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Zhou X, Guo J, Pandey MK, Varshney RK, Huang L, Luo H, Liu N, Chen W, Lei Y, Liao B, Jiang H. 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; 12:637284. [PMID: 34093605 PMCID: PMC8174301 DOI: 10.3389/fpls.2021.637284] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Accepted: 03/24/2021] [Indexed: 06/09/2023]
Abstract
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.
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Affiliation(s)
- Xiaojing Zhou
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Jianbin Guo
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Manish K. Pandey
- Center of Excellence in Genomics & Systems Biology, International Crops Research Institute for the Semi-Arid Tropics, Hyderabad, India
| | - Rajeev K. Varshney
- Center of Excellence in Genomics & Systems Biology, International Crops Research Institute for the Semi-Arid Tropics, Hyderabad, India
| | - Li Huang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Huaiyong Luo
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Nian Liu
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Weigang Chen
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Yong Lei
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - 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, Wuhan, China
| | - Huifang Jiang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
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Zeng D, Teixeira da Silva JA, Zhang M, Yu Z, Si C, Zhao C, Dai G, He C, Duan J. Genome-Wide Identification and Analysis of the APETALA2 (AP2) Transcription Factor in Dendrobium officinale. Int J Mol Sci 2021; 22:5221. [PMID: 34069261 PMCID: PMC8156592 DOI: 10.3390/ijms22105221] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 05/09/2021] [Accepted: 05/11/2021] [Indexed: 11/17/2022] Open
Abstract
The APETALA2 (AP2) transcription factors (TFs) play crucial roles in regulating development in plants. However, a comprehensive analysis of the AP2 family members in a valuable Chinese herbal orchid, Dendrobium officinale, or in other orchids, is limited. In this study, the 14 DoAP2 TFs that were identified from the D. officinale genome and named DoAP2-1 to DoAP2-14 were divided into three clades: euAP2, euANT, and basalANT. The promoters of all DoAP2 genes contained cis-regulatory elements related to plant development and also responsive to plant hormones and stress. qRT-PCR analysis showed the abundant expression of DoAP2-2, DoAP2-5, DoAP2-7, DoAP2-8 and DoAP2-12 genes in protocorm-like bodies (PLBs), while DoAP2-3, DoAP2-4, DoAP2-6, DoAP2-9, DoAP2-10 and DoAP2-11 expression was strong in plantlets. In addition, the expression of some DoAP2 genes was down-regulated during flower development. These results suggest that DoAP2 genes may play roles in plant regeneration and flower development in D. officinale. Four DoAP2 genes (DoAP2-1 from euAP2, DoAP2-2 from euANT, and DoAP2-6 and DoAP2-11 from basal ANT) were selected for further analyses. The transcriptional activation of DoAP2-1, DoAP2-2, DoAP2-6 and DoAP2-11 proteins, which were localized in the nucleus of Arabidopsis thaliana mesophyll protoplasts, was further analyzed by a dual-luciferase reporter gene system in Nicotiana benthamiana leaves. Our data showed that pBD-DoAP2-1, pBD-DoAP2-2, pBD-DoAP2-6 and pBD-DoAP2-11 significantly repressed the expression of the LUC reporter compared with the negative control (pBD), suggesting that these DoAP2 proteins may act as transcriptional repressors in the nucleus of plant cells. Our findings on AP2 genes in D. officinale shed light on the function of AP2 genes in this orchid and other plant species.
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Affiliation(s)
- Danqi Zeng
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China; (D.Z.); (M.Z.); (Z.Y.); (C.S.); (C.Z.)
- College of Life Sciences, University of the Chinese Academy of Sciences, No. 19A Yuquan Road, Shijingshan District, Beijing 100049, China
| | | | - Mingze Zhang
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China; (D.Z.); (M.Z.); (Z.Y.); (C.S.); (C.Z.)
- College of Life Sciences, University of the Chinese Academy of Sciences, No. 19A Yuquan Road, Shijingshan District, Beijing 100049, China
| | - Zhenming Yu
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China; (D.Z.); (M.Z.); (Z.Y.); (C.S.); (C.Z.)
| | - Can Si
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China; (D.Z.); (M.Z.); (Z.Y.); (C.S.); (C.Z.)
| | - Conghui Zhao
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China; (D.Z.); (M.Z.); (Z.Y.); (C.S.); (C.Z.)
- College of Life Sciences, University of the Chinese Academy of Sciences, No. 19A Yuquan Road, Shijingshan District, Beijing 100049, China
| | - Guangyi Dai
- Opening Public Laboratory, Chinese Academy of Sciences, Guangzhou 510650, China;
| | - Chunmei He
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China; (D.Z.); (M.Z.); (Z.Y.); (C.S.); (C.Z.)
| | - Juan Duan
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China; (D.Z.); (M.Z.); (Z.Y.); (C.S.); (C.Z.)
- Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Guangzhou 510650, China
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Wang Y, Wang J, Guo S, Tian S, Zhang J, Ren Y, Li M, Gong G, Zhang H, Xu Y. CRISPR/Cas9-mediated mutagenesis of ClBG1 decreased seed size and promoted seed germination in watermelon. HORTICULTURE RESEARCH 2021; 8:70. [PMID: 33790265 PMCID: PMC8012358 DOI: 10.1038/s41438-021-00506-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 12/29/2020] [Accepted: 01/03/2021] [Indexed: 05/11/2023]
Abstract
Abscisic acid (ABA) is a critical regulator of seed development and germination. β-glucosidases (BGs) have been suggested to be contributors to increased ABA content because they catalyze the hydrolysis of ABA-glucose ester to release free ABA. However, whether BGs are involved in seed development is unclear. In this study, a candidate gene, ClBG1, in watermelon was selected for targeted mutagenesis via the CRISPR/Cas9 system. Seed size and weight were significantly reduced in the Clbg1-mutant watermelon lines, which was mainly attributed to decreased cell number resulting from decreased ABA levels. A transcriptome analysis showed that the expression of 1015 and 1429 unique genes was changed 10 and 18 days after pollination (DAP), respectively. Cytoskeleton- and cell cycle-related genes were enriched in the differentially expressed genes of wild type and Clbg1-mutant lines during seed development. Moreover, the expression of genes in the major signaling pathways of seed size control was also changed. In addition, seed germination was promoted in the Clbg1-mutant lines due to decreased ABA content. These results indicate that ClBG1 may be critical for watermelon seed size regulation and germination mainly through the modulation of ABA content and thereby the transcriptional regulation of cytoskeleton-, cell cycle- and signaling-related genes. Our results lay a foundation for dissecting the molecular mechanisms of controlling watermelon seed size, a key agricultural trait of significant economic importance.
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Affiliation(s)
- Yanping Wang
- National Watermelon and Melon Improvement Center, Beijing Academy of Agricultural and Forestry Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing, 100097, China
| | - Jinfang Wang
- National Watermelon and Melon Improvement Center, Beijing Academy of Agricultural and Forestry Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing, 100097, China
| | - Shaogui Guo
- National Watermelon and Melon Improvement Center, Beijing Academy of Agricultural and Forestry Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing, 100097, China
| | - Shouwei Tian
- National Watermelon and Melon Improvement Center, Beijing Academy of Agricultural and Forestry Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing, 100097, China
| | - Jie Zhang
- National Watermelon and Melon Improvement Center, Beijing Academy of Agricultural and Forestry Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing, 100097, China
| | - Yi Ren
- National Watermelon and Melon Improvement Center, Beijing Academy of Agricultural and Forestry Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing, 100097, China
| | - Maoying Li
- National Watermelon and Melon Improvement Center, Beijing Academy of Agricultural and Forestry Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing, 100097, China
| | - Guoyi Gong
- National Watermelon and Melon Improvement Center, Beijing Academy of Agricultural and Forestry Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing, 100097, China
| | - Haiying Zhang
- National Watermelon and Melon Improvement Center, Beijing Academy of Agricultural and Forestry Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing, 100097, China
| | - Yong Xu
- National Watermelon and Melon Improvement Center, Beijing Academy of Agricultural and Forestry Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing, 100097, China.
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Riaz MW, Lu J, Shah L, Yang L, Chen C, Mei XD, Xue L, Manzoor MA, Abdullah M, Rehman S, Si H, Ma C. Expansion and Molecular Characterization of AP2/ERF Gene Family in Wheat ( Triticum aestivum L.). Front Genet 2021; 12:632155. [PMID: 33868370 PMCID: PMC8044323 DOI: 10.3389/fgene.2021.632155] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Accepted: 02/04/2021] [Indexed: 01/02/2023] Open
Abstract
The AP2/ERF is a large protein family of transcription factors, playing an important role in signal transduction, plant growth, development, and response to various stresses. AP2/ERF super-family is identified and functionalized in a different plant but no comprehensive and systematic analysis in wheat (Triticum aestivum L.) has been reported. However, a genome-wide and functional analysis was performed and identified 322 TaAP2/ERF putative genes from the wheat genome. According to the phylogenetic and structural analysis, TaAP2/ERF genes were divided into 12 subfamilies (Ia, Ib, Ic, IIa, IIb, IIc, IIIa, IIIb, IIIc, IVa, IVb, and IVc). Furthermore, conserved motifs and introns/exons analysis revealed may lead to functional divergence within clades. Cis-Acting analysis indicated that many elements were involved in stress-related and plant development. Chromosomal location showed that 320 AP2/ERF genes were distributed among 21 chromosomes and 2 genes were present in a scaffold. Interspecies microsynteny analysis revealed that maximum orthologous between Arabidopsis, rice followed by wheat. Segment duplication events have contributed to the expansion of the AP2/ERF family and made this family larger than rice and Arabidopsis. Additionally, AP2/ERF genes were differentially expressed in wheat seedlings under the stress treatments of heat, salt, and drought, and expression profiles were verified by qRT-PCR. Remarkably, the RNA-seq data exposed that AP2/ERF gene family might play a vital role in stress-related. Taken together, our findings provided useful and helpful information to understand the molecular mechanism and evolution of the AP2/ERF gene family in wheat.
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Affiliation(s)
- Muhammad Waheed Riaz
- College of Agronomy, Anhui Agricultural University, Hefei, China.,Key Laboratory of Wheat Biology and Genetic Improvement on Southern Yellow & Huai River Valley, Ministry of Agriculture and Rural Affairs, Hefei, China
| | - Jie Lu
- College of Agronomy, Anhui Agricultural University, Hefei, China.,Key Laboratory of Wheat Biology and Genetic Improvement on Southern Yellow & Huai River Valley, Ministry of Agriculture and Rural Affairs, Hefei, China
| | - Liaqat Shah
- Department of Botany, Mir Chakar Khan Rind University, Sibi, Pakistan
| | - Liu Yang
- College of Agronomy, Anhui Agricultural University, Hefei, China.,Key Laboratory of Wheat Biology and Genetic Improvement on Southern Yellow & Huai River Valley, Ministry of Agriculture and Rural Affairs, Hefei, China
| | - Can Chen
- College of Agronomy, Anhui Agricultural University, Hefei, China.,Key Laboratory of Wheat Biology and Genetic Improvement on Southern Yellow & Huai River Valley, Ministry of Agriculture and Rural Affairs, Hefei, China
| | - Xu Dong Mei
- College of Agronomy, Anhui Agricultural University, Hefei, China.,Key Laboratory of Wheat Biology and Genetic Improvement on Southern Yellow & Huai River Valley, Ministry of Agriculture and Rural Affairs, Hefei, China
| | - Liu Xue
- College of Agronomy, Anhui Agricultural University, Hefei, China.,Key Laboratory of Wheat Biology and Genetic Improvement on Southern Yellow & Huai River Valley, Ministry of Agriculture and Rural Affairs, Hefei, China
| | | | - Muhammad Abdullah
- School of Life Sciences, Anhui Agricultural University, Hefei, China
| | - Shamsur Rehman
- National Engineering Laboratory of Crop Stress Resistance Breeding, School of Life Sciences, Anhui Agricultural University, Hefei, China
| | - Hongqi Si
- College of Agronomy, Anhui Agricultural University, Hefei, China.,Key Laboratory of Wheat Biology and Genetic Improvement on Southern Yellow & Huai River Valley, Ministry of Agriculture and Rural Affairs, Hefei, China
| | - Chuanxi Ma
- College of Agronomy, Anhui Agricultural University, Hefei, China.,Key Laboratory of Wheat Biology and Genetic Improvement on Southern Yellow & Huai River Valley, Ministry of Agriculture and Rural Affairs, Hefei, China.,National United Engineering Laboratory for Crop Stress Resistance Breeding, Hefei, China.,Anhui Key Laboratory of Crop Biology, Hefei, China
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Liu Z, Wang Y, Pu W, Zhu H, Liang J, Wu J, Hong L, Guan P, Hu J. 4-CPA (4-Chlorophenoxyacetic Acid) Induces the Formation and Development of Defective "Fenghou" ( Vitis vinifera × V. labrusca) Grape Seeds. Biomolecules 2021; 11:biom11040515. [PMID: 33808413 PMCID: PMC8067128 DOI: 10.3390/biom11040515] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 03/19/2021] [Accepted: 03/22/2021] [Indexed: 12/13/2022] Open
Abstract
For some horticultural plants, auxins can not only induce normal fruit setting but also form fake seeds in the induced fruits. This phenomenon is relatively rare, and, so far, the underlying mechanism remains unclear. In this study, “Fenghou” (Vitis vinifera × V. labrusca) grapes were artificially emasculated before flowering and then sprayed with 4-CPA (4-chlorophenoxyacetic acid) to analyze its effect on seed formation. The results show that 4-CPA can induce normal fruit setting in “Fenghou” grapes. Although more seeds were detected in the fruits of the 4-CPA-treated grapevine, most seeds were immature. There was no significant difference in the seed shape; namely, both fruit seeds of the grapevines with and without 4-CPA treatment contained a hard seed coat. However, the immature seeds lacked embryo and endosperm tissue and could not germinate successfully; these were considered defective seeds. Tissue structure observation of defective seeds revealed that a lot of tissue redifferentiation occurred at the top of the ovule, which increased the number of cell layers of the outer integument; some even differentiated into new ovule primordia. The qRT-PCR results demonstrated that 4-CPA application regulated the expression of the genes VvARF2 and VvAP2, which are associated with integument development in “Fenghou” grape ovules. Together, this study evokes the regulatory role of 4-CPA in the division and continuous redifferentiation of integument cells, which eventually develop into defective seeds with thick seed coats in grapes.
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Affiliation(s)
- Zhenhua Liu
- College of Horticulture, China Agricultural University, Beijing 100193, China; (Z.L.); (Y.W.); (W.P.); (H.Z.); (J.L.); (J.W.); (L.H.)
| | - Yan Wang
- College of Horticulture, China Agricultural University, Beijing 100193, China; (Z.L.); (Y.W.); (W.P.); (H.Z.); (J.L.); (J.W.); (L.H.)
| | - Wenjiang Pu
- College of Horticulture, China Agricultural University, Beijing 100193, China; (Z.L.); (Y.W.); (W.P.); (H.Z.); (J.L.); (J.W.); (L.H.)
| | - Haifeng Zhu
- College of Horticulture, China Agricultural University, Beijing 100193, China; (Z.L.); (Y.W.); (W.P.); (H.Z.); (J.L.); (J.W.); (L.H.)
| | - Jinjun Liang
- College of Horticulture, China Agricultural University, Beijing 100193, China; (Z.L.); (Y.W.); (W.P.); (H.Z.); (J.L.); (J.W.); (L.H.)
| | - Jiang Wu
- College of Horticulture, China Agricultural University, Beijing 100193, China; (Z.L.); (Y.W.); (W.P.); (H.Z.); (J.L.); (J.W.); (L.H.)
| | - Liang Hong
- College of Horticulture, China Agricultural University, Beijing 100193, China; (Z.L.); (Y.W.); (W.P.); (H.Z.); (J.L.); (J.W.); (L.H.)
| | - Pingyin Guan
- Molecular Cell Biology, Botanical Institute, Karlsruhe Institute of Technology, 76131 Karlsruhe, Germany;
| | - Jianfang Hu
- College of Horticulture, China Agricultural University, Beijing 100193, China; (Z.L.); (Y.W.); (W.P.); (H.Z.); (J.L.); (J.W.); (L.H.)
