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Luo D, Shi L, Sun Z, Qi F, Liu H, Xue L, Li X, Liu H, Qu P, Zhao H, Dai X, Dong W, Zheng Z, Huang B, Fu L, Zhang X. Genome-Wide Association Studies of Embryogenic Callus Induction Rate in Peanut ( Arachis hypogaea L.). Genes (Basel) 2024; 15:160. [PMID: 38397150 PMCID: PMC10887910 DOI: 10.3390/genes15020160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Revised: 01/22/2024] [Accepted: 01/24/2024] [Indexed: 02/25/2024] Open
Abstract
The capability of embryogenic callus induction is a prerequisite for in vitro plant regeneration. However, embryogenic callus induction is strongly genotype-dependent, thus hindering the development of in vitro plant genetic engineering technology. In this study, to examine the genetic variation in embryogenic callus induction rate (CIR) in peanut (Arachis hypogaea L.) at the seventh, eighth, and ninth subcultures (T7, T8, and T9, respectively), we performed genome-wide association studies (GWAS) for CIR in a population of 353 peanut accessions. The coefficient of variation of CIR among the genotypes was high in the T7, T8, and T9 subcultures (33.06%, 34.18%, and 35.54%, respectively), and the average CIR ranged from 1.58 to 1.66. A total of 53 significant single-nucleotide polymorphisms (SNPs) were detected (based on the threshold value -log10(p) = 4.5). Among these SNPs, SNPB03-83801701 showed high phenotypic variance and neared a gene that encodes a peroxisomal ABC transporter 1. SNPA05-94095749, representing a nonsynonymous mutation, was located in the Arahy.MIX90M locus (encoding an auxin response factor 19 protein) at T8, which was associated with callus formation. These results provide guidance for future elucidation of the regulatory mechanism of embryogenic callus induction in peanut.
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Affiliation(s)
- Dandan Luo
- School of Life Sciences, Zhengzhou University, Zhengzhou 450001, China
- Institute of Crop Molecular Breeding, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China
| | - Lei Shi
- Institute of Crop Molecular Breeding, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China
- Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Ministry of Agriculture, Zhengzhou 450002, China
- Henan Provincial Key Laboratory for Oil Crops Improvement, Zhengzhou 450002, China
- The Shennong Laboratory, Zhengzhou 450002, China
| | - Ziqi Sun
- Institute of Crop Molecular Breeding, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China
- Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Ministry of Agriculture, Zhengzhou 450002, China
- Henan Provincial Key Laboratory for Oil Crops Improvement, Zhengzhou 450002, China
- The Shennong Laboratory, Zhengzhou 450002, China
| | - Feiyan Qi
- Institute of Crop Molecular Breeding, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China
- Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Ministry of Agriculture, Zhengzhou 450002, China
- Henan Provincial Key Laboratory for Oil Crops Improvement, Zhengzhou 450002, China
- The Shennong Laboratory, Zhengzhou 450002, China
| | - Hongfei Liu
- Institute of Crop Molecular Breeding, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Lulu Xue
- Institute of Crop Molecular Breeding, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China
| | - Xiaona Li
- Institute of Crop Molecular Breeding, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Han Liu
- Institute of Crop Molecular Breeding, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Pengyu Qu
- School of Life Sciences, Zhengzhou University, Zhengzhou 450001, China
- Institute of Crop Molecular Breeding, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China
| | - Huanhuan Zhao
- Institute of Crop Molecular Breeding, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China
| | - Xiaodong Dai
- Institute of Crop Molecular Breeding, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China
- Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Ministry of Agriculture, Zhengzhou 450002, China
- Henan Provincial Key Laboratory for Oil Crops Improvement, Zhengzhou 450002, China
| | - Wenzhao Dong
- Institute of Crop Molecular Breeding, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China
- Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Ministry of Agriculture, Zhengzhou 450002, China
- Henan Provincial Key Laboratory for Oil Crops Improvement, Zhengzhou 450002, China
| | - Zheng Zheng
- Institute of Crop Molecular Breeding, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China
- Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Ministry of Agriculture, Zhengzhou 450002, China
- Henan Provincial Key Laboratory for Oil Crops Improvement, Zhengzhou 450002, China
