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Science China(Life Sciences) 2019年第6期62卷 746-757页

作者： Xiaoling Dun Jiaqin Shi Huiping Liu Jie Wang Xinfa Wang Hanzhong Wang oil crops Research Institute of the Chinese Academy of Agricultural Sciences/key laboratory of biology and genetic improvement of oil crops Ministry of Agriculture

To reveal the genetic basis of potassium use efficiency(KUE) in rapeseed, root morphology(RM), biomass and KUE-related traits were measured in a recombinant inbred line population with 175 F7 lines that were subjected to high-potassium(HK) and low-potassium(LK) treatments by hydroponics. A total of 109 significant QTLs were identified to be associated with the examined traits. Sixty-one of these QTLs were integrated into nine stable QTLs. The higher heritability for RM and biomass traits and lower heritability for KUE-related traits, as well as nine stable QTLs for RM traits and only two for KUE-related traits,suggested that regulating RM traits would be more effective than selecting KUE traits directly to improve KUE by markerassisted selection. Furthermore, the integration of stable QTLs identified in the HK, LK, high-nitrogen(HN) and low-nitrogen(LN) conditions gave 10 QTL clusters. Seven of these clusters were classified into major QTLs that explained 7.4%–23.7% of the total phenotypic variation. Five of the major QTL clusters were detected under all of the treated conditions, and four clusters were specifically detected under the LK and LN conditions. These common and specific QTL clusters may be useful for the simultaneous improvement of multiple traits by marker-assisted selection.

关键词： Brassica napus L. root traits potassium efficiency QTL mapping QTL cluster

Comparison of transcriptomes undergoing waterlogging at the seedling stage between tolerant and sensitive varieties of Brassica napus L.

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Journal of Integrative Agriculture 2015年第9期14卷 1723-1734页

作者： ZOU Xi-ling ZENG Liu LU Guang-yuan CHENG Yong XU Jin-song ZHANG Xue-kun key laboratory of biology and genetic improvement of oil crops Ministry of Agriculture/Oil Crops Research InstituteChinese Academy of Agricultural Sciences

RNA sequencing of the sensitive GH01 variety of Brassica napus L. seedling roots under 12 h of waterlogging was compared with previously published data of the ZS9 tolerant variety to unravel genetic mechanisms of waterlogging tolerance beyond natural variation. A total of 2 977 genes with similar expression patterns and 17 genes with opposite expression patterns were identiifed in the transcription proifles of ZS9 and GH01. An additional 1 438 genes in ZS9 and 1 861 genes in GH01 showed strain speciifc regulation. Analysis of the overlapped genes between ZS9 and GH01 revealed that waterlogging tolerance is determined by ability to regulate genes with similar expression patterns. Moreover, differences in both gene expression proifles and abscisic acid (ABA) contents between the two varieties suggest that ABA may play some role in waterlogging tolerance. This study identiifes a subset of candidate genes for further functional analysis.

关键词： rapeseed(Brassica napus L.) waterlogging digital gene expression(DGE) roots transcriptome comparative analysis

Association Analysis for Quality Traits in a Diverse Panel of Chinese Sesame(Sesamum indicum L.)Germplasm

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Journal of Integrative Plant biology 2013年第8期55卷 745-758页

作者： Wenliang Wei Yanxin Zhang Haixia Lü Donghua Li Linhai Wang Xiurong Zhang oil crops Research Institute of the Chinese Academy of Agricultural Sciences Key Laboratory of Biology and Genetic Improvement of Oil CropsMinistry of Agriculture

The main objective of this study was to evaluate the potential of a sesame （Sesamum indicum L.） panel for association analysis, and investigate the genetic basis of oil content （OC）, protein content, oleic acid concentration, and linoleic acid concentration using association mapping. A panel of 216 sesame accessions was phenotyped in a multi-environment trial and fingerprinted with 608 polymorphic loci produced by 79 primers, including simple sequence repeats （SSRs）, sequence-related amplified polymorphisms （SRAPs）, and amplified fragment length polymorphisms （AFLPs）. Population structure analysis revealed two subgroups in the population. The Q model performed better for its ability to re-identify associations for the four traits at highly significant P-values compared to the other three mixed models. And a total of 35 and 25 associations for the four traits in 2010 and 2011 were identified, respectively, with the Q model after Bonferroni correction. Among those associations, only one for OC was re-identified in two environments, and several markers associated simultaneously with multiple traits were discovered. These results suggest the power and stability of the Q model for association analysis of nutritional traits in this sesame panel for its slight population stratification and familial relationship, which could aid in dissecting complex traits, and could help to develop strategies for improving nutritional quality.

