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Genome-Wide Identification and Expression Profiling Suggest that Invertase Genes Function in Silique Development and the Response to Sclerotinia sclerotiorum in Brassica napus

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Phyton-International Journal of Experimental Botany 2020年第2期89卷 253-273页

作者： Jingsen Liu Jinqi Ma Ai Lin Chao Zhang Bo Yang Liyuan Zhang Lin Huang Jiana Li chongqing rapeseed engineering research center College of Agronomy and BiotechnologyChongqing400715China Academy of Agricultural Sciences Southwest UniversityChongqing400715China

Invertase(INV),a key enzyme in sucrose metabolism,irreversibly catalyzes the hydrolysis of sucrose to glucose and fructose,thus playing important roles in plant growth,development,and biotic and abiotic stress *** this study,we identified 27 members of the BnaINV family in Brassica *** constructed a phylogenetic tree of the family and predicted the gene structures,conserved motifs,cis-acting elements in promoters,physicochemical properties of encoded proteins,and chromosomal distribution of the *** also analyzed the expression of the BnaINVs in different tissues and developmental stages in the *** cultivar Zhongshuang 11 using *** addition,we analyzed RNA-sequencing data to explore the expression patterns of the BnaINVs in four cultivars with different harvest indices and in plants inoculated with the pathogenic fungus Sclerotinia *** used WGCNA(weighted coexpression network analysis)to uncover BnaINV regulatory ***,we explored the expression patterns of several BnaINV genes in cultivars with long(Zhongshuang 4)and short(Ningyou 12)*** results suggest that BnaINVs play important roles in the growth and development of rapeseed siliques and the defense response against *** findings could facilitate the breeding of high-yielding *** cultivars with strong disease resistance.

关键词： Brassica napus invertase Sclerotinia WGCNA RNA-seq

Two types of cinnamoyl-Co A reductase function divergently in accumulation of lignins,flavonoids and glucosinolates and enhance lodging resistance in Brassica napus

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The Crop Journal 2022年第3期10卷 647-660页

作者： Nengwen Yin Bo Li Xue Liu Ying Liang Jianping Lian Yufei Xue Cunmin Qu Kun Lu Lijuan Wei Rui Wang Jiana Li Yourong Chai chongqing engineering research center for rapeseed Chongqing Key Laboratory of Crop Quality ImprovementCollege of Agronomy and BiotechnologySouthwest UniversityChongqing 400715China engineering research center of South Upland Agriculture of Ministry of Education Academy of Agricultural SciencesSouthwest UniversityChongqing 400715China

Brassica crops,which are of worldwide importance,provide various oil,vegetable and ornamental products,as well as feedstocks for animal husbandry and biofuel ***-Co A reductase(CCR)is the entry point to the lignin pathway and a crucial locus in manipulation of associated traits,but CCRassociated metabolism and traits in Brassica crops have remained largely unstudied except in Arabidopsis *** report the identification of 16 CCR genes from Brassica napus and its parental species *** and *** Bn CCR1 and Bn CCR2 subfamilies displayed divergent organ-specificity and participation in the yellow-seed *** functions were dissected via overexpression of representative paralogs in *** CCR1 was expressed preferentially in G-and H-lignin biosynthesis and vascular development,while Bn CCR2 was expressed in S-lignin biosynthesis and interfascicular fiber *** CCR1 showed stronger effects on lignification-related development,lodging resistance,phenylpropanoid flux control,and seed coat pigmentation,whereas Bn CCR2 showed a stronger effect on sinapate *** CCR1 upregulation delayed bolting and flowering time,while Bn CCR2 upregulation weakened the leaf vascular system in consequence of suppressed G-lignin *** CCR1 and Bn CCR2 were closely but almost oppositely linked with glucosinolate metabolism via inter-pathway *** conclude that Bn CCR1 and Bn CCR2 subfamilies offer great but differing potential for manipulating traits associated with phenylpropanoids and *** study reveals the CCR1–CCR2 divergence in Brassicaceae and offers a resource for rapeseed breeding for lodging resistance,yellowseed traits,and glucosinolate traits.