| | - Bingyan Huang
- Institute of Crop Molecular Breeding, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China
- Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Ministry of Agriculture, Zhengzhou 450002, China
- Henan Provincial Key Laboratory for Oil Crops Improvement, Zhengzhou 450002, China
| | - Liuyang Fu
- School of Life Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Xinyou Zhang
- Institute of Crop Molecular Breeding, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China
- Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Ministry of Agriculture, Zhengzhou 450002, China
- Henan Provincial Key Laboratory for Oil Crops Improvement, Zhengzhou 450002, China
- The Shennong Laboratory, Zhengzhou 450002, China
- National Innovation Center for Bio-Breeding Industry, Xinxiang 453500, China
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Huang C, Zhang J, Zhou D, Huang Y, Su L, Yang G, Luo W, Chen Z, Wang H, Guo T. Identification and candidate gene screening of qCIR9.1, a novel QTL associated with anther culturability in rice (Oryza sativa L.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2021; 134:2097-2111. [PMID: 33713337 DOI: 10.1007/s00122-021-03808-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Accepted: 02/27/2021] [Indexed: 06/12/2023]
Abstract
A novel QTL, qCIR9.1, that controls callus induction rate in anther culture was identified on chromosome 9 in rice, and based on RNA-seq data, Os09g0551600 was the most promising candidate gene. Anther culture, a doubled haploid (DH) technique, has become an important technology in many plant-breeding programmes. Although anther culturability is the key factor in this technique, its genetic mechanisms in rice remain poorly understood. In this study, we mapped quantitative trait loci (QTLs) responsible for anther culturability by using 192 recombinant inbred lines (RILs) derived from YZX (Oryza sativa ssp. indica) × 02428 (Oryza sativa ssp. japonica) and a high-density bin map. A total of eight QTLs for anther culturability were detected in three environments. Among these QTLs, a novel major QTL for callus induction rate (CIR) named qCIR9.1 was repeatedly mapped to a ~ 100 kb genomic interval on chromosome 9 and explained 8.39-14.14% of the phenotypic variation. Additionally, RNA sequencing (RNA-seq) was performed for the parents (YZX and 02428), low- (L-Pool) and high-CIR RILs (H-Pool) after 16 and 26 days of culture. By using the RNA of the bulked RILs for background normalization, the number of differentially expressed genes (DEGs) both between the parents and between the bulked RILs after 26 days of culture was drastically reduced to only 78. Among these DEGs, only one gene, Os09g0551600, encoding a high-mobility group (HMG) protein, was located in the candidate region of qCIR9.1. qRT-PCR analysis of Os09g0551600 showed the same results as RNA-seq, and the expression of this gene was decreased in the low-callus-induction parent (YZX) and L-Pool. Our results provide a foundational step for further cloning of qCIR9.1 and will be very useful for improving anther culturability in rice.
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Affiliation(s)
- Cuihong Huang
- National Engineering Research Center of Plant Space Breeding, South China Agricultural University, Guangzhou, 510642, People's Republic of China
| | - Jian Zhang
- National Engineering Research Center of Plant Space Breeding, South China Agricultural University, Guangzhou, 510642, People's Republic of China
| | - Danhua Zhou
- National Engineering Research Center of Plant Space Breeding, South China Agricultural University, Guangzhou, 510642, People's Republic of China
| | - Yuting Huang
- National Engineering Research Center of Plant Space Breeding, South China Agricultural University, Guangzhou, 510642, People's Republic of China
| | - Ling Su
- National Engineering Research Center of Plant Space Breeding, South China Agricultural University, Guangzhou, 510642, People's Republic of China
| | - Guili Yang
- National Engineering Research Center of Plant Space Breeding, South China Agricultural University, Guangzhou, 510642, People's Republic of China
| | - Wenlong Luo
- Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, People's Republic of China
| | - Zhiqiang Chen
- National Engineering Research Center of Plant Space Breeding, South China Agricultural University, Guangzhou, 510642, People's Republic of China
| | - Hui Wang
- National Engineering Research Center of Plant Space Breeding, South China Agricultural University, Guangzhou, 510642, People's Republic of China.
| | - Tao Guo
- National Engineering Research Center of Plant Space Breeding, South China Agricultural University, Guangzhou, 510642, People's Republic of China.