- Correspondence: ; Tel.: +86-010-62732488
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Luo C, Wang S, Ning K, Chen Z, Wang Y, Yang J, Qi M, Wang Q. The APETALA2 transcription factor LsAP2 regulates seed shape in lettuce. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:2463-2476. [PMID: 33340036 DOI: 10.1093/jxb/eraa592] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Accepted: 12/15/2020] [Indexed: 05/28/2023]
Abstract
Seeds are major vehicles of propagation and dispersal in plants. A number of transcription factors, including APETALA2 (AP2), play crucial roles during the seed development process in various plant species. However, genes essential for seed development and the regulatory networks that operate during seed development remain unclear in lettuce. Here, we identified a lettuce AP2 (LsAP2) gene that was highly expressed during the early stages of seed development. LsAP2 knockout plants obtained by the CRISPR/Cas9 system were used to explore the biological function of LsAP2. Compared with the wild type, the seeds of Lsap2 mutant plants were longer and narrower, and developed an extended tip at the seed top. After further investigating the structural characteristics of the seeds of Lsap2 mutant plants, we proposed a new function of LsAP2 in seed dispersal. Moreover, we identified several interactors of LsAP2. Our results showed that LsAP2 directly interacted with the lettuce homolog of BREVIPEDICELLUS (LsBP) and promoted the expression of LsBP. Transcriptome analysis revealed that LsAP2 might also be involved in brassinosteroid biosynthesis and signaling pathways. Taken together, our data indicate that LsAP2 has a significant function in regulating seed shape in lettuce.
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Affiliation(s)
- Chen Luo
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, Department of Vegetable Science, College of Horticulture, China Agricultural University, Beijing, China
| | - Shenglin Wang
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, Department of Vegetable Science, College of Horticulture, China Agricultural University, Beijing, China
| | - Kang Ning
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, Department of Vegetable Science, College of Horticulture, China Agricultural University, Beijing, China
| | - Zijing Chen
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, Department of Vegetable Science, College of Horticulture, China Agricultural University, Beijing, China
| | - Yixin Wang
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, Department of Vegetable Science, College of Horticulture, China Agricultural University, Beijing, China
| | - Jingjing Yang
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, Department of Vegetable Science, College of Horticulture, China Agricultural University, Beijing, China
| | - Meixia Qi
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, Department of Vegetable Science, College of Horticulture, China Agricultural University, Beijing, China
| | - Qian Wang
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, Department of Vegetable Science, College of Horticulture, China Agricultural University, Beijing, China
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57
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Zhu X, Zhang S, Chen Y, Mou C, Huang Y, Liu X, Ji J, Yu J, Hao Q, Yang C, Cai M, Nguyen T, Song W, Wang P, Dong H, Liu S, Jiang L, Wan J. Decreased grain size1, a C3HC4-type RING protein, influences grain size in rice (Oryza sativa L.). PLANT MOLECULAR BIOLOGY 2021; 105:405-417. [PMID: 33387175 DOI: 10.1007/s11103-020-01096-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2020] [Accepted: 11/08/2020] [Indexed: 05/16/2023]
Abstract
We reported that DGS1 plays a positive role in regulating grain size in rice and was regulated by OsBZR1. Grain size is an important agronomic trait that contributes to grain yield. However, the underlying molecular mechanisms that determine final grain size are still largely unknown. We isolated a rice mutant showing reduced grain size in a 60Co-irradiated variety Nanjing 35 population. We named the mutant decreased grain size1 (dgs1). Map-based cloning and subsequent transgenic CRISPR and complementation assays indicated that a mutation had occurred in LOC_Os03g49900 and that the DGS1 allele regulated grain size. DGS1 encodes a protein with a 7-transmembrane domain and C3HC4 type RING domain. It was widely expressed, especially in young tissues. DGS1 is a membrane-located protein. OsBZR1 (BRASSINAZOLE-RESISTANT1), a core transcription activator of BR signaling, also plays a positive role in grain size. We provided preliminary evidence that OsBZR1 can bind to the DGS1 promoter to activate expression of DGS1.
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Affiliation(s)
- Xingjie Zhu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China
| | - Shengzhong Zhang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yaping Chen
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China
| | - Changlin Mou
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yunshuai Huang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China
| | - Xi Liu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China
| | - Jingli Ji
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China
| | - Jiangfeng Yu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China
| | - Qixian Hao
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China
| | - Chunyan Yang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China
| | - Mengying Cai
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China
| | - Thanhliem Nguyen
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China
- Department of Biology and Agricultural Engineering, Quynhon University, Quynhon, Binhdinh, 590000, Vietnam
| | - Weihan Song
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China
| | - Ping Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China
| | - Hui Dong
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China
| | - Shijia Liu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China
| | - Ling Jiang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China.
| | - Jianmin Wan
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China.
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
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Sun F, Ding L, Feng W, Cao Y, Lu F, Yang Q, Li W, Lu Y, Shabek N, Fu F, Yu H. Maize transcription factor ZmBES1/BZR1-5 positively regulates kernel size. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:1714-1726. [PMID: 33206180 DOI: 10.1093/jxb/eraa544] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Accepted: 11/11/2020] [Indexed: 05/25/2023]
Abstract
The BES1/BZR1 transcription factors regulate the expression of genes responsive to brassinosteroids and play pivotal roles in plant development, but their role in regulating kernel development in maize remains unclear. In this study, we found that ZmBES1/BZR1-5 positively regulates kernel size. Association analysis of candidate genes in 513 diverse maize inbred lines indicated that three SNPs related to ZmBES1/BZR1-5 were significantly associated with kernel width and whilst four SNPs were related to 100-kernel weight. Overexpression of ZmBES1/BZR1-5 in Arabidopsis and rice both significantly increased seed size and weight, and smaller kernels were produced in maize Mu transposon insertion and EMS mutants. The ZmBES1/BZR1-5 protein locates in the nucleus, contains bHLH and BAM domains, and shows no transcriptional activity as a monomer but forms a homodimer through the BAM domain. ChIP-sequencing analysis, and yeast one-hybrid and dual-luciferase assays demonstrated that the protein binds to the promoters of AP2/EREBP genes (Zm00001d010676 and Zm00001d032077) and inhibits their transcription. cDNA library screening showed that ZmBES1/BZR1-5 interacts with casein kinase II subunit β4 (ZmCKIIβ4) and ferredoxin 2 (ZmFdx2) in vitro and in vivo, respectively. Taken together, our study suggests that ZmBES1/BZR1-5 positively regulates kernel size, and provides new insights into understanding the mechanisms of kernel development in maize.
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Affiliation(s)
- Fuai Sun
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture; Maize Research Institute, Sichuan Agricultural University, Chengdu, China
- Department of Plant Biology, University of California, Davis, CA, USA
| | - Lei Ding
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture; Maize Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Wenqi Feng
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture; Maize Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Yang Cao
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture; Maize Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Fengzhong Lu
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture; Maize Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Qingqing Yang
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture; Maize Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Wanchen Li
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture; Maize Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Yanli Lu
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture; Maize Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Nitzan Shabek
- Department of Plant Biology, University of California, Davis, CA, USA
| | - Fengling Fu
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture; Maize Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Haoqiang Yu
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture; Maize Research Institute, Sichuan Agricultural University, Chengdu, China
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Li Q, Chakrabarti M, Taitano NK, Okazaki Y, Saito K, Al-Abdallat AM, van der Knaap E. Differential expression of SlKLUH controlling fruit and seed weight is associated with changes in lipid metabolism and photosynthesis-related genes. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:1225-1244. [PMID: 33159787 PMCID: PMC7904157 DOI: 10.1093/jxb/eraa518] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Accepted: 11/02/2020] [Indexed: 05/21/2023]
Abstract
The sizes of plant organs such as fruit and seed are crucial yield components. Tomato KLUH underlies the locus fw3.2, an important regulator of fruit and seed weight. However, the mechanism by which the expression levels of KLUH affect organ size is poorly understood. We found that higher expression of SlKLUH increased cell proliferation in the pericarp within 5 d post-anthesis in tomato near-isogenic lines. Differential gene expression analyses showed that lower expression of SlKLUH was associated with increased expression of genes involved in lipid metabolism. Lipidomic analysis revealed that repression of SlKLUH mainly increased the contents of certain non-phosphorus glycerolipids and phospholipids and decreased the contents of four unknown lipids. Co-expression network analyses revealed that lipid metabolism was possibly associated with but not directly controlled by SlKLUH, and that this gene instead controls photosynthesis-related processes. In addition, many transcription factors putatively involved in the KLUH pathway were identified. Collectively, we show that SlKLUH regulates fruit and seed weight which is associated with altered lipid metabolism. The results expand our understanding of fruit and seed weight regulation and offer a valuable resource for functional studies of candidate genes putatively involved in regulation of organ size in tomato and other crops.
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Affiliation(s)
- Qiang Li
- State Key Laboratory of North China Crop Improvement and Regulation, Key Laboratory of Vegetable Germplasm Innovation and Utilization of Hebei, Collaborative Innovation Center of Vegetable Industry in Hebei, College of Horticulture, Hebei Agricultural University, Baoding, China
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA, USA
| | - Manohar Chakrabarti
- Department of Plant and Soil Sciences, University of Kentucky, Lexington, KY, USA
| | - Nathan K Taitano
- Institute for Plant Breeding, Genetics and Genomics, University of Georgia, Athens, GA, USA
| | - Yozo Okazaki
- RIKEN Center for Sustainable Resource Science, Yokohama, Japan
- Graduate School of Bioresources, Mie University, Tsu, Japan
| | - Kazuki Saito
- RIKEN Center for Sustainable Resource Science, Yokohama, Japan
- Graduate School of Pharmaceutical Sciences, Chiba University, Chiba, Japan
| | | | - Esther van der Knaap
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA, USA
- Institute for Plant Breeding, Genetics and Genomics, University of Georgia, Athens, GA, USA
- Department of Horticulture, University of Georgia, Athens, GA, USA
- Correspondence:
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Li W, Geng Z, Zhang C, Wang K, Jiang X. Whole-genome characterization of Rosa chinensis AP2/ERF transcription factors and analysis of negative regulator RcDREB2B in Arabidopsis. BMC Genomics 2021; 22:90. [PMID: 33509074 PMCID: PMC7844920 DOI: 10.1186/s12864-021-07396-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Accepted: 01/19/2021] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Rose (Rosa chinensis) is a traditional famous flower with valuable ornamental characteristics. However, drought stress restricts its growth and development, leading to an abnormal phenotype. One of the main transcription factor (TF) protein groups in the plant kingdom are the APETALA2/ethylene-responsive factor (AP2/ERF) proteins and are potentially involved in the growth and stress responses of various plants. RESULTS Our investigation mainly focused on exploring the genome of rose and thereby we discovered 135 apparent AP2/ERF TFs. Phylogenic analyses revealed that RcAP2/ERF genes are categorized into DREB, Soloist, AP2, and ERF subfamilies, and are further classified these into 17 groups, with the same as Malus domestica and Arabidopsis thaliana. The analysis of the gene structure revealed that the introns ranged from 0 to 9 in number. Pattern examination demonstrated that the RcAP2/ERF predominantly consists of typical AP2 domains, of which the 2nd motif is the most ubiquitous. Distributions of cis-acting elements indicated that members of the AP2/ERF family are frequently involved in growth and development, phytohormone and stress response in rose species. Also, the distribution mapping of the rose chromosomes indicated that AP2/ERF class genes are dispersed among all seven chromosomes. Additionally, we isolated a novel DREB A2 subgroup gene and named it RcDREB2B. Subsequently, the RcDREB2B transcript accumulation was repressed under the mild and severe drought stress in the root samples of rose. RcDREB2B was targeted to the nucleus and exhibited transactivation in yeast cells. The overexpression of RcDREB2B was found to promote sensitivity to a higher salt concentration, ABA, and PEG at the germination and post-germination stages. Twelve putative osmotic and ABA-related genes were impaired in RcDREB2B-overexpressing plants. CONCLUSIONS The results provide comprehensive information regarding the gene structure, phylogenic, and distribution of the rose AP2/ERF family and bring insight into the complex transcriptional gene regulation of RcAP2/ERF. Findings in this study would also contribute to further understanding of the RcDREB2B gene in rose.
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Affiliation(s)
- Wei Li
- College of Landscape Architecture and Forestry, Qingdao Agricultural University, Qingdao, 266000, China
| | - Ziwen Geng
- College of Landscape Architecture and Forestry, Qingdao Agricultural University, Qingdao, 266000, China
| | - Cuiping Zhang
- College of Landscape Architecture and Forestry, Qingdao Agricultural University, Qingdao, 266000, China
| | - Kuiling Wang
- College of Landscape Architecture and Forestry, Qingdao Agricultural University, Qingdao, 266000, China
| | - Xinqiang Jiang
- College of Landscape Architecture and Forestry, Qingdao Agricultural University, Qingdao, 266000, China.
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Zhang H, Pan X, Liu S, Lin W, Li Y, Zhang X. Genome-wide analysis of AP2/ERF transcription factors in pineapple reveals functional divergence during flowering induction mediated by ethylene and floral organ development. Genomics 2021; 113:474-489. [PMID: 33359830 DOI: 10.1016/j.ygeno.2020.10.040] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2020] [Revised: 10/03/2020] [Accepted: 10/20/2020] [Indexed: 02/06/2023]
Abstract
The APETALA2/ethylene-responsive factor (AP2/ERF) has important roles in regulating developmental processes and hormone signaling transduction in plants. Pineapple demonstrates a special sensitivity to ethylene, and AP2/ERFs may contribute to this distinct sensitivity of pineapples to ethylene. However, little information is available on the AP2/ERF of pineapple. In this study, 97 AP2/ERF family members were identified from the pineapple genome. The AcAP2/ERF superfamily could be further divided into five subfamilies, and different subfamily existed functional divergence in multifarious biological processes. ERF and RAV subfamily genes might play important roles in the process of ethylene response of pineapple; ERF and DREB subfamily genes had particular functions in the floral organ development. This study is the first to provide detailed information on the features of AP2/ERFs in pineapple, provide new insights into the potential functional roles of the AP2/ERF superfamily members, and will facilitate a better understanding of the molecular mechanism of flower in pineapple.
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Affiliation(s)
- Hongna Zhang
- Key Laboratory of Ministry of Agriculture for Tropical Fruit Biology, South Subtropical Crops Research Institute, Chinese Academy of Tropical Agricultural Sciences, Zhanjiang 524091, PR China; Hainan University, Key Laboratory for Quality Regulation of Tropical Horticultural Crops of Hainan Province, Tropical Crop New Variety Breeding Education Engineering Center, Haikou 570102, PR China
| | - Xiaolu Pan
- Key Laboratory of Ministry of Agriculture for Tropical Fruit Biology, South Subtropical Crops Research Institute, Chinese Academy of Tropical Agricultural Sciences, Zhanjiang 524091, PR China; Hainan University, Key Laboratory for Quality Regulation of Tropical Horticultural Crops of Hainan Province, Tropical Crop New Variety Breeding Education Engineering Center, Haikou 570102, PR China
| | - Shenghui Liu
- Key Laboratory of Ministry of Agriculture for Tropical Fruit Biology, South Subtropical Crops Research Institute, Chinese Academy of Tropical Agricultural Sciences, Zhanjiang 524091, PR China
| | - Wenqiu Lin
- Key Laboratory of Ministry of Agriculture for Tropical Fruit Biology, South Subtropical Crops Research Institute, Chinese Academy of Tropical Agricultural Sciences, Zhanjiang 524091, PR China
| | - Yunhe Li
- Key Laboratory of Ministry of Agriculture for Tropical Fruit Biology, South Subtropical Crops Research Institute, Chinese Academy of Tropical Agricultural Sciences, Zhanjiang 524091, PR China
| | - Xiumei Zhang
- Key Laboratory of Ministry of Agriculture for Tropical Fruit Biology, South Subtropical Crops Research Institute, Chinese Academy of Tropical Agricultural Sciences, Zhanjiang 524091, PR China.
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The AP2/ERF Gene Family in Triticum durum: Genome-Wide Identification and Expression Analysis under Drought and Salinity Stresses. Genes (Basel) 2020; 11:genes11121464. [PMID: 33297327 PMCID: PMC7762271 DOI: 10.3390/genes11121464] [Citation(s) in RCA: 62] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 11/30/2020] [Accepted: 12/03/2020] [Indexed: 12/27/2022] Open
Abstract
Members of the AP2/ERF transcription factor family play critical roles in plant development, biosynthesis of key metabolites, and stress response. A detailed study was performed to identify TtAP2s/ERFs in the durum wheat (Triticum turgidum ssp. durum) genome, which resulted in the identification of 271 genes distributed on chromosomes 1A-7B. By carrying 27 genes, chromosome 6A had the highest number of TtAP2s/ERFs. Furthermore, a duplication assay of TtAP2s/ERFs demonstrated that 70 duplicated gene pairs had undergone purifying selection. According to RNA-seq analysis, the highest expression levels in all tissues and in response to stimuli were associated with DRF and ERF subfamily genes. In addition, the results revealed that TtAP2/ERF genes have tissue-specific expression patterns, and most TtAP2/ERF genes were significantly induced in the root tissue. Additionally, 13 TtAP2/ERF genes (six ERFs, three DREBs, two DRFs, one AP2, and one RAV) were selected for further analysis via qRT-PCR of their potential in coping with drought and salinity stresses. The TtAP2/ERF genes belonging to the DREB subfamily were markedly induced under both drought-stress and salinity-stress conditions. Furthermore, docking simulations revealed several residues in the pocket sites of the proteins associated with the stress response, which may be useful in future site-directed mutagenesis studies to increase the stress tolerance of durum wheat. This study could provide valuable insights for further evolutionary and functional assays of this important gene family in durum wheat.
