub et al., 2014）, and Brassica nigra and Brassica juncea in 2016 （Yana et al.. 2016）. The first released B.

关键词： Brassica rapa includes important crops vegetables

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