关键词： Brassica napus Cinnamoyl-CoA reductase(CCR) Lignin Flavonoids Lodging

Identification and characterization of a curly-leaf locus CL1 encoding an IAA2 protein in Brassica napus

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The Crop Journal 2023年第3期11卷 756-765页

作者： Yingchao Tan Lanyang Ren Jia Wang Shuyao Ran Liusha Wu Ziyi Cheng Cunmin Qu Jiana Li Liezhao Liu college of agronomy and biotechnology Southwest UniversityChongqing 400715China chongqing engineering research center for rapeseed Academy of Agricultural SciencesState Cultivation Base of Crop Stress Biology for Southern Mountainous LandSouthwest UniversityChongqing 400715China

The leaf is the main organ for rapeseed photosynthesis,and its morphology influences photosynthetic efficiency and supports increased planting density and ***,the molecular regulatory mechanism of leaf morphology in Brassica napus is poorly understood,restricting progress in breeding for the *** describe a novel dominant mutation,curly leaf 1(cl1),which confers uneven dorsal–ventral axis development,irregular cellular structure and influenced gravitropic response in the seedling *** CL1 locus was mapped to a 1.573-Mb interval on chromosome A05 using simple sequence repeat(SSR)markers,and co-segregated with the phenotype of plants in the curly F2 population.A substitution(P62S)was identified in the highly conserved degron motif(GWSPV)of the IAA2 protein in the cl1mutant,and the P62S substitution impaired the interaction between IAA2 and TIR1 in the presence of auxin,influencing auxin *** P62S substitution-induced curly leaf phenotype was verified by ectopic expression of Bna ***2 in Arabidopsis and *** findings explain the function of IAA2 in rapeseed,providing a foundation for future investigation of auxin signaling and the mechanisms underlying leaf development in ***.

关键词： Brassica napus Curly leaf Auxin IAA2 protein

Identification of quantitative trait loci and candidate genes controlling seed pigments of rapeseed

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Journal of Integrative Agriculture 2021年第11期20卷 2862-2879页

作者： ZHU Mei-chen HU Ran ZHAO Hui-yan TANG Yun-shan SHI Xiang-tian JIANG Hai-yan ZHANG Zhi-yuan FU Fu-you XU Xin-fu TANG Zhang-lin LIU Lie-zhao LU Kun LI Jia-na QU Cun-min chongqing engineering research center for rapeseed/college of agronomy and biotechnology Southwest University/Academy of Agricultural SciencesSouthwest UniversityChongqing 400716P.R.China Agriculture and Agri-Food Canada Saskatoon Research CentreSaskatoon S7N02XCanada

rapeseed(Brassica napus L.)is an important source of edible vegetable oil and feed protein;however,seed pigments affect the quality of rapeseed oil and the feed value of the residue from oil ***,we used a population of rapeseed recombinant inbred lines(RILs)derived from the black-seeded male parent cultivar Zhongyou 821 and the yellow-seeded female parent line GH06 to map candidate genes controlling seed pigments in embryos and the seed *** detected 94 quantitative trait loci(QTLs)for seed pigments(44 for embryos and 50 for seed coat),distributed over 15 of the 19 rapeseed *** included 28 QTLs for anthocyanidin content,explaining 2.41–44.66% of phenotypic variation;24 QTLs for flavonoid content,explaining 2.41–20.26% of phenotypic variation;16 QTLs for total phenol content,accounting for 2.74–23.68% of phenotypic variation;and 26 QTLs for melanin content,accounting for 2.37–24.82% of phenotypic variation,indicating that these traits are under multigenic *** regions on chromosomes A06,A09 and C08 were associated with multiple seed pigment traits,including 15,19 and 10 QTLs,respectively,most of which were major QTLs explaining>10% of the phenotypic *** on the annotation of the ***"Darmor-bzh"reference genome,67 candidate genes were predicted from these consensus QTLs regions,and 12 candidate genes were identified as potentially involved in pigment accumulation by RNA-seq and qRT-PCR *** preliminary results provide insight into the genetic architecture of pigment biosynthesis and lay a foundation for exploring the molecular mechanisms underlying seed coat color in ***.

关键词： Brassica napus L. embryo seed coat pigments QTL

QTL analysis of leaf photosynthesis rate and related physiological traits in Brassica napus

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Journal of Integrative Agriculture 2015年第7期14卷 1261-1268页