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Gao Y, Han D, Jia W, Ma X, Yang Y, Xu Z. Molecular characterization and systematic analysis of NtAP2/ERF in tobacco and functional determination of NtRAV-4 under drought stress. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2020; 156:420-435. [PMID: 33011644 DOI: 10.1016/j.plaphy.2020.09.027] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2020] [Accepted: 09/20/2020] [Indexed: 06/11/2023]
Abstract
The APETALA2/ethylene response factor (AP2/ERF) transcription factor (TF) superfamily play crucial roles in plant growth and development as well as biotic and abiotic stresses response. Here, we systematically characterized 375 AP2/ERF TFs in the Nicotiana tabacum genome. Phylogenetic tree topology and conserved domain number allowed TF classifications into three families of 29 AP2, 341 ERF, and 5 RAV genes, which were unevenly distributed throughout 24 tobacco chromosomes. Gene family expansions were retained from whole genome or segmental duplications followed by tandem duplication. Gene structure and motif analysis revealed intra-group conservation. MicroRNA target site prediction identified nine miR172 family members targeting six NtAP2-family genes; 41 NtAP2/ERFs participated in protein co-regulatory networks. NtAP2/ERF gene global expression profiles ascertained by RNA-seq displayed diverse expression patterns across tissues and under different abiotic and biotic stresses (including drought, cold, and Phytopthora parasitica inoculation). As determined by qRT-PCR, the expression of NtAP2/ERF were induced by five hormone and four abiotic stress. RNA interference of NtRAV-4 in tobacco accelerates seed germination, enhance root development and leaf photosynthetic ability. Suppression of NtRAV-4 increases drought tolerance by improving antioxidant defense ability and reduced relative electrolyte leakage under drought stress. These results enhance understanding of NtAP2/ERF gene function and will facilitate genetic improvement of tobacco stress tolerance.
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Affiliation(s)
- Yun Gao
- National Tobacco Cultivation & Physiology & Biochemistry Research Centre, College of Tobacco Science, Henan Agricultural University, Zhengzhou, 450002, China.
| | - Dan Han
- National Tobacco Cultivation & Physiology & Biochemistry Research Centre, College of Tobacco Science, Henan Agricultural University, Zhengzhou, 450002, China.
| | - Wei Jia
- National Tobacco Cultivation & Physiology & Biochemistry Research Centre, College of Tobacco Science, Henan Agricultural University, Zhengzhou, 450002, China.
| | - Xiaohan Ma
- National Tobacco Cultivation & Physiology & Biochemistry Research Centre, College of Tobacco Science, Henan Agricultural University, Zhengzhou, 450002, China.
| | - Yongxia Yang
- National Tobacco Cultivation & Physiology & Biochemistry Research Centre, College of Tobacco Science, Henan Agricultural University, Zhengzhou, 450002, China.
| | - Zicheng Xu
- National Tobacco Cultivation & Physiology & Biochemistry Research Centre, College of Tobacco Science, Henan Agricultural University, Zhengzhou, 450002, China.
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Sallam AH, Manan F, Bajgain P, Martin M, Szinyei T, Conley E, Brown-Guedira G, Muehlbauer GJ, Anderson JA, Steffenson BJ. Genetic architecture of agronomic and quality traits in a nested association mapping population of spring wheat. THE PLANT GENOME 2020; 13:e20051. [PMID: 33217209 DOI: 10.1002/tpg2.20051] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Accepted: 07/03/2020] [Indexed: 06/11/2023]
Abstract
Germplasm collections are rich sources of genetic variation to improve crops for many valuable traits. Nested association mapping (NAM) populations can overcome the limitations of genome-wide association studies (GWAS) in germplasm collections by reducing the effect of population structure. We exploited the genetic diversity of the USDA-ARS wheat (Triticum aestivum L.) core collection by developing the Spring Wheat Multiparent Introgression Population (SWMIP). To develop this population, twenty-five core parents were crossed and backcrossed to the Minnesota spring wheat cultivar RB07. The NAM population and 26 founder parents were genotyped using genotyping-by-sequencing and phenotyped for heading date, height, test weight, and grain protein content. After quality control, 20,312 markers with physical map positions were generated for 2,038 recombinant inbred lines (RILs). The number of RILs in each family varied between 58 and 96. Three GWAS models were utilized for quantitative trait loci (QTL) detection and accounted for known family stratification, genetic kinship, and both covariates. GWAS was performed on the whole population and also by bootstrap sampling of an equal number of RILs from each family. Greater power of QTL detection was achieved by treating families equally through bootstrapping. In total 16, 15, 12, and 13 marker-trait associations (MTAs) were identified for heading date, height, test weight, and grain protein content, respectively. Some of these MTAs were coincident with major genes known to control the traits, but others were novel and contributed by the wheat core parents. The SWMIP will be a valuable source of genetic variation for spring wheat breeding.
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Affiliation(s)
- Ahmad H Sallam
- Department of Plant Pathology, University of Minnesota, St. Paul, MN, 55108, USA
| | - Fazal Manan
- Department of Plant Pathology, University of Minnesota, St. Paul, MN, 55108, USA
| | - Prabin Bajgain
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN, 55108, USA
| | - Matthew Martin
- Department of Plant Pathology, University of Minnesota, St. Paul, MN, 55108, USA
| | - Tamas Szinyei
- Department of Plant Pathology, University of Minnesota, St. Paul, MN, 55108, USA
| | - Emily Conley
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN, 55108, USA
| | | | - Gary J Muehlbauer
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN, 55108, USA
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, MN, 55108, USA
| | - James A Anderson
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN, 55108, USA
| | - Brian J Steffenson
- Department of Plant Pathology, University of Minnesota, St. Paul, MN, 55108, USA
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Korwin Krukowski P, Ellenberger J, Röhlen-Schmittgen S, Schubert A, Cardinale F. Phenotyping in Arabidopsis and Crops-Are We Addressing the Same Traits? A Case Study in Tomato. Genes (Basel) 2020; 11:E1011. [PMID: 32867311 PMCID: PMC7564427 DOI: 10.3390/genes11091011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Revised: 08/21/2020] [Accepted: 08/24/2020] [Indexed: 11/18/2022] Open
Abstract
The convenient model Arabidopsis thaliana has allowed tremendous advances in plant genetics and physiology, in spite of only being a weed. It has also unveiled the main molecular networks governing, among others, abiotic stress responses. Through the use of the latest genomic tools, Arabidopsis research is nowadays being translated to agronomically interesting crop models such as tomato, but at a lagging pace. Knowledge transfer has been hindered by invariable differences in plant architecture and behaviour, as well as the divergent direct objectives of research in Arabidopsis versus crops compromise transferability. In this sense, phenotype translation is still a very complex matter. Here, we point out the challenges of "translational phenotyping" in the case study of drought stress phenotyping in Arabidopsis and tomato. After briefly defining and describing drought stress and survival strategies, we compare drought stress protocols and phenotyping techniques most commonly used in the two species, and discuss their potential to gain insights, which are truly transferable between species. This review is intended to be a starting point for discussion about translational phenotyping approaches among plant scientists, and provides a useful compendium of methods and techniques used in modern phenotyping for this specific plant pair as a case study.
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Affiliation(s)
- Paolo Korwin Krukowski
- Plant Stress Lab, Department of Agriculture, Forestry and Food Sciences DISAFA-Turin University, 10095 Grugliasco, Italy; (A.S.); (F.C.)
| | - Jan Ellenberger
- INRES Horticultural Sciences, University of Bonn, 53121 Bonn, Germany;
| | | | - Andrea Schubert
- Plant Stress Lab, Department of Agriculture, Forestry and Food Sciences DISAFA-Turin University, 10095 Grugliasco, Italy; (A.S.); (F.C.)
| | - Francesca Cardinale
- Plant Stress Lab, Department of Agriculture, Forestry and Food Sciences DISAFA-Turin University, 10095 Grugliasco, Italy; (A.S.); (F.C.)
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Rodríguez-Cazorla E, Ripoll JJ, Ortuño-Miquel S, Martínez-Laborda A, Vera A. Dissection of the Arabidopsis HUA-PEP gene activity reveals that ovule fate specification requires restriction of the floral A-function. THE NEW PHYTOLOGIST 2020; 227:1222-1234. [PMID: 32259283 DOI: 10.1111/nph.16589] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2019] [Accepted: 03/25/2020] [Indexed: 06/11/2023]
Abstract
Ovules are essential for sexual plant reproduction and seed formation, and are fundamental for agriculture. However, our understanding of the molecular mechanisms governing ovule development is far from complete. In Arabidopsis, ovule identity is determined by homeotic MADS-domain proteins that define the floral C- (AG) and D- (SHP1/SHP2, STK) functions. Pre-mRNA processing of these genes is critical and mediated by HUA-PEP activity, composed of genes encoding RNA-binding proteins. In strong hua-pep mutants, functional transcripts for C- and D-function genes are reduced, resulting in homeotic transformation of ovules. Thus, hua-pep mutants provide an unique sensitized background to study ovule morphogenesis when C- and D-functions are simultaneously compromised. We found that hua-pep ovules are morphologically sepaloid and show ectopic expression of the homeotic class-A gene AP1. Inactivation of AP1 or AP2 (A-function genes) in hua-pep mutants reduced homeotic conversions, rescuing ovule identity while promoting carpelloid traits in transformed ovules. Interestingly, increased AG dosage led to similar results. Our findings strongly suggest that HUA-PEP activity is required for correct C and D floral functions, which in turn prevents ectopic expression of class-A genes in ovules for their proper morphogenesis, evoking the classic A-C antagonism of the ABC model for floral organ development.
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Affiliation(s)
| | - Juan-José Ripoll
- Division of Biological Sciences, Section of Cell and Developmental Biology, University of California San Diego, La Jolla, CA, 92093, USA
- TATA Institute for Genetics and Society (TIGS), University of California San Diego, La Jolla, CA, 92093, USA
| | - Samanta Ortuño-Miquel
- Area de Genética, Universidad Miguel Hernández, Campus de Sant Joan, Alicante, 03550, Spain
| | | | - Antonio Vera
- Area de Genética, Universidad Miguel Hernández, Campus de Sant Joan, Alicante, 03550, Spain
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Hasrak S, Lohrasebi T, Bagheri A, Shariati V, Marashi H, Razavi K. A Study to Assess the Role of Gluten Encoded Genes and Their Regulatory Elements in Bread Making Quality of Wheat. IRANIAN JOURNAL OF BIOTECHNOLOGY 2020; 17:e2164. [PMID: 32671123 PMCID: PMC7357697 DOI: 10.30498/ijb.2019.82861] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Background: Quality of bread baking is affected by gluten genes and balance between their expressions. Hence, it is necessary for a comprehensive
research to study and compare all gluten genes and their regulating elements simultaneously. Objectives: The aim of this study was to evaluate the molecular mechanism of bread quality at the level of coding genes and regulating elements via comparative
transcriptome analysis of two extreme wheat cultivars. Materials and Methods: RNAs were extracted from the grain of two wheat cultivars with high (Pishtaz) and low (Navid) bread making qualities, collected during endosperm
development at five stages. mRNAs were sequenced and gluten transcripts were assessed to find differentially expressed genes. Then, transcription
factors interacting with gluten genes were detected and evaluated for expression. Results: Results showed that Ɣ-gliadin and LMW-GS genes had a higher expression in Pishtaz and Navid, respectively. Most identified transcription
factors were active at the early stage of growth and it seemed that NAC and ERF transcription factors had significant roles in regulating genes
with different expressions. There was no significant difference in the expression level of NACs between two cultivars. It is proposed that
the ERF transcription factor which classified as BREB2C transcription factor could control the expression of LMW-GS genes in two cultivars and
functionally act as a repressor for their target genes. Conclusion: The priority of Pishtaz wheat cultivar in bread quality originated from high expression levels of Ɣ-gliadin gene and ERF transcription factor.
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Affiliation(s)
- Shabnam Hasrak
- Biotechnology and Plant Breeding Department, Faculty of Agriculture, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Tahmineh Lohrasebi
- Agricultural Biotechnology Department, National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran, Iran
| | - Abdolreza Bagheri
- Biotechnology and Plant Breeding Department, Faculty of Agriculture, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Vahid Shariati
- Agricultural Biotechnology Department, National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran, Iran
| | - Hasan Marashi
- Biotechnology and Plant Breeding Department, Faculty of Agriculture, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Khadijeh Razavi
- Agricultural Biotechnology Department, National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran, Iran
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Ikram M, Han X, Zuo JF, Song J, Han CY, Zhang YW, Zhang YM. Identification of QTNs and Their Candidate Genes for 100-Seed Weight in Soybean (Glycine max L.) Using Multi-Locus Genome-Wide Association Studies. Genes (Basel) 2020; 11:E714. [PMID: 32604988 PMCID: PMC7397327 DOI: 10.3390/genes11070714] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Revised: 06/18/2020] [Accepted: 06/24/2020] [Indexed: 12/29/2022] Open
Abstract
100-seed weight (100-SW) in soybeans is a yield component trait and controlled by multiple genes with different effects, but limited information is available for its quantitative trait nucleotides (QTNs) and candidate genes. To better understand the genetic architecture underlying the trait and improve the precision of marker-assisted selection, a total of 43,834 single nucleotide polymorphisms (SNPs) in 250 soybean accessions were used to identify significant QTNs for 100-SW in four environments and their BLUP values using six multi-locus and one single-locus genome-wide association study methods. As a result, a total of 218 significant QTNs were detected using multi-locus methods, whereas eight QTNs were identified by a single-locus method. Among 43 QTNs or QTN clusters identified repeatedly across various environments and/or approaches, all of them exhibited significant trait differences between their corresponding alleles, 33 were found in the genomic region of previously reported QTLs, 10 were identified as new QTNs, and three (qHSW-4-1, qcHSW-7-3, and qcHSW-10-4) were detected in all the four environments. The number of seed weight (SW) increasing alleles for each accession ranged from 8 (18.6%) to 36 (83.72%), and three accessions (Yixingwuhuangdou, Nannong 95C-5, and Yafanzaodou) had more than 35 SW increasing alleles. Among 36 homologous seed-weight genes in Arabidopsis underlying the above 43 stable QTNs, more importantly, Glyma05g34120, GmCRY1, and GmCPK11 had known seed-size/weight-related genes in soybean, and Glyma07g07850, Glyma10g03440, and Glyma10g36070 were candidate genes identified in this study. These results provide useful information for genetic foundation, marker-assisted selection, genomic prediction, and functional genomics of 100-SW.
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Affiliation(s)
- Muhammad Ikram
- Crop Information Center, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (M.I.); (X.H.); (J.-F.Z.); (C.-Y.H.); (Y.-W.Z.)
| | - Xu Han
- Crop Information Center, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (M.I.); (X.H.); (J.-F.Z.); (C.-Y.H.); (Y.-W.Z.)
| | - Jian-Fang Zuo
- Crop Information Center, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (M.I.); (X.H.); (J.-F.Z.); (C.-Y.H.); (Y.-W.Z.)
| | - Jian Song
- College of Agriculture, Nanjing Agricultural University, Nanjing 210095, China;
| | - Chun-Yu Han
- Crop Information Center, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (M.I.); (X.H.); (J.-F.Z.); (C.-Y.H.); (Y.-W.Z.)
| | - Ya-Wen Zhang
- Crop Information Center, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (M.I.); (X.H.); (J.-F.Z.); (C.-Y.H.); (Y.-W.Z.)
| | - Yuan-Ming Zhang
- Crop Information Center, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (M.I.); (X.H.); (J.-F.Z.); (C.-Y.H.); (Y.-W.Z.)