关键词： Association mapping nutritional trait population structure Sesamum indicum L.

Molecular evidence for blocking erucic acid synthesis in rapeseed(Brassica napus L.) by a two-base-pair deletion in FAE1(fatty acid elongase 1)

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Journal of Integrative Agriculture 2015年第7期14卷 1251-1260页

作者： WU Lei JIA Yan-li WU Gang LU Chang-ming oil crops Research Institute Chinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetic Improvement of Oil CropsMinistry of Agriculture

DNA sequences of fatty acid elongase 1 genes FAE1.1 （EA） and FAE1.2 （Ec） were isolated and characterized for 30 com- mercialized low erucic acid rapeseed （LEAR） cultivars in China. Four types of independent mutation leading to low erucic acid trait were found, i.e., a single-base transition （eAl）, a two-base deletion （ec2） and four-base deletion （eC4） as well as single-base transition with a four-base deletion （eA.）. Three genotypes, i.e., eA1eA1eC2eC2, eA1eA1eC4eC4 and ***4ec4 were responsible for LEA content in storage Iipids of different rapeseed cultivars. Most of the LEAR cultivars had a genotype of eA1eA1ec2ec2, which were descended from the first LEAR cultivar, Oro. Yeast expression analysis revealed that two-base-pair （AA） deletion （ec2） at the base sites of 1 422-1 423 in the C genome FAE1 gene resulted in the absence of the condensing enzyme and led to the failure to produce erucic acid. Coexpression of FAE1 and ketoacyI-CoA reductase （KCR） or enoyI-CoA reductase （ECR） was found in high erucic acid rapeseed （HEAR） but not in LEAR （eA1eA1ec2ec2oreA1eA1ec4ec4）. Moreover, KCR and ECR were still coordinately regulated in eA1eA1ec2ec2 or eA1eA1ec4ec4 genotypes, suggesting that the expression of two genes was tightly linked. In addition, specific detection methods were developed by high-resolution melting curve analysis in order to detect eA1 and ec4.

关键词： erucic acid fatty acid elongase 1 natural mutation Brassica napus L.

Diversity characterization and association analysis of agronomic traits in a Chinese peanut (Arachis hypogaea L.) mini-core collection

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Journal of Integrative Plant biology 2014年第2期56卷 159-169页

作者： Huifang Jiang Li Huang Xiaoping Ren Yuning Chen Xiaojing Zhou Youlin Xia Jiaquan Huang Yong Lei Liying Yan Liyun Wan Boshou Liao key laboratory of biology and genetic improvement of oil crops Ministry of Agriculture Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences Nanchong Academy of Agricultural Sciences

Association mapping is a powerful approach for exploring the molecular basis of phenotypic variations in plants. A peanut （Arachis hypogaea L.） mini-core collection in China comprising 298 accessions was genotyped using lo9 simple sequence repeat （SSR） markers, which identified 554 SSR alleles and phenotyped for 15 agronomic traits in three different environments, exhibiting abundant genetic and phenotypic diversity within the panel. A model-based structure analysis assigned all accessions to three groups. Most of the accessions had the relative kinship of less than o.05, indicating that there were no or weak relationships between accessions of the mini- core collection. For 15 agronomic traits in the peanut panel, generally the Q ＋ K model exhibited the best performance to eliminate the false associated positives compared to the Q model and the general linear model-simple model. In total, 89 SSR alleles were identified to be associated with 15 agronomic traits of three environments by the Q＋K model-based association analysis. Of these, eight alleles were repeatedly detected in two or three environments, and 15 alleles were commonly detected to be associated with multiple agronomic traits. Simple sequence repeat allelic effects confirmed significant differences between different genotypes of these repeatedly detected markers. Our results demonstrate the great potential of integrating the association analysis and marker-assisted breeding by utilizing the peanut mini-core collection.