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Abd El-Fatah BES, Sayed MA, El-Sanusy SA. Genetic analysis of anther culture response and identification of QTLs associated with response traits in wheat (Triticum aestivum L.). Mol Biol Rep 2020; 47:9289-9300. [PMID: 33230785 DOI: 10.1007/s11033-020-06007-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Accepted: 11/16/2020] [Indexed: 10/22/2022]
Abstract
Anther culture is the most effective tool for doubled haploid production of wheat. This investigation was conducted to estimate genetic parameters of anther culture response in wheat and identification of putative Quantitative trait loci (QTLs) associated with response traits. Two varieties of wheat, namely ICR-DH (P1) and Sle 1 × 15 (P2) and their F1 and F2 progenies were used in the present investigation to estimate genetic parameters of anther culture response. Two molecular marker systems, SRAP and SSR markers were used to detect the polymorphism between two anther donor parents. Single marker analysis (SMA) and Composite interval mapping (CIM) were used to localize the putative QTL associated with four anther culture response in wheat using 100 plants of F2 population derived from F1 cross 'ICR-DH' × 'Sel 1 × 15'. Analyses of variance indicated significant differences between four populations (P1, P2, F1 and F2) for callus induction (CAL), number of green plants per 100 anther (GR), number of albino plant per 100 anther (AR) and total regenerated plants per 100 anther (TR). The additive effects were more important than dominance effects in controlling these traits. The two molecular marker systems were sufficient in detecting polymorphism between two parents. Thirty two putative QTLs were detected on eight linkage groups. Our study indicated that the additive effects of genes and detection of new QTLs permit marker-assisted selection of genotypes with high green plantlet regeneration efficiency in anther culture, and therefore favor efficient use of anther culture in wheat breeding programs.
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Affiliation(s)
- Bahaa E S Abd El-Fatah
- Department of Genetics, Faculty of Agriculture, Assiut University, Assiut, 71526, Egypt.
| | - Mohammed A Sayed
- Department of Agronomy, Faculty of Agriculture, Assiut University, Assiut, 71526, Egypt
| | - Sahar A El-Sanusy
- Department of Genetics, Faculty of Agriculture, Assiut University, Assiut, 71526, Egypt
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Natural Variation in Plant Pluripotency and Regeneration. PLANTS 2020; 9:plants9101261. [PMID: 32987766 PMCID: PMC7598583 DOI: 10.3390/plants9101261] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Revised: 09/03/2020] [Accepted: 09/21/2020] [Indexed: 12/14/2022]
Abstract
Plant regeneration is essential for survival upon wounding and is, hence, considered to be a strong natural selective trait. The capacity of plant tissues to regenerate in vitro, however, varies substantially between and within species and depends on the applied incubation conditions. Insight into the genetic factors underlying this variation may help to improve numerous biotechnological applications that exploit in vitro regeneration. Here, we review the state of the art on the molecular framework of de novo shoot organogenesis from root explants in Arabidopsis, which is a complex process controlled by multiple quantitative trait loci of various effect sizes. Two types of factors are distinguished that contribute to natural regenerative variation: master regulators that are conserved in all experimental systems (e.g., WUSCHEL and related homeobox genes) and conditional regulators whose relative role depends on the explant and the incubation settings. We further elaborate on epigenetic variation and protocol variables that likely contribute to differential explant responsivity within species and conclude that in vitro shoot organogenesis occurs at the intersection between (epi) genetics, endogenous hormone levels, and environmental influences.
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Kim K, Kang Y, Lee SJ, Choi SH, Jeon DH, Park MY, Park S, Lim YP, Kim C. Quantitative Trait Loci (QTLs) Associated with Microspore Culture in Raphanus sativus L. (Radish). Genes (Basel) 2020; 11:genes11030337. [PMID: 32245207 PMCID: PMC7141118 DOI: 10.3390/genes11030337] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Revised: 03/19/2020] [Accepted: 03/20/2020] [Indexed: 11/25/2022] Open
Abstract
The radish is a highly self-incompatible plant, and consequently it is difficult to produce homozygous lines. Bud pollination in cross-fertilization plants should be done by opening immature pollen and attaching pollen to mature flowers. It accordingly takes a lot of time and effort to develop lines with fixed alleles. In the current study, a haploid breeding method has been applied to obtain homozygous plants in a short period of time by doubling chromosomes through the induction of a plant body in the haploid cells, in order to shorten the time to breed inbred lines. We constructed genetic maps with an F1 population derived by crossing parents that show a superior and inferior ability to regenerate microspores, respectively. Genetic maps were constructed from the maternal and parental maps, separately, using the two-way pseudo-testcross model. The phenotype of the regeneration rate was examined by microspore cultures and a quantitative trait loci (QTL) analysis was performed based on the regeneration rate. From the results of the culture of microspores in the F1 population, more than half of the group did not regenerate, and only a few showed a high regeneration rate. A total of five significant QTLs were detected in the F1 population, and five candidate genes were found based on the results. These candidate genes are divided into two classes, and appear to be related to either PRC2 subunits or auxin synthesis.