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Feng K, Hou XL, Xing GM, Liu JX, Duan AQ, Xu ZS, Li MY, Zhuang J, Xiong AS. Advances in AP2/ERF super-family transcription factors in plant. Crit Rev Biotechnol 2020; 40:750-776. [PMID: 32522044 DOI: 10.1080/07388551.2020.1768509] [Citation(s) in RCA: 217] [Impact Index Per Article: 54.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
In the whole life process, many factors including external and internal factors affect plant growth and development. The morphogenesis, growth, and development of plants are controlled by genetic elements and are influenced by environmental stress. Transcription factors contain one or more specific DNA-binding domains, which are essential in the whole life cycle of higher plants. The AP2/ERF (APETALA2/ethylene-responsive element binding factors) transcription factors are a large group of factors that are mainly found in plants. The transcription factors of this family serve as important regulators in many biological and physiological processes, such as plant morphogenesis, responsive mechanisms to various stresses, hormone signal transduction, and metabolite regulation. In this review, we summarized the advances in identification, classification, function, regulatory mechanisms, and the evolution of AP2/ERF transcription factors in plants. AP2/ERF family factors are mainly classified into four major subfamilies: DREB (Dehydration Responsive Element-Binding), ERF (Ethylene-Responsive-Element-Binding protein), AP2 (APETALA2) and RAV (Related to ABI3/VP), and Soloists (few unclassified factors). The review summarized the reports about multiple regulatory functions of AP2/ERF transcription factors in plants. In addition to growth regulation and stress responses, the regulatory functions of AP2/ERF in plant metabolite biosynthesis have been described. We also discussed the roles of AP2/ERF transcription factors in different phytohormone-mediated signaling pathways in plants. Genomic-wide analysis indicated that AP2/ERF transcription factors were highly conserved during plant evolution. Some public databases containing the information of AP2/ERF have been introduced. The studies of AP2/ERF factors will provide important bases for plant regulatory mechanisms and molecular breeding.
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Affiliation(s)
- Kai Feng
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Ministry of Agriculture and Rural Affairs Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Xi-Lin Hou
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Ministry of Agriculture and Rural Affairs Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Guo-Ming Xing
- Collaborative Innovation Center for Improving Quality and Increased Profits of Protected Vegetables in Shanxi, Taigu, China
| | - Jie-Xia Liu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Ministry of Agriculture and Rural Affairs Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Ao-Qi Duan
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Ministry of Agriculture and Rural Affairs Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Zhi-Sheng Xu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Ministry of Agriculture and Rural Affairs Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Meng-Yao Li
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Ministry of Agriculture and Rural Affairs Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Jing Zhuang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Ministry of Agriculture and Rural Affairs Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Ai-Sheng Xiong
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Ministry of Agriculture and Rural Affairs Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, College of Horticulture, Nanjing Agricultural University, Nanjing, China
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Liu N, Cheng F. Association mapping for yield traits in Paeonia rockii based on SSR markers within transcription factors of comparative transcriptome. BMC PLANT BIOLOGY 2020; 20:245. [PMID: 32487017 PMCID: PMC7265254 DOI: 10.1186/s12870-020-02449-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2019] [Accepted: 05/18/2020] [Indexed: 05/30/2023]
Abstract
BACKGROUND Allelic variation underlying the quantitative traits in plants is caused by the extremely complex regulation process. Tree peony originated in China is a peculiar ornamental, medicinal and oil woody plant. Paeonia rockii, one of tree peony species, is a precious emerging woody oil crop. However, in this valuable plant, the study of functional loci associated with yield traits has rarely been identified. Therefore, to explore the genetic architecture of 24 yield quantitative traits, the association mapping was first reported in 420 unrelated cultivated P. rockii individuals based on the next-generation sequencing (NGS) and single-molecule long-read sequencing (SMLRS). RESULTS The developed 58 pairs of polymorphic expressed sequence tag-simple sequence repeat (EST-SSR) markers from 959 candidate transcription factors (TFs) associated with yield were used for genotyping the 420 P. rockii accessions. We observed a high level of genetic diversity (polymorphic information content, PIC = 0.514) and low linkage disequilibrium (LD) between EST-SSRs. Moreover, four subpopulations in the association population were revealed by STRUCTURE analyses. Further, single-marker association analysis identified 141 significant associations, involving 17 quantitative traits and 41 EST-SSRs. These loci were mainly from AP2, TCP, MYB, HSF, bHLH, GATA, and B3 gene families and showed a small proportion of the phenotypic variance (3.79 to 37.45%). CONCLUSIONS Our results summarize a valuable collection of functional loci associated with yield traits in P. rockii, and provide a precious resource that reveals allelic variation underlying quantitative traits in Paeonia and other woody oil crops.
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Affiliation(s)
- Na Liu
- Peony International Institute, Beijing Advanced Innovation Center of Tree Breeding by Molecular Design, Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, Beijing, 100083, China
| | - Fangyun Cheng
- Peony International Institute, Beijing Advanced Innovation Center of Tree Breeding by Molecular Design, Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, Beijing, 100083, China.
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Geleta M, Gustafsson C, Glaubitz JC, Ortiz R. High-Density Genetic Linkage Mapping of Lepidium Based on Genotyping-by-Sequencing SNPs and Segregating Contig Tag Haplotypes. FRONTIERS IN PLANT SCIENCE 2020; 11:448. [PMID: 32425961 PMCID: PMC7204607 DOI: 10.3389/fpls.2020.00448] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Accepted: 03/26/2020] [Indexed: 05/09/2023]
Abstract
Lepidium campestre has been targeted for domestication as future oilseed and catch crop. Three hundred eighty plants comprising genotypes of L. campestre, Lepidium heterophyllum, and their interspecific F2 mapping population were genotyped using genotyping by sequencing (GBS), and the generated polymorphic markers were used for the construction of high-density genetic linkage map. TASSEL-GBS, a reference genome-based pipeline, was used for this analysis using a draft L. campestre whole genome sequence. The analysis resulted in 120,438 biallelic single-nucleotide polymorphisms (SNPs) with minor allele frequency (MAF) above 0.01. The construction of genetic linkage map was conducted using MSTMap based on phased SNPs segregating in 1:2:1 ratio for the F2 individuals, followed by genetic mapping of segregating contig tag haplotypes as dominant markers against the linkage map. The final linkage map consisted of eight linkage groups (LGs) containing 2,330 SNP markers and spanned 881 Kosambi cM. Contigs (10,302) were genetically mapped to the eight LGs, which were assembled into pseudomolecules that covered a total of ∼120.6 Mbp. The final size of the pseudomolecules ranged from 9.4 Mbp (LG-4) to 20.4 Mpb (LG-7). The following major correspondence between the eight Lepidium LGs (LG-1 to LG-8) and the five Arabidopsis thaliana (At) chromosomes (Atx-1-Atx-5) was revealed through comparative genomics analysis: LG-1&2_Atx-1, LG-3_Atx-2&3, LG-4_Atx-2, LG-5_Atx-2&Atx-3, LG-6_Atx-4&5, LG-7_Atx-4, and LG-8_Atx-5. This analysis revealed that at least 66% of the sequences of the LGs showed high collinearity with At chromosomes. The sequence identity between the corresponding regions of the LGs and At chromosomes ranged from 80.6% (LG-6) to 86.4% (LG-8) with overall mean of 82.9%. The map positions on Lepidium LGs of the homologs of 24 genes that regulate various traits in A. thaliana were also identified. The eight LGs revealed in this study confirm the previously reported (1) haploid chromosome number of eight in L. campestre and L. heterophyllum and (2) chromosomal fusion, translocation, and inversion events during the evolution of n = 8 karyotype in ancestral species shared by Lepidium and Arabidopsis to n = 5 karyotype in A. thaliana. This study generated highly useful genomic tools and resources for Lepidium that can be used to accelerate its domestication.
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Affiliation(s)
- Mulatu Geleta
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Alnarp, Sweden
| | - Cecilia Gustafsson
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Alnarp, Sweden
| | | | - Rodomiro Ortiz
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Alnarp, Sweden
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Cao S, Wang Y, Li X, Gao F, Feng J, Zhou Y. Characterization of the AP2/ERF Transcription Factor Family and Expression Profiling of DREB Subfamily under Cold and Osmotic Stresses in Ammopiptanthus nanus. PLANTS (BASEL, SWITZERLAND) 2020; 9:E455. [PMID: 32260365 PMCID: PMC7238250 DOI: 10.3390/plants9040455] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Revised: 03/11/2020] [Accepted: 04/02/2020] [Indexed: 02/02/2023]
Abstract
APETALA2/ethylene-responsive factor (AP2/ERF) is one of the largest transcription factor (TF) families in plants, which play important roles in regulating plant growth, development, and response to environmental stresses. Ammopiptanthus nanus, an unusual evergreen broad-leaved shrub in the arid region in the northern temperate zone, demonstrates a strong tolerance to low temperature and drought stresses, and AP2/ERF transcription factors may contribute to the stress tolerance of A. nanus. In the current study, 174 AP2/ERF family members were identified from the A. nanus genome, and they were divided into five subfamilies, including 92 ERF members, 55 dehydration-responsive element binding (DREB) members, 24 AP2 members, 2 RAV members, and 1 Soloist member. Compared with the other leguminous plants, A. nanus has more members of the DREB subfamily and the B1 group of the ERF subfamily, and gene expansion in the AP2/ERF family is primarily driven by tandem and segmental duplications. Promoter analysis showed that many stress-related cis-acting elements existed in promoter regions of the DREB genes, implying that MYB, ICE1, and WRKY transcription factors regulate the expression of DREB genes in A. nanus. Expression profiling revealed that the majority of DREB members were responsive to osmotic and cold stresses, and several DREB genes such as EVM0023336.1 and EVM0013392.1 were highly induced by cold stress, which may play important roles in cold response in A. nanus. This study provided important data for understanding the evolution and functions of AP2/ERF and DREB transcription factors in A. nanus.
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Affiliation(s)
| | | | | | - Fei Gao
- College of Life and Environmental Sciences, Minzu University of China, Beijing 100081, China; (S.C.); (Y.W.); (X.L.); (J.F.)
| | | | - Yijun Zhou
- College of Life and Environmental Sciences, Minzu University of China, Beijing 100081, China; (S.C.); (Y.W.); (X.L.); (J.F.)
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Zhang Z, Li A, Song G, Geng S, Gill BS, Faris JD, Mao L. Comprehensive analysis of Q gene near-isogenic lines reveals key molecular pathways for wheat domestication and improvement. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 102:299-310. [PMID: 31778224 DOI: 10.1111/tpj.14624] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2019] [Revised: 10/14/2019] [Accepted: 11/12/2019] [Indexed: 06/10/2023]
Abstract
The wheat AP2-like transcription factor gene Q has played a major role in domestication by conferring the free-threshing character and pleiotropically affecting numerous other traits. However, little information is known regarding the molecular mechanisms associated with the regulation of these traits by Q, especially for the structural determination of threshability. Here, transcriptome analysis of immature spike tissues in three lines nearly isogenic for Q revealed over 3000 differentially expressed genes (DEGs) involved in a number of pathways. Using phenotypic, microscopic, transcriptomic, and tissue-specific gene expression analyses, we demonstrated that Q governs threshability through extensive modification of wheat glumes including their structure, cell wall thickness, and chemical composition. Critical DEGs and pathways involved in secondary cell wall synthesis and regulation of the chemical composition of glumes were identified. We also showed that the mutation giving rise to the Q allele synchronized the expression of genes for micro-sporogenesis that affected pollen fertility, and may determine the final grain number for wheat spikes. Transcriptome dissection of genes and genetic pathways regulated by Q should further our understanding of wheat domestication and improvement.
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Affiliation(s)
- Zengcui Zhang
- Cereal Crops Research Unit, Edward T. Schafer Agricultural Research Center, USDA-ARS, Fargo, ND, 58102, USA
| | - Aili Li
- Institute of Crop Science (ICS), Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, China
| | - Gaoyuan Song
- Institute of Crop Science (ICS), Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, China
| | - Shuaifeng Geng
- Institute of Crop Science (ICS), Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, China
| | - Bikram S Gill
- Wheat Genetics Resource Center and Department of Plant Pathology, Kansas State University, Manhattan, 66506, KS, USA
| | - Justin D Faris
- Cereal Crops Research Unit, Edward T. Schafer Agricultural Research Center, USDA-ARS, Fargo, ND, 58102, USA
| | - Long Mao
- Institute of Crop Science (ICS), Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, China
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Guo Y, Gao M, Liang X, Xu M, Liu X, Zhang Y, Liu X, Liu J, Gao Y, Qu S, Luan F. Quantitative Trait Loci for Seed Size Variation in Cucurbits - A Review. FRONTIERS IN PLANT SCIENCE 2020; 11:304. [PMID: 32265957 PMCID: PMC7099056 DOI: 10.3389/fpls.2020.00304] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Accepted: 03/03/2020] [Indexed: 05/17/2023]
Abstract
Cucurbits (Cucurbitaceae family) include many economically important fruit vegetable crops such as watermelon, pumpkin/squash, cucumber, and melon. Seed size (SS) is an important trait in cucurbits breeding, which is controlled by quantitative trait loci (QTL). Recent advances have deciphered several signaling pathways underlying seed size variation in model plants such as Arabidopsis and rice, but little is known on the genetic basis of SS variation in cucurbits. Here we conducted literature review on seed size QTL identified in watermelon, pumpkin/squash, cucumber and melon, and inferred 14, 9 and 13 consensus SS QTL based on their physical positions in respective draft genomes. Among them, four from watermelon (ClSS2.2, ClSS6.1, ClSS6.2, and ClSS8.2), two from cucumber (CsSS4.1 and CsSS5.1), and one from melon (CmSS11.1) were major-effect, stable QTL for seed size and weight. Whole genome sequence alignment revealed that these major-effect QTL were located in syntenic regions across different genomes suggesting possible structural and functional conservation of some important genes for seed size control in cucurbit crops. Annotation of genes in the four watermelon consensus SS QTL regions identified genes that are known to play important roles in seed size control including members of the zinc finger protein and the E3 ubiquitin-protein ligase families. The present work highlights the utility of comparative analysis in understanding the genetic basis of seed size variation, which may help future mapping and cloning of seed size QTL in cucurbits.
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Affiliation(s)
- Yu Guo
- College of Life Sciences, Agriculture and Forestry, Qiqihar University, Qiqihar, China
- Heilongjiang Provincial Key Laboratory of Resistance Gene Engineering and Preservation of Biodiversity in Cold Areas, Qiqihar, China
| | - Meiling Gao
- College of Life Sciences, Agriculture and Forestry, Qiqihar University, Qiqihar, China
- Heilongjiang Provincial Key Laboratory of Resistance Gene Engineering and Preservation of Biodiversity in Cold Areas, Qiqihar, China
| | - Xiaoxue Liang
- College of Life Sciences, Agriculture and Forestry, Qiqihar University, Qiqihar, China
| | - Ming Xu
- College of Life Sciences, Agriculture and Forestry, Qiqihar University, Qiqihar, China
| | - Xiaosong Liu
- College of Life Sciences, Agriculture and Forestry, Qiqihar University, Qiqihar, China
| | - Yanling Zhang
- College of Life Sciences, Agriculture and Forestry, Qiqihar University, Qiqihar, China
| | - Xiujie Liu
- Qiqihar Horticultural Research Institute, Qiqihar, China
| | - Jixiu Liu
- Qiqihar Horticultural Research Institute, Qiqihar, China
| | - Yue Gao
- Qiqihar Horticultural Research Institute, Qiqihar, China
| | - Shuping Qu
- College of Horticulture, Landscape Architecture, Northeast Agricultural University, Harbin, China
| | - Feishi Luan
- College of Horticulture, Landscape Architecture, Northeast Agricultural University, Harbin, China
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Chun Y, Fang J, Zafar SA, Shang J, Zhao J, Yuan S, Li X. MINI SEED 2 (MIS2) Encodes a Receptor-like Kinase that Controls Grain Size and Shape in Rice. RICE (NEW YORK, N.Y.) 2020; 13:7. [PMID: 32006119 PMCID: PMC6994593 DOI: 10.1186/s12284-020-0368-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Accepted: 01/20/2020] [Indexed: 05/22/2023]
Abstract
BACKGROUND Grain size is a key agronomic trait that is directly associated with grain yield in rice. Although several genes related to grain size in rice have been identified, our understanding of the mechanism of grain development is still limited. RESULTS In this study, we reported the characterization of a novel seed size mutant mini seed 2 (mis2), in which the grain showed reduced length, width and thickness along with wrinkled surface. Microscopic analysis revealed that the spikelet epidermal cell size was reduced but the cell number was increased in the mis2 mutant, suggesting that MIS2 controls grain size by coordinately regulating epidermal cell size and cell number. Map-based cloning revealed that MIS2 encodes a receptor-like kinase CRINKLY4 (CR4) which showed the highest expression in developing panicles. The MIS2 protein is localized primarily on the plasma membrane along with the endosome. However, the Arg258Gln mutation located in extracellular domain in the mis2 mutant disturbed its subcellular localization. Additionally, three major haplotypes of MIS2 were identified in the japonica, indica and aus rice cultivars. The 18-bp InDel (insertion and deletion) in the 5'-UTR (untranslated region) caused different expression level of MIS2 in haplotypes. CONCLUSIONS We reported a key role of OsCR4 in controlling grain size and shape by coordinately regulating epidermal cell size and cell number. The Arg258 in the extracellular seven-repeat domain is essential for the correct subcellular behavior and function of the OsCR4 protein.