作者： YAN Xing-ying QU Cun-min LI Jia-na CHEN Li LIU Lie-zhao college of agronomy and biotechnology Southwest University biotechnology research center Southwest University

rapeseed （Brassica napus L.） oil is the crucial source of edible oil in China. In addition, it can become a major renewable and sustainable feedstock for biodiesel production in the future. It is known that photosynthesis products are the primary sources for dry matter accumulation in rapeseed. Therefore, increasing the photosynthetic efficiency is desirable for the raise of rapeseed yield. The objective of the present study was to identify the genetic mechanism of photosynthesis based on the description of relationships between different photosynthetic traits and their quantitative trait loci （QTL） by using a recombinant inbred line （RIL） population with 172 lines. Specifically, correlation analysis in this study showed that internal CO2 concentration has negative correlations with other three physiological traits under two different stages. Totally, 11 and 12 QTLs of the four physiological traits measured at the stages 1 and 2 were detected by using a high-density single nu- cleotidepolymorphism （SNP） markers linkage map with composite interval mapping （CIM）, respectively. Three co-localized QTLs on A03 were detected at stage 1 with 5, 5, and 10% of the phenotypic variation, respectively. Other two co-localized QTLs were located on A05 at stage 2, which explained up to 12 and 5% of the phenotypic variation, respectively. The results are beneficial for our understanding of genetic control of photosynthetic physiological characterizations and improvement of rapeseed yield in the future.

关键词： Brassica napus photosynthesis quantitative trait loci (QTL)

Identification of a candidate QTG for seed number per silique by integrating QTL mapping and RNA-seq in Brassica napus L.

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The Crop Journal 2023年第1期11卷 189-197页

作者： Shuangshuang Xin Hongli Dong Yixin Cui Yilin Liu Guifu Tian Nanxi Deng Huafang Wan Zhi Liu Xiaorong Li Wei Qian college of agronomy and biotechnology Southwest UniversityChongqing 400715China engineering research center of South Upland Agriculture Ministry of EducationChongqing 400715China college of Pharmaceutical Sciences and Chinese Medicine Southwest UniversityChongqing 400715China

Seed number per silique(SNPS)is one of seed yield components in rapeseed,but its genetic mechanism remains *** a double haploid(DH)population derived from a hybrid between female 6Q006with 35–40 SNPS and male 6W26 with 10–15 SNPS was investigated for SNPS in the year 2017,2018,2019 and 2021,and genotyped with Brassica 60K Illumina Infinium SNP *** overlapping major QTL(qSNPS.C09)explaining 51.50%of phenotypic variance on average was narrowed to a 0.90 Mb region from 44.87 Mb to 45.77 Mb on chromosome C09 by ***,two DEGs in this interval were detected between extreme individuals in DH and F_2populations by transcriptome sequencing at7 and 14 days after pollination *** which,BnaC09g45400D encoded an adenine phosphoribosyltransferase 5(APT5)has a 48-bp InDel variation in the promoter of two *** gene association analysis showed that this InDel variation was associated with SNPS in a nature population of rapeseed,where 54 accessions carrying the same haplotype as parent 6Q006 had higher SNPS than103 accessions carrying the same haplotype as parent ***,the findings are helpful for rapeseed molecular breeding of SNPS,and provide new insight into the genetic and molecular mechanism of SNPS in rapeseed.

关键词： Adenine phosphoribosyltransferase 5 Brassica napus QTL mapping RNA-seq Seed number per silique

New Insights into Nested Long Terminal Repeat Retrotransposons in Brassica Species

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Molecular Plant 2013年第2期6卷 470-482页

作者： Lijuan Wei Meili Xiaoa Zeshan An Bi Ma Annaliese S. Mason Wei Qian Jiana Li Donghui Fu chongqing engineering research center for rapeseed College of Agronomy and Biotechnology Southwest University Chongqing 400716 China School of Agriculture and Food Sciences and centre for Integrative I~egume-research The University of Queensland 1:he Universit'y of QueenslandBrisbane 4072 Australia Key Laboratory of Crop Physiology Ecology and Genetic Breeding Ministry of Education Agronomy College Jiangxi Agricultural University Nanchang330045 China

Long terminal repeat （LTR） retrotransposons, one of the foremost types of transposons, continually change or modify gene function and reorganize the genome through bursts of dramatic proliferation. Many LTR-TEs preferen-tially insert within other LTR-TEs, but the cause and evolutionary significance of these nested LTR-TEs are not well under-stood. In this study, a total of 1.52 Gb of Brassica sequence containing 2020 bacterial artificial chromosomes （BACs） was scanned, and six bacterial artificial chromosome （BAC） clones with extremely nested LTR-TEs （LTR-TEs density： 7.24/kb） were selected for further analysis. The majority of the LTR-TEs in four of the six BACs were found to be derived from the rapid proliferation of retrotransposons originating within the BAC regions, with only a few LTR-TEs originating from the proliferation and insertion of retrotransposons from outside the BAC regions approximately 5-23 Mya. LTR-TEs also pref-erably inserted into TA-rich repeat regions. Gene prediction by Genescan identified 207 genes in the 0.84Mb of total BAC sequences. Only a few genes （3/207） could be matched to the Brassica expressed sequence tag （EST） database, indicating that most genes were inactive after retrotransposon insertion. Five of the six BACs were putatively centromeric. Hence, nested LTR-TEs in centromere regions are rapidly duplicated, repeatedly inserted, and act to suppress activity of genes and to reshuffle the structure of the centromeric sequences. Our results suggest that LTR-TEs burst and proliferate on a local scale to create nested LTR-TE regions, and that these nested LTR-TEs play a role in the formation of centromeres.

