Xiaojing Zhou

Zhejiang Chinese Medical University

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Boshou Liao

National Institutes for Food and Drug Control

Huifang Jiang

Tongde Hospital of Zhejiang Province

Yong Lei

Oil Crops Research Institute

Yuning Chen

Oil Crops Research Institute

Li Huang

Harbin Veterinary Research Institute

Huaiyong Luo

Chinese Academy of Agricultural Sciences

Nian Liu

Chinese Academy of Agricultural Sciences

Weigang Chen

Shihezi University

Manish K. Pandey

International Crops Research Institute for the Semi-Arid Tropics

Rajeev K. Varshney

Murdoch University

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Chinese Academy of Agricultural Sciences

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Oil Crops Research Institute

Ministry of Agriculture and Rural Affairs

Heilongjiang Bayi Agricultural University

Huazhong Agricultural University

Chinese Academy of Sciences

Nanjing University

Zhejiang University

Central South University

Sichuan University

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Additional file 3: Table S3. of Genomic survey sequencing for development and validation of single-locus SSR markers in peanut (Arachis hypogaea L.)

Figshare (2016)

Xiaojing Zhou Yang Dong Jiaojiao Zhao Huang Li Xiaoping Ren

List of 96 A. hypogaea accessions used in this study. The table includes information about locality, accession code, subspecies and varieties. The ICRISAT codes, which can correspond to the accession code in the National Medium-term Peanut Genebank of China, are presented in parentheses. (XLSX 12Â kb)

Arachis hypogaea

Table (database)

10.6084/m9.figshare.c.3632819_d4

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Citations (0)

Safe conservation and utilization of peanut germplasm resources in the Oil Crops Middle-term Genebank of China

Oil Crop Science (2022)

Xiaojing Zhou Xiaoping Ren Huaiyong Luo Li Huang Nian Liu

Peanut (Arachis hypogaea L.) is an important oil and cash crop in the world. Peanut germplasm collected in China are abundant, which provides important material guarantee for peanut breeding and industrial development. Here, the safe conservation technology and indicators of peanut germplasm resources in the Oil Crops Middle-term Genebank of China were expounded from three processes of storage, monitoring, reproduction and renewal. We summarized and reviewed the situation of conservation and utilization of peanut germplasm resources in the Middle-term Genebank in the past 20 years. The future research direction of peanut resources in the Oil Crops Middle-term Genebank of China is prospected.

Germ plasm

Arachis hypogaea

Cash crop

Genetic Resources

10.1016/j.ocsci.2021.12.001

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Citations (12)

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

The Crop Journal (2019)

Yuning Chen Zhihui Wang Xiaoping Ren Li Huang Jianbin Guo

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 (N1PP, N2PP, and N3PP) 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 qN3PPA5.2, qN3PPA5.4, qN3PPA5.5, and qN3PPA5.7 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 N3PP were suggested. These findings shed light on the genetic basis of PSNT. Major QTL for N3PP could be used as candidates for further positional cloning.

Arachis hypogaea

Arachis

10.1016/j.cj.2018.09.002

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Citations (14)

Dissection of the Genetic Basis of Yield-Related Traits in the Chinese Peanut Mini-Core Collection Through Genome-Wide Association Studies

Frontiers in Plant Science (2021)

Xiaojing Zhou Jianbin Guo Manish K. Pandey Rajeev K. Varshney Li Huang

Peanut is an important legume crop worldwide. To uncover the genetic basis of yield features and assist breeding in the future, we conducted genome-wide association studies (GWAS) for six yield-related traits of the Chinese peanut mini-core collection. The seed (pod) size and weight of the population were investigated under four different environments, and these traits showed highly positive correlations in pairwise combinations. We sequenced the Chinese peanut mini-core collection using genotyping-by-sequencing approach and identified 105,814 high-quality single-nucleotide polymorphisms (SNPs). The population structure analysis showed essentially subspecies patterns in groups and obvious geographical distribution patterns in subgroups. A total of 79 significantly associated loci ( P < 4.73 × 10 –7 ) were detected for the six yield-related traits through GWAS. Of these, 31 associations were consistently detected in multiple environments, and 15 loci were commonly detected to be associated with multiple traits. Two major loci located on chromosomal pseudomolecules A06 and A02 showed pleiotropic effects on yield-related traits, explaining ∼20% phenotypic variations across environments. The two genomic regions were found 46 putative candidate genes based on gene annotation and expression profile. The diagnostic marker for the yield-related traits from non-synonymous SNP (Aradu-A06-107901527) was successfully validated, achieving a high correlation between nucleotide polymorphism and phenotypic variation. This study provided insights into the genetic basis of yield-related traits in peanut and verified one diagnostic marker to facilitate marker-assisted selection for developing high-yield peanut varieties.