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Affiliation(s)
- Yan Chun
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Jingjing Fang
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Syed Adeel Zafar
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Jiangyuan Shang
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Jinfeng Zhao
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | | | - Xueyong Li
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
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Li H, Dong Q, Zhao Q, Shi S, Ran K. Isolation, sequencing, and expression analysis of 30 AP2/ERF transcription factors in apple. PeerJ 2020; 8:e8391. [PMID: 31988809 PMCID: PMC6970539 DOI: 10.7717/peerj.8391] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Accepted: 12/13/2019] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND AP2/ERF transcription factors are involved in the regulation of plant growth, development, and stress responses. Our research objective was to characterize novel apple (Malus × domestica Borkh.) genes encoding AP2/ERF transcription factors involved in regulation of plant growth, development, and stress response. The transcriptional level of apple AP2/ERF genes in different tissues and under various biotic and abiotic stress was determined to provide valuable insights into the function of AP2/ERF transcription factors in apple. METHODS Thirty full-length cDNA sequences of apple AP2/ERF genes were isolated from 'Zihong Fuji' apple (Malus × domestica cv. Zihong Fuji) via homologous comparison and RT-PCR confirmation, and the obtained cDNA sequences and the deduced amino acid sequences were analyzed with bioinformatics methods. Expression levels of apple AP2/ERF genes were detected in 16 different tissues using a known array. Expression patterns of apple AP2/ERF genes were detected in response to Alternaria alternata apple pathotype (AAAP) infection using RNA-seq with existing data, and the expression of apple AP2/ERF genes was analyzed under NaCl and mannitol treatments using qRT-PCR. RESULTS The sequencing results produced 30 cDNAs (designated as MdERF3-8, MdERF11, MdERF16-19, MdERF22-28, MdERF31-35, MdERF39, MdAP2D60, MdAP2D62-65, and MdRAV2). Phylogenetic analysis revealed that MdERF11/16, MdERF33/35, MdERF34/39, and MdERF18/23 belonged to groups A-2, A-4, A-5, and A-6 of the DREB subfamily, respectively; MdERF31, MdERF19, MdERF4/25/28/32, MdERF24, MdERF5/6/27, and MdERF3/7/8/17/22/26 belonged to groups B-1, B-2, B-3, B-4, B-5, and B-6 of the ERF subfamily, respectively; MdAP2D60 and MdAP2D62/63/64/65 belonged to the AP2 subfamily; and MdRAV2 belonged to the RAV subfamily. Array results indicated that 30 apple AP2/ERF genes were expressed in all examined tissues to different degrees. RNA-seq results using previously reported data showed that many members of the apple ERF and DREB subfamilies were induced by Alternaria alternate apple pathotype (AAAP) infection. Under salt treatment, many members in the apple ERF and DREB subfamilies were transcriptionally up or down-regulated. Under mannitol treatment, many members of the apple ERF, DREB, and AP2 subfamilies were induced at the transcriptional level. Taken together, the results indicated that the cloned apple AP2/ERF genes were expressed in all examined tissues. These genes were up-regulated or down-regulated in response to AAAP infection and to salt or mannitol treatment, which suggested they may be involved in regulating growth, development, and stress response in apple.
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Affiliation(s)
- Huifeng Li
- Shandong Institute of Pomology, Tai’an, China
| | - Qinglong Dong
- College of Horticulture, Northwest A and F University, Yangling, China
| | - Qiang Zhao
- College of Horticulture, Qingdao Agricultural University, Qingdao, China
| | - Song Shi
- Nanjing Agricultural University, Nanjing, China
| | - Kun Ran
- Shandong Institute of Pomology, Tai’an, China
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Jiang W, Zhang X, Song X, Yang J, Pang Y. Genome-Wide Identification and Characterization of APETALA2/Ethylene-Responsive Element Binding Factor Superfamily Genes in Soybean Seed Development. FRONTIERS IN PLANT SCIENCE 2020; 11:566647. [PMID: 33013987 PMCID: PMC7498640 DOI: 10.3389/fpls.2020.566647] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Accepted: 08/17/2020] [Indexed: 05/15/2023]
Abstract
Glycine max is one of the most important grain and oil crops, and improvement of seed yield is one of the major objectives in soybean breeding. The AP2/ERF superfamily members are involved in regulating flower and seed development in many species, and therefore play key roles in seed yield. However, it is still unknown that how many AP2/ERF members were presented in the G. max genome and whether these AP2/ERF family members function in flower and seed development in G. max. Here, we identified 380 AP2/ERF superfamily genes in the G. max genome. Phylogenetic analysis showed that 323 members were grouped into the ERF family, and 49 into the AP2 family. Among the AP2 family, 14 members of the euAP2 lineage showed high identity with their orthologs, and eight member of the ANT lineage were expressed highly in the seeds. Furthermore, seven of them (GmAP2-1 to GmAP2-7) were successfully cloned and over-expressed in Arabidopsis thaliana. The transgenic Arabidopsis plants over-expressing these GmAP2 genes flowered earlier relative to the wild type control. The seed length and width, and seed area of these over-expression lines were increased compared with the wild type, and seed weight of over-expression lines of GmAP2-1, GmAP2-4, GmAP2-5, and GmAP2-6 were greater than those of the wild type. Furthermore, the seed number per silique of the over-expression lines for GmAP2 genes were not affected except GmAP2-5. Collectively, GmAP2-1, GmAP2-4, and GmAP2-6 played important roles in regulating seed weight by affecting seed length, width and area, and further controlling seed yield.
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Affiliation(s)
- Wenbo Jiang
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xuejing Zhang
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
- Key Laboratory of Plant Resources and Beijing Botanical Garden, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Xuewei Song
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
- Key Laboratory of Plant Resources and Beijing Botanical Garden, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Junfeng Yang
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
- Key Laboratory of Plant Resources and Beijing Botanical Garden, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Yongzhen Pang
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
- *Correspondence: Yongzhen Pang,
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Solomon CU, Drea S. Besides and Beyond Flowering: Other roles of EuAP2 Genes in Plant Development. Genes (Basel) 2019; 10:genes10120994. [PMID: 31805740 PMCID: PMC6947164 DOI: 10.3390/genes10120994] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Revised: 11/27/2019] [Accepted: 11/27/2019] [Indexed: 12/18/2022] Open
Abstract
EuAP2 genes are well-known for their role in flower development, a legacy of the founding member of this subfamily of transcription factors, whose mutants lacked petals in Arabidopsis. However, studies of euAP2 genes in several species have accumulated evidence highlighting the diverse roles of euAP2 genes in other aspects of plant development. Here, we emphasize other developmental roles of euAP2 genes in various species and suggest a shift from regarding euAP2 genes as just flowering genes to consider the global role they may be playing in plant development. We hypothesize that their almost universal expression profile and pleiotropic effects of their mutation suggest their involvement in fundamental plant development processes.
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Affiliation(s)
- Charles U. Solomon
- Department of Genetics and Genome Biology, University of Leicester, Leicester LE1 7RH, UK
- Department of Plant Science and Biotechnology, Abia State University, PMB 2000, Uturu 441107, Nigeria
- Correspondence:
| | - Sinéad Drea
- Department of Genetics and Genome Biology, University of Leicester, Leicester LE1 7RH, UK
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Abstract
The plant haploid generation is specified late in higher plant development, and post-meiotic haploid plant cells divide mitotically to produce a haploid gametophyte, in which a subset of cells differentiates into the gametes. The immediate mother of the angiosperm seed is the female gametophyte, also called the embryo sac. In most flowering plants the embryo sac is comprised of two kinds of gametes (egg and central cell) and two kinds of subsidiary cells (antipodals and synergids) all of which descend from a single haploid spore produced by meiosis. The embryo sac develops within a specialized organ of the flower called the ovule, which supports and controls many steps in the development of both the embryo sac and the seed. Double fertilization of the central cell and egg cell by the two sperm cells of a pollen grain produce the endosperm and embryo of the seed, respectively. The endosperm and embryo develop under the influence of their precursor gametes and the surrounding tissues of the ovule and the gametophyte. The final size and pattern of the angiosperm seed then is the result of complex interactions across multiple tissues of three different generations (maternal sporophyte, maternal gametophyte, and the fertilization products) and three different ploidies (haploid gametophyte, diploid parental sporophyte and embryo, and triploid endosperm).
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Lo S, Muñoz-Amatriaín M, Hokin SA, Cisse N, Roberts PA, Farmer AD, Xu S, Close TJ. A genome-wide association and meta-analysis reveal regions associated with seed size in cowpea [Vigna unguiculata (L.) Walp]. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2019; 132:3079-3087. [PMID: 31367839 PMCID: PMC6791911 DOI: 10.1007/s00122-019-03407-z] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Accepted: 07/24/2019] [Indexed: 05/19/2023]
Abstract
This paper combined GWAS, meta-analysis and sequence homology comparison with common bean to identify regions associated with seed size variation in domesticated cowpea. Seed size is an important trait for yield and commercial value in dry-grain cowpea. Seed size varies widely among different cowpea accessions, and the genetic basis of such variation is not yet well understood. To better decipher the genetic basis of seed size, a genome-wide association study (GWAS) and meta-analysis were conducted on a panel of 368 cowpea diverse accessions from 51 countries. Four traits, including seed weight, length, width and density were evaluated across three locations. Using 51,128 single nucleotide polymorphisms covering the cowpea genome, 17 loci were identified for these traits. One locus was common to weight, width and length, suggesting pleiotropy. By integrating synteny-based analysis with common bean, six candidate genes (Vigun05g036000, Vigun05g039600, Vigun05g204200, Vigun08g217000, Vigun11g187000, and Vigun11g191300) which are implicated in multiple functional categories related to seed size such as endosperm development, embryo development, and cell elongation were identified. These results suggest that a combination of GWAS meta-analysis with synteny comparison in a related plant is an efficient approach to identify candidate gene (s) for complex traits in cowpea. The identified loci and candidate genes provide useful information for improving cowpea varieties and for molecular investigation of seed size.
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Affiliation(s)
- Sassoum Lo
- Department of Botany and Plant Sciences, University of California, Riverside, CA, 92521, USA.
| | - María Muñoz-Amatriaín
- Department of Botany and Plant Sciences, University of California, Riverside, CA, 92521, USA
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO, 80523, USA
| | - Samuel A Hokin
- National Center for Genome Resources, Santa Fe, NM, 87505, USA
| | - Ndiaga Cisse
- Centre d'Etude Régional pour l'Amélioration de l'Adaptation à la Sècheresse, ISRA/CERAAS, Thies, Senegal
| | - Philip A Roberts
- Department of Nematology, University of California, Riverside, CA, 92521, USA
| | - Andrew D Farmer
- National Center for Genome Resources, Santa Fe, NM, 87505, USA
| | - Shizhong Xu
- Department of Botany and Plant Sciences, University of California, Riverside, CA, 92521, USA
| | - Timothy J Close
- Department of Botany and Plant Sciences, University of California, Riverside, CA, 92521, USA
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81
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Zhao Y, Ma R, Xu D, Bi H, Xia Z, Peng H. Genome-Wide Identification and Analysis of the AP2 Transcription Factor Gene Family in Wheat ( Triticum aestivum L.). FRONTIERS IN PLANT SCIENCE 2019; 10:1286. [PMID: 31681381 PMCID: PMC6797823 DOI: 10.3389/fpls.2019.01286] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Accepted: 09/13/2019] [Indexed: 05/23/2023]
Abstract
The AP2 transcription factors play important roles in regulating plant growth and development. However, limited data are available on the contributions of AP2 transcription factors in wheat (Triticum aestivum L.). In the present study, a total of 62 AP2 genes were identified in wheat from a genome-wide search against the latest wheat genome data. Phylogenetic and sequence alignment analyses divided the wheat AP2 genes into 3 clusters, euAP2, euANT, and basalANT. Chromosomal distribution, gene structure and duplication, and motif composition were subsequently investigated. The 62 TaAP2 genes were unevenly distributed on 21 chromosomes. Twenty-four homologous gene sets among A, B, and D sub-genomes were detected, which contributed to the expansion of the wheat AP2 gene family. The expression levels of TaAP2 genes were examined using the WheatExp database; most detected genes exhibited tissue-specific expression patterns. The transcript levels of 9 randomly selected TaAP2 genes were validated through qPCR analyses. Overexpression of TaAP2-10-5D, the most likely homolog of Arabidopsis ANT gene, increased organ sizes in Arabidopsis. Our results extend our knowledge of the AP2 gene family in wheat, and contribute to further functional characterization of AP2s during wheat development with the ultimate goal of improving crop production.
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Affiliation(s)
- Yue Zhao
- College of Life Science, Henan Agricultural University, Zhengzhou, China
| | - Renyi Ma
- College of Life Science, Henan Agricultural University, Zhengzhou, China
| | - Dongliang Xu
- College of Life Science, Henan Agricultural University, Zhengzhou, China
| | - Huihui Bi
- College of Agronomy/Collaborative Innovation Center of Henan Grain Crops/National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, China
| | - Zongliang Xia
- College of Life Science, Henan Agricultural University, Zhengzhou, China
| | - Huiru Peng
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, China
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82
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Transcriptome Analysis Reveals Key Seed-Development Genes in Common Buckwheat ( Fagopyrum esculentum). Int J Mol Sci 2019; 20:ijms20174303. [PMID: 31484314 PMCID: PMC6747174 DOI: 10.3390/ijms20174303] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Revised: 08/16/2019] [Accepted: 08/28/2019] [Indexed: 12/12/2022] Open
Abstract
Seed development is an essential and complex process, which is involved in seed size change and various nutrients accumulation, and determines crop yield and quality. Common buckwheat (Fagopyrum esculentum Moench) is a widely cultivated minor crop with excellent economic and nutritional value in temperate zones. However, little is known about the molecular mechanisms of seed development in common buckwheat (Fagopyrum esculentum). In this study, we performed RNA-Seq to investigate the transcriptional dynamics and identify the key genes involved in common buckwheat seed development at three different developmental stages. A total of 4619 differentially expressed genes (DEGs) were identified. Based on the results of Gene Ontology (GO) and KEGG analysis of DEGs, many key genes involved in the seed development, including the Ca2+ signal transduction pathway, the hormone signal transduction pathways, transcription factors (TFs), and starch biosynthesis-related genes, were identified. More importantly, 18 DEGs were identified as the key candidate genes for seed size through homologous query using the known seed size-related genes from different seed plants. Furthermore, 15 DEGs from these identified as the key genes of seed development were selected to confirm the validity of the data by using quantitative real-time PCR (qRT-PCR), and the results show high consistency with the RNA-Seq results. Taken together, our results revealed the underlying molecular mechanisms of common buckwheat seed development and could provide valuable information for further studies, especially for common buckwheat seed improvement.
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83
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Fang X, Zhang Y, Zhang Y, Huang K, Yang W, Li X, Zhang Z, Wu K, Xu X, Ruan R, Yuan X, Zhang Z, Yi Z. De novo transcriptome assembly and identification of genes related to seed size in common buckwheat ( Fagopyrum esculentum M.). BREEDING SCIENCE 2019; 69:487-497. [PMID: 31598082 PMCID: PMC6776140 DOI: 10.1270/jsbbs.18194] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Accepted: 06/15/2019] [Indexed: 05/23/2023]
Abstract
Common buckwheat (Fagopyrum esculentum M.) belongs to the eudicot family Polygonaceae, Fagopyrum Mill, and its seeds have high nutritional value. The mechanism of seed development of common buckwheat remains unclear at the molecular level and no genes related to seed size have been identified. In this study, we performed genome-wide transcriptome sequencing and analysis using common buckwheat seeds at 5 days post anthesis (DPA) and 10 DPA from two cultivars (large-seeded and small-seeded). A total of 259,895 transcripts were assembled, resulting in 187,034 unigenes with average length of 1097 bp and N50 of 1538 bp. Based on gene expression profiles, 9127 differentially expressed genes (DEGs) were identified and analyzed in GO enrichment and KEGG analysis. In addition, genes related to seed size in the IKU pathway, ubiquitin-proteasome pathway, MAPK signaling pathway, TFs and phytohormones were identified and analyzed. AP2 and bZIP transcription factors, BR-signal and ABA were considered to be important regulators of seed size. This study provides a valuable genetic resource for future identification and functional analysis of candidate genes regulating seed size in common buckwheat and will be useful for improving seed yield in common buckwheat through molecular breeding in the future.
