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Yi X, Chen W, Guan J, Zhu J, Zhang Q, Yang H, Yang H, Zhong S, Chen C, Tan F, Ren T, Luo P. Genome-Wide Analysis of the Polygalacturonase Gene Family Sheds Light on the Characteristics, Evolutionary History, and Putative Function of Akebia trifoliata. Int J Mol Sci 2023; 24:16973. [PMID: 38069295 PMCID: PMC10707396 DOI: 10.3390/ijms242316973] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 11/26/2023] [Accepted: 11/27/2023] [Indexed: 12/18/2023] Open
Abstract
Polygalacturonase (PG) is one of the largest families of hydrolytic enzymes in plants. It is involved in the breakdown of pectin in the plant cell wall and even contributes to peel cracks. Here, we characterize PGs and outline their expression profiles using the available reference genome and transcriptome of Akebia trifoliata. The average length and exon number of the 47 identified AktPGs, unevenly assigned on 14 chromosomes and two unassembled contigs, were 5399 bp and 7, respectively. The phylogenetic tree of 191 PGs, including 47, 57, 51, and 36 from A. trifoliata, Durio zibethinus, Actinidia chinensis, and Vitis vinifera, respectively, showed that AktPGs were distributed in all groups except group G and that 10 AktPGs in group E were older, while the remaining 37 AktPGs were younger. Evolutionarily, all AktPGs generally experienced whole-genome duplication (WGD)/segmental repeats and purifying selection. Additionally, the origin of conserved domain III was possibly associated with a histidine residue (H) substitute in motif 8. The results of both the phylogenetic tree and expression profiling indicated that five AktPGs, especially AktPG25, could be associated with the cracking process. Detailed information and data on the PG family are beneficial for further study of the postharvest biology of A. trifoliata.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | - Peigao Luo
- Key Laboratory of Plant Genetics and Breeding, Sichuan Agricultural University, Chengdu 611130, China; (X.Y.); (W.C.); (J.G.); (J.Z.); (Q.Z.); (H.Y.); (H.Y.); (S.Z.); (C.C.); (F.T.); (T.R.)
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Zou SY, Feng C, Gao PX, Li TJ, Jia TJ, Huang H. Germplasm resources and genetic improvement of Akebia: A new fruit crop in China. PLANT DIVERSITY 2023; 45:712-721. [PMID: 38197008 PMCID: PMC10772107 DOI: 10.1016/j.pld.2022.12.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 11/29/2022] [Accepted: 12/02/2022] [Indexed: 01/11/2024]
Abstract
Akebia species, belonging to Lardizabalaceae, are widespread from subtropical to temperate environments of China, Japan, and Korea. All known Akebia species have medicinal and dietary value and have been widely cultivated as a new fruit crop in many areas of China. However, compared with other crop species, the breeding improvement and commercial cultivation of Akebia remain in their infancy. This review systematically introduces the present germplasm resources, geographical distribution, biological characteristics, interspecific and intraspecific cross compatibility, molecular biology, and breeding progress in Akebia species. Akebia plants are widely distributed in Shanxi, Henan, Sichuan, Chongqing, Hunan, Hubei, Jiangxi, Zhejiang, and Fujian provinces of China, and wild Akebia plants exhibit abundant phenotypic and genetic diversity due to their wide range of geographical distribution and high adaptability in different habitats. Interspecific artificial hybridization experiments have been conducted in our Akebia germplasm resources nursery. The results showed that there was no reproductive isolation between Akebia species, and fertile progeny could be produced. The synthesis of knowledge on these species provides insights for the rational development and utilization of these germplasm resources, and can facilitate the development of new breeding lines or varieties for commercial cultivation or production. Finally, perspectives on Akebia breeding research are discussed and conclusions are provided. This review provided breeders with new insights into Akebia domestication and breeding, and we also proposed five basic steps in the domestication of new fruit crops.