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Affiliation(s)
- Kyeongmin Kim
- Department of Crop Science, College of Agricultural and Life Sciences, Chungnam National University, Daejeon 34134, Korea; (K.K.); (Y.K.); (S.-J.L.); (S.-H.C.); (D.-H.J.)
| | - Yuna Kang
- Department of Crop Science, College of Agricultural and Life Sciences, Chungnam National University, Daejeon 34134, Korea; (K.K.); (Y.K.); (S.-J.L.); (S.-H.C.); (D.-H.J.)
| | - Sol-Ji Lee
- Department of Crop Science, College of Agricultural and Life Sciences, Chungnam National University, Daejeon 34134, Korea; (K.K.); (Y.K.); (S.-J.L.); (S.-H.C.); (D.-H.J.)
| | - Se-Hyun Choi
- Department of Crop Science, College of Agricultural and Life Sciences, Chungnam National University, Daejeon 34134, Korea; (K.K.); (Y.K.); (S.-J.L.); (S.-H.C.); (D.-H.J.)
| | - Dong-Hyun Jeon
- Department of Crop Science, College of Agricultural and Life Sciences, Chungnam National University, Daejeon 34134, Korea; (K.K.); (Y.K.); (S.-J.L.); (S.-H.C.); (D.-H.J.)
| | - Min-Young Park
- National Institute of Horticultural & Herbal Science, Rural Development Administration (RDA), Wanju 55365, Korea; (M.-Y.P.); (S.P.)
| | - Suhyoung Park
- National Institute of Horticultural & Herbal Science, Rural Development Administration (RDA), Wanju 55365, Korea; (M.-Y.P.); (S.P.)
| | - Yong Pyo Lim
- Department of Horticultural Science, College of Agricultural and Life Sciences, Chungnam National University, Daejeon 34134, Korea;
| | - Changsoo Kim
- Department of Crop Science, College of Agricultural and Life Sciences, Chungnam National University, Daejeon 34134, Korea; (K.K.); (Y.K.); (S.-J.L.); (S.-H.C.); (D.-H.J.)
- Department of Smart Agriculture Systems, College of Agricultural and Life Sciences, Chungnam National University, Daejeon 34134, Korea
- Correspondence: ; Tel.: +82-42-821-5729
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Li SN, Cheng P, Bai YQ, Shi Y, Yu JY, Li RC, Zhou RN, Zhang ZG, Wu XX, Chen QS. Analysis of Soybean Somatic Embryogenesis Using Chromosome Segment Substitution Lines and Transcriptome Sequencing. Genes (Basel) 2019; 10:E943. [PMID: 31752416 PMCID: PMC6896167 DOI: 10.3390/genes10110943] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2019] [Revised: 11/05/2019] [Accepted: 11/18/2019] [Indexed: 12/15/2022] Open
Abstract
Soybean is an important cash crop that is widely used as a source of vegetable protein and edible oil. The regeneration ability of soybean directly affects the application of biotechnology. In this study, we used the exogenous hormone 2,4-D to treat immature embryos. Different levels of somatic incidence were selected from the chromosome segment substitution lines (CSSLs) constructed by SN14 and ZYD00006. Transcriptome sequencing of extreme materials was performed, and 2666 differentially expressed genes were obtained. At the same time, a difference table was generated by combining the data on CSSL rearrangement. In the extreme materials, a total of 93 differentially expressed genes were predicted and were then analyzed by cluster analysis and Gene Ontology (GO) annotation. After screening and annotating the target genes, three differentially expressed genes with hormone pathways were identified. The expression patterns of the target genes were verified by real-time quantitative PCR (qRT-PCR). Haplotype polymorphism detection and linkage disequilibrium analysis were performed on the candidate gene Glyma.09g248200. This study provided more information on the regulation network of soybean somatic embryogenesis and regeneration processes, and further identified important genes in the soybean regeneration process and provided a theoretical basis for accelerating the application of biotechnology to soybean for improving its breeding efficiency.
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Affiliation(s)
| | | | | | | | | | | | | | - Zhan-Guo Zhang
- College of Agriculture, Northeast Agricultural University, Harbin 150030, Heilongjiang, China; (S.-N.L.); (P.C.); (Y.-Q.B.); (Y.S.); (J.-Y.Y.); (R.-C.L.); (R.-N.Z.)
| | - Xiao-Xia Wu
- College of Agriculture, Northeast Agricultural University, Harbin 150030, Heilongjiang, China; (S.-N.L.); (P.C.); (Y.-Q.B.); (Y.S.); (J.-Y.Y.); (R.-C.L.); (R.-N.Z.)
| | - Qing-Shan Chen
- College of Agriculture, Northeast Agricultural University, Harbin 150030, Heilongjiang, China; (S.-N.L.); (P.C.); (Y.-Q.B.); (Y.S.); (J.-Y.Y.); (R.-C.L.); (R.-N.Z.)
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