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Affiliation(s)
| | | | | | - Kehui Huang
- College of Agronomy and Biotechnology, Southwest University,
Chongqing, 400716,
People’s Republic of China
| | - Wenjuan Yang
- College of Agronomy and Biotechnology, Southwest University,
Chongqing, 400716,
People’s Republic of China
| | - Xiaoyu Li
- College of Agronomy and Biotechnology, Southwest University,
Chongqing, 400716,
People’s Republic of China
| | - Zhiyong Zhang
- College of Agronomy and Biotechnology, Southwest University,
Chongqing, 400716,
People’s Republic of China
| | - Kanghong Wu
- College of Agronomy and Biotechnology, Southwest University,
Chongqing, 400716,
People’s Republic of China
| | - Xin Xu
- College of Agronomy and Biotechnology, Southwest University,
Chongqing, 400716,
People’s Republic of China
| | - Renwu Ruan
- College of Agronomy and Biotechnology, Southwest University,
Chongqing, 400716,
People’s Republic of China
| | - Xiaohui Yuan
- College of Agronomy and Biotechnology, Southwest University,
Chongqing, 400716,
People’s Republic of China
| | - Zhengsheng Zhang
- College of Agronomy and Biotechnology, Southwest University,
Chongqing, 400716,
People’s Republic of China
| | - Zelin Yi
- College of Agronomy and Biotechnology, Southwest University,
Chongqing, 400716,
People’s Republic of China
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84
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Guan P, Di N, Mu Q, Shen X, Wang Y, Wang X, Yu K, Song W, Chen Y, Xin M, Hu Z, Guo W, Yao Y, Ni Z, Sun Q, Peng H. Use of near-isogenic lines to precisely map and validate a major QTL for grain weight on chromosome 4AL in bread wheat (Triticum aestivum L.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2019; 132:2367-2379. [PMID: 31119311 DOI: 10.1007/s00122-019-03359-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Accepted: 05/08/2019] [Indexed: 06/09/2023]
Abstract
This study precisely mapped and validated a major quantitative trait locus (QTL) on chromosome 4AL for thousand-grain weight in wheat using multiple near-isogenic lines. Thousand-grain weight (TGW) is an essential yield component. Following the previous identification of a major QTL for TGW within the interval of 15.7 cM (92.7-108.4 cM) on chromosome 4AL using the Nongda3338 (ND3338)/Jingdong6 (JD6) doubled haploid population, the aim of this study was to perform more precise mapping and validate the genetic effect of the QTL. Multiple near-isogenic lines (NILs) were developed using ND3338 as the recurrent parent through marker-assisted selection. Based on five independent BC3F3:4 segregating populations derived from BC3F3 plants with different heterozygous segments for the target QTL site and the results of genotyping analysis performed using the Wheat660 K SNP array, it was possible to delimit the QTL region to a physical interval of approximately 6.5 Mb (677.11-683.61 Mb, IWGSC Ref Seq v1.0). Field trials across multiple environments showed that NILsJD6 had a consistent effect on increasing the TGW by 5.16-27.48% and decreasing the grain number per spike (GNS) by 3.98-32.91% compared to the corresponding NILsND3338, which exhibited locus-specific TGW-GNS trade-offs. Moreover, by using RNA sequencing (RNA-Seq) of whole grains at 10 days after pollination stage of multiple NILs, we found that differentially expressed genes between the NIL pairs were significantly enriched for cell cycle and the replication of chromosome-related genes, hence affecting cell division and cell proliferation. Overall, our results provide a basis for map-based cloning of the major QTL and determining the mechanisms underlying TGW-GNS trade-offs in wheat, which would help to fine-tune these two components and maximize the grain yield for breeders.
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Affiliation(s)
- Panfeng Guan
- State Key Laboratory for Agrobiotechnology/Key Laboratory of Crop Heterosis and Utilization, Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement/College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
- College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Na Di
- College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Qing Mu
- State Key Laboratory for Agrobiotechnology/Key Laboratory of Crop Heterosis and Utilization, Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement/College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Xueyi Shen
- State Key Laboratory for Agrobiotechnology/Key Laboratory of Crop Heterosis and Utilization, Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement/College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Yongfa Wang
- State Key Laboratory for Agrobiotechnology/Key Laboratory of Crop Heterosis and Utilization, Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement/College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Xiaobo Wang
- State Key Laboratory for Agrobiotechnology/Key Laboratory of Crop Heterosis and Utilization, Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement/College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Kuohai Yu
- State Key Laboratory for Agrobiotechnology/Key Laboratory of Crop Heterosis and Utilization, Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement/College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Wanjun Song
- State Key Laboratory for Agrobiotechnology/Key Laboratory of Crop Heterosis and Utilization, Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement/College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Yongming Chen
- State Key Laboratory for Agrobiotechnology/Key Laboratory of Crop Heterosis and Utilization, Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement/College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Mingming Xin
- State Key Laboratory for Agrobiotechnology/Key Laboratory of Crop Heterosis and Utilization, Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement/College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Zhaorong Hu
- State Key Laboratory for Agrobiotechnology/Key Laboratory of Crop Heterosis and Utilization, Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement/College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Weilong Guo
- State Key Laboratory for Agrobiotechnology/Key Laboratory of Crop Heterosis and Utilization, Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement/College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Yingyin Yao
- State Key Laboratory for Agrobiotechnology/Key Laboratory of Crop Heterosis and Utilization, Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement/College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Zhongfu Ni
- State Key Laboratory for Agrobiotechnology/Key Laboratory of Crop Heterosis and Utilization, Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement/College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Qixin Sun
- State Key Laboratory for Agrobiotechnology/Key Laboratory of Crop Heterosis and Utilization, Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement/College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Huiru Peng
- State Key Laboratory for Agrobiotechnology/Key Laboratory of Crop Heterosis and Utilization, Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement/College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China.
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85
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Landrein B, Ingram G. Connected through the force: mechanical signals in plant development. JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:3507-3519. [PMID: 30821332 DOI: 10.1093/jxb/erz103] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Accepted: 02/12/2019] [Indexed: 05/12/2023]
Abstract
As multicellular organisms, plants acquire characteristic shapes through a complex set of biological processes known as morphogenesis. Biochemical signalling underlies much of development, as it allows cells to acquire specific identities based on their position within tissues and organs. However, as growing physical structures, plants, and their constituent cells, also experience internal and external physical forces that can be perceived and can influence key processes such as growth, polarity, and gene expression. This process, which adds another layer of control to growth and development, has important implications for plant morphogenesis. This review provides an overview of recent research into the role of mechanical signals in plant development and aims to show how mechanical signalling can be used, in concert with biochemical signals, as a cue allowing cells and tissues to coordinate their behaviour and to add robustness to developmental processes.
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Affiliation(s)
- Benoit Landrein
- Laboratoire Reproduction et Développement des Plantes, Université de Lyon, Ecole Normale Supérieure de Lyon, UCB Lyon 1, CNRS, INRA, Lyon Cedex, France
| | - Gwyneth Ingram
- Laboratoire Reproduction et Développement des Plantes, Université de Lyon, Ecole Normale Supérieure de Lyon, UCB Lyon 1, CNRS, INRA, Lyon Cedex, France
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86
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Cao B, Shu L, Li A. Functional characterization of LkERF- B2 for improved salt tolerance ability in Arabidopsis thaliana. 3 Biotech 2019; 9:263. [PMID: 31192088 PMCID: PMC6560127 DOI: 10.1007/s13205-019-1793-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Accepted: 06/03/2019] [Indexed: 12/29/2022] Open
Abstract
The ethylene response factors have been reported to play critical roles in developmental and environmental responses in plants. In the present study, an ERF transcription factor gene was aimed to be identified from Larix kaempferi. Molecular characteristics and function of this gene were further explored. The result showed that a 1344 bp ERF transcription factor gene containing initiation and termination codon was obtained by RT-PCR and named LkERF-B2. LkERF-B2 gene encoded 447 amino acids containing a typical AP2/ERF domain. Alignment of predicted amino acid sequence of LkERF-B2 in various plant species showed that this ERF transcription factor was highly homologous (79.0%) with that of Picea sitchensi. To elucidate the function of LkERF-B2, LkERF-B2 overexpression vector was successfully constructed and transformed to Arabidopsis thaliana via dip flower. Compared with control plant, LkERF-B2 overexpressed transgenic A. thaliana showed a significantly higher survival rate under cold, heat, NaCl and drought stresses. NaCl stress analysis revealed that control and transgenic Arabidopsis were both flowering earlier under 100 and 150 mM/L NaCl treatment. While under 200-300 mM/L NaCl treatment, the growth of control plant was significantly inhibited compared with transgenic A. thaliana. Salt injury rate and salt injury index of transgenic Arabidopsis were lower than those of the control. Further investigation showed that transgenic Arabidopsis exhibited much higher content of chloroplast pigments under different NaCl concentration. Meanwhile, the activity of SOD and POD was also enhanced in transgenic A. thaliana. These results suggested that LkERF-B2 was a key transcription factor and could lead to enhanced salt stress tolerance.
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Affiliation(s)
- Beibei Cao
- College of Horticulture and Landscape Architecture (Key Laboratory of Fruit Science), Tianjin Agricultural University, Tianjin, 300000 China
| | - Lixiang Shu
- College of Horticulture and Landscape Architecture (Key Laboratory of Fruit Science), Tianjin Agricultural University, Tianjin, 300000 China
| | - Ai Li
- College of Horticulture and Landscape Architecture (Key Laboratory of Fruit Science), Tianjin Agricultural University, Tianjin, 300000 China
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87
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Assefa T, Otyama PI, Brown AV, Kalberer SR, Kulkarni RS, Cannon SB. Genome-wide associations and epistatic interactions for internode number, plant height, seed weight and seed yield in soybean. BMC Genomics 2019; 20:527. [PMID: 31242867 PMCID: PMC6595607 DOI: 10.1186/s12864-019-5907-7] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Accepted: 06/17/2019] [Indexed: 01/29/2023] Open
Abstract
BACKGROUND Breeding programs benefit from information about marker-trait associations for many traits, whether the goal is to place those traits under active selection or to maintain them through background selection. Association studies are also important for identifying accessions bearing potentially useful alleles by characterizing marker-trait associations and allelic states across germplasm collections. This study reports the results of a genome-wide association study and evaluation of epistatic interactions for four agronomic and seed-related traits in soybean. RESULTS Using 419 diverse soybean accessions, together with genotyping data from the SoySNP50K Illumina Infinium BeadChip, we identified marker-trait associations for internode number (IN), plant height (PH), seed weight (SW), and seed yield per plant (SYP). We conducted a genome-wide epistatic study (GWES), identifying candidate genes that show evidence of SNP-SNP interactions. Although these candidate genes will require further experimental validation, several appear to be involved in developmental processes related to the respective traits. For IN and PH, these include the Dt1 determinacy locus (a soybean meristematic transcription factor), as well as a pectinesterase gene and a squamosa promoter binding gene that in other plants are involved in cell elongation and the vegetative-to-reproductive transition, respectively. For SW, candidate genes include an ortholog of the AP2 gene, which in other species is involved in maintaining seed size, embryo size, seed weight and seed yield. Another SW candidate gene is a histidine phosphotransfer protein - orthologs of which are involved in cytokinin-mediated seed weight regulating pathways. The SYP association loci overlap with regions reported in previous QTL studies to be involved in seed yield. CONCLUSIONS This study further confirms the utility of GWAS and GWES approaches for identifying marker-trait associations and interactions within a diverse germplasm collection.
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Affiliation(s)
- Teshale Assefa
- ORISE Fellow, USDA-ARS, Corn Insects and Crop Genetics Research Unit, Ames, Iowa USA
| | - Paul I. Otyama
- Agronomy Department, Iowa State University, Ames, IA USA
| | - Anne V. Brown
- USDA-ARS, Corn Insects and Crop Genetics Research Unit, Ames, Iowa USA
| | - Scott R. Kalberer
- USDA-ARS, Corn Insects and Crop Genetics Research Unit, Ames, Iowa USA
| | | | - Steven B. Cannon
- USDA-ARS, Corn Insects and Crop Genetics Research Unit, Ames, Iowa USA
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Lei M, Li ZY, Wang JB, Fu YL, Xu L. Ectopic expression of the Aechmea fasciata APETALA2 gene AfAP2-2 reduces seed size and delays flowering in Arabidopsis. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2019; 139:642-650. [PMID: 31048121 DOI: 10.1016/j.plaphy.2019.03.034] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Revised: 02/18/2019] [Accepted: 03/23/2019] [Indexed: 05/07/2023]
Abstract
The Bromeliaceae family, which is distributed pantropically, is one of the most morphologically diverse families. Except for the edible pineapple (Ananas comosus), the vast majority of bromeliads cultivated worldwide are appreciated mainly for their ornamental value. As subtropical and tropical flowering plants, these bromeliads, among with Aechmea fasciata, have significant economic importance. However, the molecular mechanism of flowering in bromeliads remains unrevealed. In this study, an APETALA2 (AP2) homologue, AfAP2-2, which belongs to the AP2/ethylene response element binding protein (AP2/EREBP) transcription factor superfamily, was identified in A. fasciata. AfAP2-2 contains two conserved AP2 domains and is a nuclear-localized transactivator. The expression level of AfAP2-2 was predominantly higher in vegetative organs of the reproductive phase than in those of the vegetative phase. Ectopic expression of AfAP2-2 in Arabidopsis specifically delayed flowering in short-day (SD) conditions. Furthermore, the size and weight of seeds of AfAP2-2-overexpressing Arabidopsis plants were significantly reduced compared to those of the wild type (WT). Our findings suggest that AfAP2-2 might be a negative regulator of flowering and seed size and weight. These results may help facilitate the molecular breeding of bromeliads.
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Affiliation(s)
- Ming Lei
- Institute of Tropical Crop Genetic Resources, Chinese Academy of Tropical Agricultural Sciences, Danzhou, 571737, China; Guangxi Key Laboratory of Medicinal Resources Protection and Genetic Improvement, Guangxi Botanical Garden of Medicinal Plants, Nanning, Guangxi, 530023, China; Key Laboratory of Crop Gene Resources and Germplasm Enhancement in Southern China, Danzhou, 571737, China; Key Laboratory of Tropical Crops Germplasm Resources Genetic Improvement and Innovation, Danzhou, 571737, China; Mid Tropical Crop Gene Bank of National Crop Resources, Danzhou, 571737, China.
| | - Zhi-Ying Li
- Institute of Tropical Crop Genetic Resources, Chinese Academy of Tropical Agricultural Sciences, Danzhou, 571737, China; Key Laboratory of Crop Gene Resources and Germplasm Enhancement in Southern China, Danzhou, 571737, China; Key Laboratory of Tropical Crops Germplasm Resources Genetic Improvement and Innovation, Danzhou, 571737, China; Mid Tropical Crop Gene Bank of National Crop Resources, Danzhou, 571737, China.
| | - Jia-Bin Wang
- Institute of Tropical Crop Genetic Resources, Chinese Academy of Tropical Agricultural Sciences, Danzhou, 571737, China; Key Laboratory of Crop Gene Resources and Germplasm Enhancement in Southern China, Danzhou, 571737, China; Key Laboratory of Tropical Crops Germplasm Resources Genetic Improvement and Innovation, Danzhou, 571737, China; Mid Tropical Crop Gene Bank of National Crop Resources, Danzhou, 571737, China.
| | - Yun-Liu Fu
- Institute of Tropical Crop Genetic Resources, Chinese Academy of Tropical Agricultural Sciences, Danzhou, 571737, China; Key Laboratory of Crop Gene Resources and Germplasm Enhancement in Southern China, Danzhou, 571737, China; Key Laboratory of Tropical Crops Germplasm Resources Genetic Improvement and Innovation, Danzhou, 571737, China; Mid Tropical Crop Gene Bank of National Crop Resources, Danzhou, 571737, China.
| | - Li Xu
- Institute of Tropical Crop Genetic Resources, Chinese Academy of Tropical Agricultural Sciences, Danzhou, 571737, China; Key Laboratory of Crop Gene Resources and Germplasm Enhancement in Southern China, Danzhou, 571737, China; Key Laboratory of Tropical Crops Germplasm Resources Genetic Improvement and Innovation, Danzhou, 571737, China; Mid Tropical Crop Gene Bank of National Crop Resources, Danzhou, 571737, China.