Genome-wide Association Study

Genetic Association

10.3389/fpls.2021.637284

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High-Density Genetic Linkage Map Construction Using Whole-Genome Resequencing for Mapping Qtls of Resistance to Aspergillus Flavus Infection in Peanut

Research Square (Research Square) (2021)

Yifei Jiang Huaiyong Luo Bolun Yu Yingbin Ding Yanping Kang

Abstract Cultivated peanut ( Arachis hypogaea L.) is rich in edible oil and protein, which is widely planted around the world as an oil and cash crop. However, aflatoxin contamination seriously affects the quality safety of peanut, hindering the development of peanut industry and threatening consumers’ health. Breeding peanut varieties with resistance to Aspergillus flavus infection is important for control the aflatoxin contamination, and understanding of the genetic basis of resistance is vital to its genetic enhancement. In this study, we report the QTL mapping of resistance to A. flavus infection of a well-known resistant variety J11. A recombination inbred line (RIL) population was constructed by crossing a susceptible variety Zhonghua 16 and J11. Through whole-genome resequencing, a genetic linkage map was constructed with 2,802 recombination bins and an average inter-bin distance of 0.58 cM. Combined with phenotypic data of infection index in four consecutive years, six novel resistant QTLs were identified and they explained 5.03-10.87% phenotypic variances. The favorable alleles of five QTLs were from J11 while that of one QTL were from Zhonghua 16. The pyramiding of these favorable alleles significantly improved the resistance to A. flavus infection. These results could contribute greatly to understanding of genetic basis of A. flavus resistance and could be meaningful in further resistance improvement in peanut.

Genetic linkage

10.21203/rs.3.rs-538664/v1

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Design and synthesis of 2-styryl of 5-Nitroimidazole derivatives and antimicrobial activities as FabH inhibitors

European Journal of Medicinal Chemistry (2014)

Yongtao Duan Zhong‐Chang Wang Ya-Li Sang Xiang-Xiang Tao Shashikant B. Teraiya

Bacillus thuringiensis

Docking (animal)

10.1016/j.ejmech.2014.02.004

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Characterization of genomic imprinting effects and patterns with parametric accelerated failure time model

Molecular Genetics and Genomics (2011)

Xiaojing Zhou Ming Fang Jiahan Li Daniel R. Prows Runqing Yang

Genomic Imprinting

Imprinting (psychology)

10.1007/s00438-011-0661-9

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Construction of a high-quality genomic BAC library for Chinese peanut cultivar Zhonghua 8 with high oil content

Botanical studies (2014)

Yuning Chen Wenhui Wei Xiaoping Ren Xueya Zhao Xiaojing Zhou

Arachis hypogaea L. (2n = 4× = 40, AABB) is one of the most important oil and economic crop plants in the word. This species has the largest genome size of about 2,813 Mb among the oil crop species. Zhonghua 8 is a peanut cultivar planted widely in central China and has several superior traits including high oil content, high yield and disease resistance. A high-quality BAC library of Zhonghua 8 was constructed for future researches on the genomics of Chinese peanut cultivars.A Hin d III-digested genomic BAC (bacterial artificial chromosome) library was constructed with the genomic DNA from leaves of Zhonghua 8. This BAC library consists of 160,512 clones and the average insert is estimated about 102 kb ranging from 30 to 150 kb. The library represents about 5.55× haploid genome equivalents, and provides a 99.71% probability of finding specific genes. The empty-vector rate is under 5 percent detected from 200 randomly selected clones. Probing of 384 clones with the psbA gene of barley chloroplast and the atp6 gene of rice mitochondrion indicated that the contamination with organellar DNA is insignificant. Successive subculture of three clones showed that the inserts are stable in one hundred generations.This study presented the construction of a high-quality BAC library for the genome of Chinese cultivated peanut. Many essential experiences were summarized in the present study. This BAC library can serve as a substantial platform for development of molecular marker, isolation of genes and further genome research.