关键词： LTR retrotransposons Brassica centromere retrotransposon-rich transposon burst.

Complete genome sequences of four isolates of Citrus leaf blotch virus from citrus in China

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Journal of Integrative Agriculture 2018年第3期17卷 712-715页

作者： LI Ping LI Min ZHANG Song WANG Jun YANG Fang-yun CAO Meng-ji LI Zhong-an National Citrus engineering research center Citrus Research Institute Southwest University college of agronomy and biotechnology Southwest University

Citrus leaf blotch virus （CLBV） is a member of the genus Citrivirus, in the family Betaflexiviridae. It has been reported CLBV could infect kiwi, citrus and sweet cherry in China. Of 289 citrus samples from six regions of China, 15 were detected to be infected with CLBV in this study. The complete genome of four isolates of CLBV was obtained from Reikou in Sichuan （CLBV-LH）, Yura Wase in Zhejiang （CLBV-YL）, Bingtangcheng in Hunan （CLBV-BT）, Fengjie 72-1 in chongqing （CLBV- F J）, respectively. While they all represented 8 747 nucleotides in monopartite size, excluding the poly（A） tail, each of the isolates coded three open reading frames （ORFs）. Identity of the four isolates ranged from 98.9 to 99.8% to each other and from 96.8 to 98.1% to the citrus references in GenBank by multiple alignment of genomes. A phylogenetic tree based on the genome sequences of available CLBV isolates indicated that the four isolates were clustered together, suggesting that CLBV isolates from citrus in China did not have obvious variation. This is the first report of the complete nucleotide sequences of CLBV isolates infecting citrus in China.

关键词： Citrus leaf blotch virus (CLBV) genome sequence Citrivirus

ISSR-Based Molecular Characterization of an Elite Germplasm Collection of Sweet Potato(Ipomoea batatas L.) in China

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Journal of Integrative Agriculture 2014年第11期13卷 2346-2361页

作者： ZHANG Kai WU Zheng-dan LI Yan-hua ZHANG Han WANG Liang-ping ZHOU Quan-lu TANG Dao-bin FU Yu-fan HE Feng-fa JIANG Yu-chun YANG Hang WANG Ji-chun college of agronomy and biotechnology Southwest University Sweet Potato engineering and Technology research center engineering research center of South Upland Agriculture Ministry of Education The chongqing Three Gorges Academy of Agricultural Sciences Nanchong Institute of Agricultural Sciences college of Life Science Southwest University

To determine the genetic diversity and population structure of sweet potato accessions cultivated in China, and to establish the genetic relationships among their germplasm types, a representative collection of 240 accessions was analyzed using inter-simple sequence repeat （ISSR） markers. The mean genetic similarity coefifcient, Nei’s gene diversity, and shared allele distance of tested sweet potato accessions were 0.7302, 0.3167 and 0.2698, respectively. The 240 accessions could be divided into six subgroups and ifve subpopulations based on neighbor-joining （NJ） clustering and STRUCTURE results, and obvious genetic relationships among the tested sweet potato accessions were identiifed. The marker-based NJ clustering and population structure showed no distinct assignment pattern corresponding to lfesh color or geographical ecotype of the tested sweet potato germplasm. Analysis of molecular variance （AMOVA） revealed small but signiifcant difference between white and orange-lfeshed sweet potato accessions. Small but signiifcant difference were also observed among sweet potato accessions from the Southern summer-autumn sweet potato region, the Yellow River Basin spring and summer sweet potato region and the Yangtze River Basin summer sweet potato region. This study demonstrates that genetic diversity in the tested sweet potato germplasm collection in China is lower than that in some reported sweet potato germplasm collections from other regions. Pedigree investigations suggest that more diverse Chinese sweet potato varieties should be formed by broadening the selection scope of breeding parents and incorporating the introduced varieties into future breeding programs.

关键词： sweet potato genetic diversity population structure agro-ecological zone lfesh color ISSR