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89
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Chen S, Zhang N, Zhang Q, Zhou G, Tian H, Hussain S, Ahmed S, Wang T, Wang S. Genome Editing to Integrate Seed Size and Abiotic Stress Tolerance Traits in Arabidopsis Reveals a Role for DPA4 and SOD7 in the Regulation of Inflorescence Architecture. Int J Mol Sci 2019; 20:ijms20112695. [PMID: 31159296 PMCID: PMC6600516 DOI: 10.3390/ijms20112695] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Revised: 05/26/2019] [Accepted: 05/27/2019] [Indexed: 01/21/2023] Open
Abstract
Both seed size and abiotic stress tolerance are important agronomic traits in crops. In Arabidopsis, two closely related transcription repressors DPA4 (Development-Related PcG Target in the APEX4)/NGAL3 and SOD7 (Suppressor of da1-1)/NGAL2 (NGATHA-like protein) function redundantly to regulate seed size, which was increased in the dpa4 sod7 double mutants. Whereas ABA-induced transcription repressors (AITRs) are involved in the regulation of ABA signaling and abiotic stress tolerance, Arabidopsis aitr2 aitr5 aitr6 (aitr256) triple mutant showed enhanced tolerance to drought and salt. Here we performed CRISPR/Cas9 genome editing to disrupt DPA4 and SOD7 in aitr256 mutant, trying to integrate seed size and abiotic stress tolerance traits in Arabidopsis, and also to examine whether DPA4 and SOD7 may regulate other aspects of plant growth and development. Indeed, seed size was increased in the dpa4 sod7 aitr256 quintuple mutants, and enhanced tolerance to drought was observed in the mutants. In addition, we found that shoot branching was affected in the dpa4 sod7 aitr256 mutants. The mutant plants failed to produce secondary branches, and flowers/siliques were distributed irregularly on the main stems of the plants. Floral organ number and fertility were also affected in the dpa4 sod7 aitr256 mutant plants. To examine if these phenotypes were dependent on loss-of-function of AITRs, dpa4 sod7 double mutants were generated in Col wild type background, and we found that the dpa4 sod7 mutant plants showed a phenotype similar to the dpa4 sod7 aitr256 quintuple mutants. Taken together, our results indicate that the integration of seed size and abiotic stress tolerance traits by CRISPR/Cas9 editing was successful, and our results also revealed a role of DPA4 and SOD7 in the regulation of inflorescence architecture in Arabidopsis.
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Affiliation(s)
- Siyu Chen
- College of Life Sciences, Linyi University, Linyi 276005, China.
- Key Laboratory of Molecular Epigenetics of MOE, Institute of Genetics and Cytology, Northeast Normal University, Changchun 130024, China.
| | - Na Zhang
- Key Laboratory of Molecular Epigenetics of MOE, Institute of Genetics and Cytology, Northeast Normal University, Changchun 130024, China.
| | - Qimeng Zhang
- Key Laboratory of Molecular Epigenetics of MOE, Institute of Genetics and Cytology, Northeast Normal University, Changchun 130024, China.
| | - Ganghua Zhou
- Key Laboratory of Molecular Epigenetics of MOE, Institute of Genetics and Cytology, Northeast Normal University, Changchun 130024, China.
| | - Hainan Tian
- Key Laboratory of Molecular Epigenetics of MOE, Institute of Genetics and Cytology, Northeast Normal University, Changchun 130024, China.
| | - Saddam Hussain
- Key Laboratory of Molecular Epigenetics of MOE, Institute of Genetics and Cytology, Northeast Normal University, Changchun 130024, China.
| | - Sajjad Ahmed
- Key Laboratory of Molecular Epigenetics of MOE, Institute of Genetics and Cytology, Northeast Normal University, Changchun 130024, China.
| | - Tianya Wang
- Key Laboratory of Molecular Epigenetics of MOE, Institute of Genetics and Cytology, Northeast Normal University, Changchun 130024, China.
| | - Shucai Wang
- College of Life Sciences, Linyi University, Linyi 276005, China.
- Key Laboratory of Molecular Epigenetics of MOE, Institute of Genetics and Cytology, Northeast Normal University, Changchun 130024, China.
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90
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Abstract
The size of seeds affects not only evolutionary fitness but also grain yield of crops. Understanding the mechanisms controlling seed size has become an important research field in plant science. Seed size is determined by the integrated signals of maternal and zygotic tissues, which control the coordinated growth of the embryo, endosperm, and seed coat. Recent advances have identified several signaling pathways that control seed size through maternal tissues, including or involving the ubiquitin-proteasome pathway, G-protein signaling, mitogen-activated protein kinase (MAPK) signaling, phytohormone perception and homeostasis, and some transcriptional regulators. Meanwhile, growth of the zygotic tissues is regulated in part by the HAIKU (IKU) pathway and phytohormones. This review provides a general overview of current findings in seed size control and discusses the emerging molecular mechanisms and regulatory networks found to be involved.
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Affiliation(s)
- Na Li
- State Key Laboratory of Plant Cell and Chromosome Engineering and Chinese Academy of Sciences Center for Excellence in Molecular Plant Sciences, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China;
| | - Ran Xu
- State Key Laboratory of Plant Cell and Chromosome Engineering and Chinese Academy of Sciences Center for Excellence in Molecular Plant Sciences, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China;
| | - Yunhai Li
- State Key Laboratory of Plant Cell and Chromosome Engineering and Chinese Academy of Sciences Center for Excellence in Molecular Plant Sciences, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China;
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91
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Ren D, Wang X, Yang M, Yang L, He G, Deng XW. A new regulator of seed size control in Arabidopsis identified by a genome-wide association study. THE NEW PHYTOLOGIST 2019; 222:895-906. [PMID: 30556142 DOI: 10.1111/nph.15642] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2018] [Accepted: 12/02/2018] [Indexed: 05/21/2023]
Abstract
Organ size in plants is controlled by the interaction between genotype and the environment. Seed size, an important agronomic trait, largely determines yield and is an important focus of research. However, the genetic components underpinning natural variation of seed size in undomesticated species remain largely unidentified. Here we report a genome-wide association study (GWAS) of seed size in Arabidopsis thaliana, which identified 38 significantly associated loci, including one locus associated with CYCB1;4. Natural variations in CYCB1;4, which encodes a cyclin protein involved in the cell cycle, significantly influence seed size in A. thaliana. Transgenic plants with enhanced CYCB1;4 expression show normal development, exhibit increased seed size as a result of an accelerated cell cycle progression, and tend to produce higher yields. By contrast, cycb1;4 mutants have smaller seeds, and the effect is especially pronounced in a large-seed accession. The temporal and spatial expression pattern of CYCB1;4 suggests that this gene may function in both maternal tissues and zygotic tissues to coordinate the final size of seeds. Taken together, our results provide genetic insights into natural variation in seed size in Arabidopsis. Moreover, CYCB1;4 homologs in other crops could have great potential as targets for efforts aimed at yield improvement.
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Affiliation(s)
- Diqiu Ren
- School of Life Sciences and School of Advanced Agricultural Sciences, State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, China
| | - Xuncheng Wang
- School of Life Sciences and School of Advanced Agricultural Sciences, State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, China
| | - Mei Yang
- School of Life Sciences and School of Advanced Agricultural Sciences, State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, China
| | - Li Yang
- School of Life Sciences and School of Advanced Agricultural Sciences, State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, China
| | - Guangming He
- School of Life Sciences and School of Advanced Agricultural Sciences, State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, China
| | - Xing Wang Deng
- School of Life Sciences and School of Advanced Agricultural Sciences, State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, China
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92
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Yu A, Wang Z, Zhang Y, Li F, Liu A. Global Gene Expression of Seed Coat Tissues Reveals a Potential Mechanism of Regulating Seed Size Formation in Castor Bean. Int J Mol Sci 2019; 20:E1282. [PMID: 30875738 PMCID: PMC6471003 DOI: 10.3390/ijms20061282] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Revised: 02/27/2019] [Accepted: 02/28/2019] [Indexed: 01/19/2023] Open
Abstract
The physiological and molecular basis of seed size formation is complex, and the development of seed coat (derived from integument cells) might be a critical factor that determines seed size formation for many endospermic seeds. Castor bean (Ricinus communis L.), a model system of studying seed biology, has large and persistent endosperm with a hard seed coat at maturity. Here, we investigated the potential molecular mechanisms underlying seed size formation in castor bean by comparing the difference between global gene expression within developing seed coat tissues between the large-seed ZB107 and small-seed ZB306. First, we observed the cell size of seed coat and concluded that the large seed coat area of ZB107 resulted from more cell numbers (rather than cell size). Furthermore, we found that the lignin proportion of seed coat was higher in ZB306. An investigation into global gene expression of developing seed coat tissues revealed that 815 genes were up-regulated and 813 were down-regulated in ZB306 relative to ZB107. Interestingly, we found that many genes involved in regulating cell division were up-regulated in ZB107, whereas many genes involved in regulating lignin biosynthesis (including several NAC members, as well as MYB46/83 and MYB58/63) and in mediating programmed cell death (such as CysEP1 and βVPE) were up-regulated in ZB306. Furthermore, the expression patterns of the genes mentioned above indicated that the lignification of seed coat tissues was enhanced and occurred earlier in the developing seeds of ZB306. Taken together, we tentatively proposed a potential scenario for explaining the molecular mechanisms of seed coat governing seed size formation in castor bean by increasing the cell number and delaying the onset of lignification in seed coat tissues in large-seed ZB107. This study not only presents new information for possible modulation of seed coat related genes to improve castor seed yield, but also provides new insights into understanding the molecular basis of seed size formation in endospermic seeds with hard seed coat.
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Affiliation(s)
- Anmin Yu
- Key Laboratory of Economic Plants and Biotechnology, Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China.
- University of the Chinese Academy of Sciences, Beijing 100049, China.
| | - Zaiqing Wang
- Key Laboratory of Economic Plants and Biotechnology, Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China.
- University of the Chinese Academy of Sciences, Beijing 100049, China.
| | - Yang Zhang
- Jiangxi Province Key Laboratory of Oil Crops Biology, Crops Research Institute of Jiangxi Academy of Agricultural Sciences, Nanchang 330200, China.
| | - Fei Li
- Key Laboratory of Economic Plants and Biotechnology, Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China.
| | - Aizhong Liu
- Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, Southwest Forestry University, Kunming 650224, China.
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93
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Liu M, Sun W, Ma Z, Zheng T, Huang L, Wu Q, Zhao G, Tang Z, Bu T, Li C, Chen H. Genome-wide investigation of the AP2/ERF gene family in tartary buckwheat (Fagopyum Tataricum). BMC PLANT BIOLOGY 2019; 19:84. [PMID: 30786863 PMCID: PMC6381666 DOI: 10.1186/s12870-019-1681-6] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Accepted: 02/08/2019] [Indexed: 05/18/2023]
Abstract
BACKGROUND AP2/ERF transcription factors perform indispensable functions in various biological processes, such as plant growth, development, biotic and abiotic stresses responses. The AP2/ERF transcription factor family has been identified in many plants, and several AP2/ERF transcription factors from Arabidopsis thaliana (A. thaliana) have been functionally characterized. However, little research has been conducted on the AP2/ERF genes of tartary buckwheat (Fagopyum tataricum), which is an important edible and medicinal crop. The recently published whole genome sequence of tartary buckwheat allowed us to study the tissue and expression profiles of AP2/ERF genes in tartary buckwheat on a genome-wide basis. RESULTS In this study, 134 AP2/ERF genes of tartary buckwheat (FtAP2/ERF) were identified and renamed according to the chromosomal distribution of the FtAP2/ERF genes. According to the number conserved domains and gene structure, the AP2/ERF genes were divided into three subfamilies by phylogenetic tree analysis, namely, AP2 (15 members), ERF (116 members) and RAV (3 members). A total of 10 motifs were detected in tartary buckwheat AP2/ERF genes, and some of the unique motifs were found to be important for the function of AP2/ERF genes. CONCLUSION A comprehensive analysis of AP2/ERF gene expression patterns in different tissues and fruit development stages by quantitative real-time PCR (qRT-PCR) showed that they played an important role in the growth and development of tartary buckwheat, and genes that might regulate flower and fruit development were preliminarily identified. This systematic analysis establishes a foundation for further studies of the functional characteristics of FtAP2/ERF genes and improvement of tartary buckwheat crops.
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Affiliation(s)
- Moyang Liu
- College of Life Science, Sichuan Agricultural University, Ya’an, China
| | - Wenjun Sun
- College of Life Science, Sichuan Agricultural University, Ya’an, China
| | - Zhaotang Ma
- College of Life Science, Sichuan Agricultural University, Ya’an, China
| | - Tianrun Zheng
- College of Life Science, Sichuan Agricultural University, Ya’an, China
| | - Li Huang
- College of Life Science, Sichuan Agricultural University, Ya’an, China
| | - Qi Wu
- College of Life Science, Sichuan Agricultural University, Ya’an, China
| | - Gang Zhao
- College of Biological Industry, Chengdu University, Chengdu, Sichuan China
| | - Zizhong Tang
- College of Life Science, Sichuan Agricultural University, Ya’an, China
| | - Tongliang Bu
- College of Life Science, Sichuan Agricultural University, Ya’an, China
| | - Chenglei Li
- College of Life Science, Sichuan Agricultural University, Ya’an, China
| | - Hui Chen
- College of Life Science, Sichuan Agricultural University, Ya’an, China
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94
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Sizani BL, Kalve S, Markakis MN, Domagalska MA, Stelmaszewska J, AbdElgawad H, Zhao X, De Veylder L, De Vos D, Broeckhove J, Schnittger A, Beemster GTS. Multiple mechanisms explain how reduced KRP expression increases leaf size of Arabidopsis thaliana. THE NEW PHYTOLOGIST 2019; 221:1345-1358. [PMID: 30267580 DOI: 10.1111/nph.15458] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2018] [Accepted: 08/26/2018] [Indexed: 05/24/2023]
Abstract
Although cell number generally correlates with organ size, the role of cell cycle control in growth regulation is still largely unsolved. We studied kip related protein (krp) 4, 6 and 7 single, double and triple mutants of Arabidopsis thaliana to understand the role of cell cycle inhibitory proteins in leaf development. We performed leaf growth and seed size analysis, kinematic analysis, flow cytometery, transcriptome analysis and mathematical modeling of G1/S and G2/M checkpoint progression of the mitotic and endoreplication cycle. Double and triple mutants progressively increased mature leaf size, because of elevated expression of cell cycle and DNA replication genes stimulating progression through the division and endoreplication cycle. However, cell number was also already increased before leaf emergence, as a result of an increased cell number in the embryo. We show that increased embryo and seed size in krp4/6/7 results from seed abortion, presumably reducing resource competition, and that seed size differences contribute to the phenotype of several large-leaf mutants. Our results provide a new mechanistic understanding of the role of cell cycle regulation in leaf development and highlight the contribution of the embryo to the development of leaves after germination in general.