10.1186/1999-3110-55-8

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High-resolution mapping of a major and consensus quantitative trait locus for oil content to a ~ 0.8-Mb region on chromosome A08 in peanut (Arachis hypogaea L.)

Theoretical and Applied Genetics (2019)

Nian Liu Jianbin Guo Xiaojing Zhou Bei Wu Li Huang

Key message ddRAD-seq-based high-density genetic map comprising 2595 loci identified a major and consensus QTL with a linked marker in a 0.8-Mb physical interval for oil content in peanut. Abstract Enhancing oil content is an important breeding objective in peanut. High-resolution mapping of quantitative trait loci (QTLs) with linked markers could facilitate marker-assisted selection in breeding for target traits. In the present study, a recombined inbred line population (Xuhua 13 × Zhonghua 6) was used to construct a genetic map based on double-digest restriction-site-associated DNA sequencing (ddRAD-seq). The resulting high-density genetic map contained 2595 loci, and spanned a length of 2465.62 cM, with an average distance of 0.95 cM/locus. Seven QTLs for oil content were identified on five linkage groups, including the major and stable QTL qOCA08.1 on chromosome A08 with 10.14–27.19% phenotypic variation explained. The physical interval of qOCA08.1 was further delimited to a ~ 0.8-Mb genomic region where two genes affecting oil synthesis had been annotated. The marker SNPOCA08 was developed targeting the SNP loci associated with oil content and validated in peanut cultivars with diverse oil contents. The major and stable QTL identified in the present study could be further dissected for gene discovery. Furthermore, the tightly linked marker for oil content would be useful in marker-assisted breeding in peanut.

Genetic linkage

Candidate gene

10.1007/s00122-019-03438-6

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Citations (50)

Genetic dissection of fatty acid components in the Chinese peanut (Arachis hypogaea L.) mini-core collection under multi-environments

PLoS ONE (2022)

Xiaojing Zhou Huaiyong Luo Bolun Yu Li Huang Nian Liu

Peanut ( Arachis hypogaea L.) is an important source of edible oil and protein for human nutrition. The quality of peanut seed oil is mainly determined by the composition of fatty acids, especially the contents of oleic acid and linoleic acid. Improving the composition of fatty acids in the seed oil is one of the main objectives for peanut breeding globally. To uncover the genetic basis of fatty acids and broaden the genetic variation in future peanut breeding programs, this study used genome-wide association studies (GWAS) to identify loci associated with target traits and developed diagnostic marker. The contents of eight fatty acid components of the Chinese peanut mini-core collection were measured under four environments. Using the phenotypic information and over one hundred thousand single nucleotide polymorphisms (SNPs), GWAS were conducted to investigate the genetics basis of fatty acids under multi-environments. Overall, 75 SNPs were identified significant trait associations with fatty acid components. Nineteen associations were repeatedly identified in multiple environments, and 13 loci were co-associated with two or three traits. Three stable major associated loci were identified, including two loci for oleic acid and linoleic acid on chromosome A09 [mean phenotypic variation explained (PVE): 38.5%, 10.35%] and one for stearic acid on B06 (mean PVE: 23%). According to functional annotations, 21 putative candidate genes related to fatty acid biosynthesis were found underlying the three associations. The allelic effect of SNP A09-114690064 showed that the base variation was highly correlated with the phenotypic variation of oleic acid and linoleic acid contents, and a cost-effective Kompetitive allele-Specific PCR (KASP) diagnostic marker was developed. Furthermore, the SNP A09-114690064 was found to change the cis-element CAAT (-) in the promoter of ahFAD2A to YACT (+), leading dozens of times higher expression level. The enhancer-like activity of ahFAD2A promoter was identified that was valuable for enriching the regulation mechanism of ahFAD2A . This study improved our understanding on the genetic architecture of fatty acid components in peanut, and the new effective diagnostic marker would be useful for marker-assisted selection of high-oleic peanut breeding.

Arachis hypogaea

Arachis

10.1371/journal.pone.0279650

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Citations (8)