关键词： Arachis hypogaea L. association analysis mini-corecollection peanut

Combining Ability and Breeding Potential of Rapeseed Elite Lines for Pod Shatter Resistance

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Journal of Integrative Agriculture 2013年第3期12卷 552-555页

作者： LIU Jia MEI De-sheng LI Yun-chang CUI Jia-cheng WANG Hui PENG Peng-fei FU Li HU Qiong key laboratory of biology and genetic improvement of oil crops Ministry of Agriculture Oil Crops Research Institute Chinese Academy of Agricultural Sciences

Pod shatter resistance of rapeseed is of great importance for modem farming practice. In order to determine the combining ability of elite inbred lines and the breeding potential of rapeseed hybrids in terms of pod shatter resistance, analysis of a 6×6 incomplete diallel cross was conducted at two locations. Results showed that a significant variation existed among breeding lines and their F1 hybrids for pod shatter resistant index （SRI）, pod length and width. Pod shatter resistance was significantly positively correlated with pod length. The general combining ability （GCA） effects （GCA=l.58） played a more important role than specific combining ability （SCA） effects （SCA=0.20） for pod shatter trait. The elite lines R1, 1019B and 1055B displayed significant positive GCA effects for pod shatter resistance. Four crosses （1019B×R1, 1015B×R1, 6098B×R1, and 8908B×R1） with high mean performance and positive SCA effects were recommended for developing new hybrids for mechanical harvest in the middle reaches of the Yangtze River.

关键词： rapeseed pod shatter resistance elite lines breeding potential

Identification of major QTL for seed number per pod on chromosome A05 of tetraploid peanut(Arachis hypogaea L.)

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The Crop Journal 2019年第2期7卷 238-248页

作者： Yuning Chen Zhihui Wang Xiaoping Ren Li Huang Jianbin Guo Jiaojiao Zhao Xiaojing Zhou Liying Yan Huaiyong Luo Nian Liu Weigang Chen Liyun Wan Yong Lei Boshou Liao Dongxin Huai Huifang Jiang oil Crop Research Institute Chinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetic Improvement of Oil CropsMinistry of Agriculture and Rural Affairs

The inheritance of pod-and seed-number traits(PSNT) in peanut(Arachis hypogaea L.) is poorly understood. In the present study, a recombinant inbred line(RIL) population of 188 lines was used to map quantitative trait loci(QTL) for number of seeds per pod(NSP),number of pods per plant(NPP), and numbers of one-, two-, and three-seeded pods per plant(N1 PP, N2 PP, and N3 PP) in four environments. A total of 28 consensus QTL and 14 single QTL were identified, including 11 major and stable QTL. Four major and stable QTL including qN3 PPA5.2, q N3 PPA5.4, qN3 PPA5.5, and qN3 PPA5.7 each explained 12.3%–33.0% of phenotype variation. By use of another integrated linkage map for the A5 group(hereafter referred to as INT A5 group), QTL for PSNT were located in seven intervals of 0.73–9.68 Mb in length on chromosome A05, and candidate genes underlying N3 PP were suggested. These findings shed light on the genetic basis of PSNT. Major QTL for N3 PP could be used as candidates for further positional cloning.

关键词： Peanut Number Pod Seed QTL

Stable major QTL on chromosomes A07 and A08 increase shelling percentage in peanut(Arachis hypogaea L.)