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Affiliation(s)
- Bulelani L Sizani
- Laboratory for Integrated Molecular Plant Physiology Research (IMPRES), Department of Biology, University of Antwerp, Antwerp, 2020, Belgium
| | - Shweta Kalve
- Laboratory for Integrated Molecular Plant Physiology Research (IMPRES), Department of Biology, University of Antwerp, Antwerp, 2020, Belgium
| | - Marios N Markakis
- Laboratory for Integrated Molecular Plant Physiology Research (IMPRES), Department of Biology, University of Antwerp, Antwerp, 2020, Belgium
| | - Malgorzata A Domagalska
- Laboratory for Integrated Molecular Plant Physiology Research (IMPRES), Department of Biology, University of Antwerp, Antwerp, 2020, Belgium
| | - Joanna Stelmaszewska
- Laboratory for Integrated Molecular Plant Physiology Research (IMPRES), Department of Biology, University of Antwerp, Antwerp, 2020, Belgium
- Department of Reproduction and Gynecological Endocrinology Medical, University of Bialystok, 15-089, Bialystok, Poland
| | - Hamada AbdElgawad
- Laboratory for Integrated Molecular Plant Physiology Research (IMPRES), Department of Biology, University of Antwerp, Antwerp, 2020, Belgium
- Department of Botany and Microbiology, Faculty of Science, Beni-Suef University, 62521, Beni-Suef, Egypt
| | - Xin'ai Zhao
- Department of Developmental Biology, University of Hamburg, Hamburg, 22609, Germany
| | - Lieven De Veylder
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, 9052, Belgium
- VIB Center for Plant Systems Biology, Ghent, 6052, Belgium
| | - Dirk De Vos
- Laboratory for Integrated Molecular Plant Physiology Research (IMPRES), Department of Biology, University of Antwerp, Antwerp, 2020, Belgium
- Department of Mathematics and Computer Science, University of Antwerp, Antwerp, 2020, Belgium
| | - Jan Broeckhove
- Department of Mathematics and Computer Science, University of Antwerp, Antwerp, 2020, Belgium
| | - Arp Schnittger
- Department of Developmental Biology, University of Hamburg, Hamburg, 22609, Germany
| | - Gerrit T S Beemster
- Laboratory for Integrated Molecular Plant Physiology Research (IMPRES), Department of Biology, University of Antwerp, Antwerp, 2020, Belgium
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95
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Evolutionary aspects of direct or indirect selection for seed size and seed metabolites in Brassica juncea and diploid progenitor species. Mol Biol Rep 2019; 46:1227-1238. [PMID: 30637624 DOI: 10.1007/s11033-019-04591-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Accepted: 01/03/2019] [Indexed: 10/27/2022]
Abstract
Seed size and seed metabolites have been the targets of direct or indirect selection during domestication and subsequent crop breeding. Understanding these traits and associated genetics can prove very useful for plant translational research. Large germplasm assemblage (235) of Brassica juncea and its progenitor species (B. rapa and B. nigra) was evaluated to establish seed trait variations for seed size and seed metabolites. Seeds were smallest in B. nigra and largest in B. juncea. Australian B. juncea and Indian B. rapa var brown sarson types averaged more seed oil content. Seed size and oil content were generally higher in modern cultivars in comparison to the land races. Allelic diversity for known associated genes for seed-size and oil-content (AP2, ARF2, TTG2, GRF2, GL2, CYP78A5, CYP78A6, MINI3, IKU2, IKU1, BRI1, DGAT, GPDH, LPAAT, GPAT and DA1) was studied so as to infer the effect of domestication on seed traits. Three genes (IKU1, IKU2, AP2) in B. rapa, two (TTG2 and GL2) in B. nigra and two (IKU1 and GRF2) in natural B. juncea were identified as targets of selection on the basis of Fst outlier and/or sequence diversity tests. We report parallel divergence for seed traits between B. juncea and B. rapa. Directional selection appeared stronger for seed-size as compared to correlated seed metabolites. Positive selection on seed-size is likely to have played a significant role in structuring regional variation in the germplasm.
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96
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Jiang L, Ma X, Zhao S, Tang Y, Liu F, Gu P, Fu Y, Zhu Z, Cai H, Sun C, Tan L. The APETALA2-Like Transcription Factor SUPERNUMERARY BRACT Controls Rice Seed Shattering and Seed Size. THE PLANT CELL 2019; 31:17-36. [PMID: 30626621 PMCID: PMC6391694 DOI: 10.1105/tpc.18.00304] [Citation(s) in RCA: 69] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2018] [Revised: 11/26/2018] [Accepted: 01/08/2019] [Indexed: 05/19/2023]
Abstract
The elimination of seed shattering was a crucial event during crop domestication. Improving and fine-tuning the regulation of this process will further enhance grain yield by avoiding seed losses during crop production. In this work, we identified the loss-of-shattering mutant suppression of shattering1 (ssh1) through a screen of mutagenized wild rice (Oryza rufipogon) introgression lines with naturally high shattering. Using the MutMap approach and transformation experiments, we isolated a genetic factor for seed shattering, SSH1, which is an allele of SUPERNUMERARY BRACT (SNB), a gene encoding a plant-specific APETALA2-like transcription factor. A C-to-A point mutation in the ninth intron of SNB altered the splicing of its messenger RNA, causing the reduced shattering of the ssh1 mutant by altering the development of the abscission layer and vascular bundle at the junction between the seed and the pedicel. Our data suggest that SNB positively regulates the expression of two rice REPLUMLESS orthologs, qSH1 and SH5 In addition, the ssh1 mutant had larger seeds and a higher grain weight, resulting from its increased elongation of the glume longitudinal cells. The further identification of favorable SNB alleles will be valuable for improving rice seed shattering and grain yield using molecular breeding strategies.
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Affiliation(s)
- Liyun Jiang
- National Center for Evaluation of Agricultural Wild Plants (Rice), MOE Laboratory of Crop Heterosis and Utilization, Department of Plant Genetics and Breeding, China Agricultural University, Beijing 100193, China
| | - Xin Ma
- National Center for Evaluation of Agricultural Wild Plants (Rice), MOE Laboratory of Crop Heterosis and Utilization, Department of Plant Genetics and Breeding, China Agricultural University, Beijing 100193, China
| | - Shuangshuang Zhao
- National Center for Evaluation of Agricultural Wild Plants (Rice), MOE Laboratory of Crop Heterosis and Utilization, Department of Plant Genetics and Breeding, China Agricultural University, Beijing 100193, China
| | - Yanyan Tang
- National Center for Evaluation of Agricultural Wild Plants (Rice), MOE Laboratory of Crop Heterosis and Utilization, Department of Plant Genetics and Breeding, China Agricultural University, Beijing 100193, China
| | - Fengxia Liu
- National Center for Evaluation of Agricultural Wild Plants (Rice), MOE Laboratory of Crop Heterosis and Utilization, Department of Plant Genetics and Breeding, China Agricultural University, Beijing 100193, China
- State Key Laboratory of Plant Physiology and Biochemistry, China Agricultural University, Beijing 100193, China
| | - Ping Gu
- National Center for Evaluation of Agricultural Wild Plants (Rice), MOE Laboratory of Crop Heterosis and Utilization, Department of Plant Genetics and Breeding, China Agricultural University, Beijing 100193, China
| | - Yongcai Fu
- National Center for Evaluation of Agricultural Wild Plants (Rice), MOE Laboratory of Crop Heterosis and Utilization, Department of Plant Genetics and Breeding, China Agricultural University, Beijing 100193, China
| | - Zuofeng Zhu
- National Center for Evaluation of Agricultural Wild Plants (Rice), MOE Laboratory of Crop Heterosis and Utilization, Department of Plant Genetics and Breeding, China Agricultural University, Beijing 100193, China
| | - Hongwei Cai
- National Center for Evaluation of Agricultural Wild Plants (Rice), MOE Laboratory of Crop Heterosis and Utilization, Department of Plant Genetics and Breeding, China Agricultural University, Beijing 100193, China
| | - Chuanqing Sun
- National Center for Evaluation of Agricultural Wild Plants (Rice), MOE Laboratory of Crop Heterosis and Utilization, Department of Plant Genetics and Breeding, China Agricultural University, Beijing 100193, China
- State Key Laboratory of Plant Physiology and Biochemistry, China Agricultural University, Beijing 100193, China
| | - Lubin Tan
- National Center for Evaluation of Agricultural Wild Plants (Rice), MOE Laboratory of Crop Heterosis and Utilization, Department of Plant Genetics and Breeding, China Agricultural University, Beijing 100193, China
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97
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Shah S, Karunarathna NL, Jung C, Emrani N. An APETALA1 ortholog affects plant architecture and seed yield component in oilseed rape (Brassica napus L.). BMC PLANT BIOLOGY 2018; 18:380. [PMID: 30594150 PMCID: PMC6310979 DOI: 10.1186/s12870-018-1606-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Accepted: 12/17/2018] [Indexed: 05/18/2023]
Abstract
BACKGROUND Increasing the productivity of rapeseed as one of the widely cultivated oil crops in the world is of upmost importance. As flowering time and plant architecture play a key role in the regulation of rapeseed yield, understanding the genetic mechanism underlying these traits can boost the rapeseed breeding. Meristem identity genes are known to have pleiotropic effects on plant architecture and seed yield in various crops. To understand the function of one of the meristem identity genes, APETALA1 (AP1) in rapeseed, we performed phenotypic analysis of TILLING mutants under greenhouse conditions. Three stop codon mutant families carrying a mutation in Bna.AP1.A02 paralog were analyzed for different plant architecture and seed yield-related traits. RESULTS It was evident that stop codon mutation in the K domain of Bna.AP1.A02 paralog caused significant changes in flower morphology as well as plant architecture related traits like plant height, branch height, and branch number. Furthermore, yield-related traits like seed yield per plant and number of seeds per plants were also significantly altered in the same mutant family. Apart from phenotypic changes, stop codon mutation in K domain of Bna.AP1.A02 paralog also altered the expression of putative downstream target genes like Bna.TFL1 and Bna.FUL in shoot apical meristem (SAM) of rapeseed. Mutant plants carrying stop codon mutations in the COOH domain of Bna.AP1.A02 paralog did not have a significant effect on plant architecture, yield-related traits or the expression of the downstream targets. CONCLUSIONS We found that Bna.AP1.A02 paralog has pleiotropic effect on plant architecture and yield-related traits in rapeseed. The allele we found in the current study with a beneficial effect on seed yield can be incorporated into rapeseed breeding pool to develop new varieties.
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Affiliation(s)
- Smit Shah
- Plant Breeding Institute, Christian-Albrechts-University of Kiel, Olshausenstr. 40, 24098 Kiel, Germany
| | - Nirosha L. Karunarathna
- Plant Breeding Institute, Christian-Albrechts-University of Kiel, Olshausenstr. 40, 24098 Kiel, Germany
| | - Christian Jung
- Plant Breeding Institute, Christian-Albrechts-University of Kiel, Olshausenstr. 40, 24098 Kiel, Germany
| | - Nazgol Emrani
- Plant Breeding Institute, Christian-Albrechts-University of Kiel, Olshausenstr. 40, 24098 Kiel, Germany
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98
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Analysis of genes encoding seed storage proteins (SSPs) in chickpea (Cicer arietinum L.) reveals co-expressing transcription factors and a seed-specific promoter. Funct Integr Genomics 2018; 19:373-390. [PMID: 30560463 DOI: 10.1007/s10142-018-0650-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Revised: 11/22/2018] [Accepted: 11/26/2018] [Indexed: 12/27/2022]
Abstract
Improvement of the quality and quantity of chickpea seed protein can be greatly facilitated by an understanding of the genic organization and the genetic architecture of the genes encoding seed storage proteins (SSPs). The aim of this study was to provide a comprehensive analysis of the chickpea SSP genes, putative co-expressing transcription factors (TFs), and to identify a seed-specific SSP gene promoter. A genome-wide identification of SSP genes in chickpea led to the identification of 21 non-redundant SSP encoding genes located on 6 chromosomes. Phylogenetic analysis grouped SSP genes into 3 subgroups where members within the same clade demonstrated similar motif composition and intron-exon organization. Tandem duplications were identified to be the major contributors to the expansion of the SSP gene family in chickpea. Co-expression analysis revealed 14 TFs having expression profiles similar to the SSP genes that included members of important TF families that are known to regulate seed development. Expression analysis of SSP genes and TFs revealed significantly higher expression in late stages of seed development as well as in high seed protein content (HPC) genotypes. In silico analysis of the promoter regions of the SSP encoding genes revealed several seed-specific cis-regulatory elements such as RY repeats, ACGT motifs, CAANTG, and GCN4. A candidate promoter was analyzed for seed specificity by generating stable transgenics in Arabidopsis. Overall, this study provides a useful resource to explore the regulatory networks involved in SSP synthesis and/or accumulation for utilization in developing nutritionally improved chickpea genotypes.
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99
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Castillo FM, Canales J, Claude A, Calderini DF. Expansin genes expression in growing ovaries and grains of sunflower are tissue-specific and associate with final grain weight. BMC PLANT BIOLOGY 2018; 18:327. [PMID: 30514222 PMCID: PMC6280438 DOI: 10.1186/s12870-018-1535-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Accepted: 11/19/2018] [Indexed: 05/07/2023]
Abstract
BACKGROUND Grain weight (GW) is a key component of sunflower yield and quality, but may be limited by maternal tissues. Cell growth is influenced by expansin proteins that loosen the plant cell wall. This study aimed to identify spatio-temporal expression of EXPN genes in sunflower reproductive organ tissues (ovary, pericarp, and embryo) and evaluate correlations between reproductive organ growth and expansin genes expression. Evaluations involved eight different developmental stages, two genotypes, two source-sink treatments and two experiments. The genotypes evaluated are contrasting in GW (Alybro and confection variety RHA280) under two source-sink treatments (control and shaded) to study the interactions between grain growth and expansin genes expression. RESULTS Ovaries and grains were sampled at pre- and post-anthesis, respectively. Final GW differed between genotypes and shading treatments. Shading treatment decreased final GW by 16.4 and 19.5% in RHA280 and Alybro, respectively. Relative expression of eight expansin genes were evaluated in grain tissues. EXPN4 was the most abundant expansin in the ovary tissue, while EXPN10 and EXPN7 act predominantly in ovary and pericarp tissues, and EXPN1 and EXPN15 in the embryo tissues. CONCLUSIONS Specific expansin genes were expressed in ovary, pericarp and embryo in a tissue-specific manner. Differential expression among grain tissues was consistent between genotypes, source-sink treatments and experiments. The correlation analysis suggests that EXPN genes could be specifically involved in grain tissue extension, and their expression could be linked to grain size in sunflower.
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Affiliation(s)
- Francisca M. Castillo
- Graduate School, Faculty of Agricultural Sciences, Universidad Austral de Chile, Valdivia, Chile
- Plant Production and Plant Protection Institute, Faculty of Agricultural Sciences, Universidad Austral de Chile, Valdivia, Chile
| | - Javier Canales
- Institute of Biochemistry and Microbiology, Faculty of Sciences, Universidad Austral de Chile, Valdivia, Chile
- Millennium Institute for Integrative Biology (iBio), Santiago, Chile
| | - Alejandro Claude
- Institute of Biochemistry and Microbiology, Faculty of Sciences, Universidad Austral de Chile, Valdivia, Chile
| | - Daniel F. Calderini
- Plant Production and Plant Protection Institute, Faculty of Agricultural Sciences, Universidad Austral de Chile, Valdivia, Chile
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100
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Gao H, Wang Y, Li W, Gu Y, Lai Y, Bi Y, He C. Transcriptomic comparison reveals genetic variation potentially underlying seed developmental evolution of soybeans. JOURNAL OF EXPERIMENTAL BOTANY 2018; 69:5089-5104. [PMID: 30113693 PMCID: PMC6184420 DOI: 10.1093/jxb/ery291] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2018] [Accepted: 07/31/2018] [Indexed: 05/22/2023]
Abstract
Soybean (Glycine max) was domesticated from its wild relative Glycine soja. However, the genetic variations underlying soybean domestication are not well known. Comparative transcriptomics revealed that a small portion of the orthologous genes might have been fast evolving. In contrast, three gene expression clusters were identified as divergent by their expression patterns, which occupied 37.44% of the total genes, hinting at an essential role for gene expression alteration in soybean domestication. Moreover, the most divergent stage in gene expression between wild and cultivated soybeans occurred during seed development around the cotyledon stage (15 d after fertilization, G15). A module in which the co-expressed genes were significantly down-regulated at G15 of wild soybeans was identified. The divergent clusters and modules included substantial differentially expressed genes (DEGs) between wild and cultivated soybeans related to cell division, storage compound accumulation, hormone response, and seed maturation processes. Chromosomal-linked DEGs, quantitative trait loci controlling seed weight and oil content, and selection sweeps revealed candidate DEGs at G15 in the fruit-related divergence of G. max and G. soja. Our work establishes a transcriptomic selection mechanism for altering gene expression during soybean domestication, thus shedding light on the molecular networks underlying soybean seed development and breeding strategy.
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Affiliation(s)
- Huihui Gao
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Xiangshan, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yan Wang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Xiangshan, Beijing, China
| | - Wei Li
- Crop Tillage and Cultivation Institute, Heilongjiang Academy of Agricultural Sciences, Harbin, Heilongjiang, China
| | - Yongzhe Gu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Xiangshan, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yongcai Lai
- Crop Tillage and Cultivation Institute, Heilongjiang Academy of Agricultural Sciences, Harbin, Heilongjiang, China
| | - Yingdong Bi
- Crop Tillage and Cultivation Institute, Heilongjiang Academy of Agricultural Sciences, Harbin, Heilongjiang, China
| | - Chaoying He
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Xiangshan, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
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