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The Crop Journal 2022年第3期10卷 820-829页

作者： Weitao Li Nian Liu Li Huang Yuning Chen Jianbin Guo Bolun Yu Huaiyong Luo Xiaojing Zhou Dongxin Huai Weigang Chen Liying Yan Xin Wang Yong Lei Boshou Liao Huifang Jiang key laboratory of biology and genetic improvement of oil crops Ministry of Agriculture and Rural AffairsOil Crops Research Institute of the Chinese Academy of Agricultural SciencesWuhan 430062HubeiChina

Peanut is a major oilseed and food *** percentage(SP),closely associated with seed yield,is a trait whose improvement is a major goal of peanut *** this study,a mapping population(Xuhua 13×Zhonghua 6)was used to map quantitative trait loci(QTL)controlling SP in four *** stable major QTL for SP were mapped on both SSR-and SNP-based genetic maps.q SPA07.1 on chromosome A07 explained up to 31.7%of phenotypic variation,and q SPA08.2 on chromosome A08 explained up to 10.8%.Favorable alleles of q SPA07.1 and q SPA08.2 were derived from the female and male parents,*** recombinant inbred lines(RILs)carrying both favorable alleles showed superiority in SP over the two parents in all environmental trials.A combination of the two favorable alleles using the linked markers was verified to increase SP by~5%in the RIL population and by~3%SP in diverse peanut cultivars.q SPA07.1 and q SPA08.2 were delimited to respectively a 0.73-Mb interval harboring 96 genes and a 3.93-Mb interval harboring 238 *** five and eight genes with high expression in pods,including enzymes and transcription factors,were assigned as candidate genes for q SPA07.1 and q *** consistent major QTL provide an opportunity for fine mapping of genes controlling SP,and the linked markers may be useful for genetic improvement of SP in peanut.

关键词： Peanut Shelling percentage QTL mapping Genomic region Candidate genes InDel marker

key genes and mechanisms underlying natural variation of silique length in oilseed rape(Brassica napus L.)germplasm

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The Crop Journal 2022年第3期10卷 617-626页

作者： Quaid Hussain Jiepeng Zhan Huabing Liang Xinfa Wang Guihua Liu Jiaqin Shi Hanzhong Wang oil crops Research Institute of the Chinese Academy of Agricultural Sciences Key Laboratory of Biology and Genetic Improvement of Oil CropsMinistry of Agriculture and Rural AffairsWuhan 430062HubeiChina

Silique length influences seed yield in oilseed *** shows extensive variation in germplasm resources,and identifying the underlying genes and regulatory mechanisms would advance breeding for the *** 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 *** 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 *** analysis showed that silique length variation was due mainly to differences in cell number followed by cell *** 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 *** GWAS,RNA-seq,and functional annotation results revealed 15 candidate genes for the major associated locus q *** these,Bna ***18 and Bna ***78 A9 were validated by haplotype analysis followed by candidate gene *** variation in the coding region of Bna ***18 and expression of Bna ***78 A9 in silique walls were strongly associated with silique *** results provide an explanation for the natural variation of silique length in oilseed rape germplasm and offer useful information for its improvement.

关键词： Brassica napus Silique length GWAS RNA-seq Phytohormones Cell number Cell size Bna A9.ARF18 Bna A9.CYP78A9

Genome editing opens a new era of genetic improvement in polyploid crops

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The Crop Journal 2019年第2期7卷 141-150页

作者： Qamar U.Zaman Chao Li Hongtao Cheng Qiong Hu oil crops Research Institute Chinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetic Improvement of Oil CropsMinistry of Agriculture Graduate School of Chinese Academy of Agricultural Sciences

Sequence-specific nucleases(SSN) that generate double-stranded DNA breaks(DSBs) in genes of interest are the key to site-specific genome editing in plants. Genome editing has developed into one method of reducing undesirable traits in crops by the induction of knockout mutations. Different SSN-mediated genome-editing systems, including LAGLIDADG homing endonucleases or meganucleases, zinc-finger nucleases, transcription activator-like effector nucleases and clustered regularly interspaced short palindromic repeats, are emerging as robust tools for introducing functional mutations in polyploid crops including citrus, wheat, cotton, soybean, rapeseed, potato, grapes, Camelina sativa,dandelion, and tobacco. The approach utilizes knowledge of biological mechanisms for targeted induction of DSBs and their error-prone repair, allowing highly specific changes at designated genome loci. In this review, we briefly describe genome-editing technologies and their application to genetic improvement of polyploid crops.

关键词： Genome editing CRISPR Site-specific mutagenesis Polyploid Crop improvement