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Affiliation(s)
- Shuai-Yu Zou
- Lushan Botanical Garden, Chinese Academy of Sciences, Jiujiang 332900, China
| | - Chen Feng
- Lushan Botanical Garden, Chinese Academy of Sciences, Jiujiang 332900, China
| | - Pu-Xin Gao
- Lushan Botanical Garden, Chinese Academy of Sciences, Jiujiang 332900, China
| | - Tong-Jian Li
- School of Pharmacy and Life Science, Jiujiang University, Jiujiang 332005, China
| | - Tian-Jiao Jia
- Lushan Botanical Garden, Chinese Academy of Sciences, Jiujiang 332900, China
| | - Hongwen Huang
- Lushan Botanical Garden, Chinese Academy of Sciences, Jiujiang 332900, China
- South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
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Zhang Y, Zhang J, Zou S, Liu Z, Huang H, Feng C. Genome-wide analysis of the cellulose toolbox of Primulina eburnea, a calcium-rich vegetable. BMC PLANT BIOLOGY 2023; 23:259. [PMID: 37189063 DOI: 10.1186/s12870-023-04266-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Accepted: 05/05/2023] [Indexed: 05/17/2023]
Abstract
BACKGROUND Human-guided crop domestication has lasted for more than 10,000 years. In terms of the domestication and breeding of vegetables, cellulose content in edible tissues is one of the most important traits. Primulina eburnea is a recently developed calcium-rich vegetable with a high soluble and bioavailable calcium content in its leaves. However, the high cellulose content in the leaves hampers the taste, and no research has been reported on the genetic basis of cellulose biosynthesis in this calcium-rich vegetable. RESULTS We identified 36 cellulose biosynthesis-involved genes belonging to eight gene families in the P. eburnea genome. The cellulose accumulated decreasingly throughout leaf development. Nineteen genes were considered core genes in cellulose biosynthesis, which were highly expressed in buds but lowly expressed in mature leaves. In the nitrogen fertilization experiment, exogenous nitrogen decreased the cellulose content in the buds. The expressing pattern of 14 genes were consistent with phenotypic variation in the nitrogen fertilization experiment, and thus they were proposed as cellulose toolbox genes. CONCLUSIONS The present study provides a strong basis for the subsequent functional research of cellulose biosynthesis-involved genes in P. eburnea, and provides a reference for breeding and/or engineering this calcium-rich vegetable with decreased leaf cellulose content to improve the taste.
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Affiliation(s)
- Yi Zhang
- College of Life Science, Nanchang University, Nanchang, China
- Jiangxi Provincial Key Laboratory of ex situ Plant Conservation and Utilization, Lushan Botanical Garden, Chinese Academy of Sciences, No. 9, Zhiqing Rd, Jiujiang, 332900, Jiangxi, China
| | - Jie Zhang
- Jiangxi Provincial Key Laboratory of ex situ Plant Conservation and Utilization, Lushan Botanical Garden, Chinese Academy of Sciences, No. 9, Zhiqing Rd, Jiujiang, 332900, Jiangxi, China
| | - Shuaiyu Zou
- Jiangxi Provincial Key Laboratory of ex situ Plant Conservation and Utilization, Lushan Botanical Garden, Chinese Academy of Sciences, No. 9, Zhiqing Rd, Jiujiang, 332900, Jiangxi, China
| | - Ziwei Liu
- Jiangxi Provincial Key Laboratory of ex situ Plant Conservation and Utilization, Lushan Botanical Garden, Chinese Academy of Sciences, No. 9, Zhiqing Rd, Jiujiang, 332900, Jiangxi, China
| | - Hongwen Huang
- College of Life Science, Nanchang University, Nanchang, China.
- Jiangxi Provincial Key Laboratory of ex situ Plant Conservation and Utilization, Lushan Botanical Garden, Chinese Academy of Sciences, No. 9, Zhiqing Rd, Jiujiang, 332900, Jiangxi, China.
- South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China.
- University of Chinese Academy of Sciences, Beijing, China.
| | - Chen Feng
- College of Life Science, Nanchang University, Nanchang, China.
- Jiangxi Provincial Key Laboratory of ex situ Plant Conservation and Utilization, Lushan Botanical Garden, Chinese Academy of Sciences, No. 9, Zhiqing Rd, Jiujiang, 332900, Jiangxi, China.
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Chen W, Yang H, Zhong S, Zhu J, Zhang Q, Li Z, Ren T, Tan F, Shen J, Li Q, Luo P. Expression Profiles of Microsatellites in Fruit Tissues of Akebia trifoliata and Development of Efficient EST-SSR Markers. Genes (Basel) 2022; 13:genes13081451. [PMID: 36011362 PMCID: PMC9408125 DOI: 10.3390/genes13081451] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 08/10/2022] [Accepted: 08/11/2022] [Indexed: 12/03/2022] Open
Abstract
Akebia trifoliata, a member of the family Lardizabalaceae, has high exploitation potential for multiple economic purposes, so genetic improvements to meet requirements for commercial demand are needed. However, this progress is largely impeded by a lack of effective selection markers. In this study, we obtained 271.49 Gb of clean transcriptomic data from 12 samples (three tissues at four developmental stages) of A. trifoliata fruit. We identified 175,604, 194,370, and 207,906 SSRs from the de novo assembled 416,363, 463,756, and 491,680 unigene sequences obtained from the flesh, seed, and rind tissues, respectively. The profile and proportion of SSR motifs expressed in each fruit tissue and developmental stage were remarkably similar, but many trinucleotide repeats had differential expression levels among different tissues or at different developmental stages. In addition, we successfully designed 16,869 functional EST-SSR primers according to the annotated unigenes. Finally, 94 and 72 primer pairs out of 100 randomly selected primer pairs produced clear bands and polymorphic bands, respectively. These results were also used to elucidate the expression profiles of different tissues at various stages. Additionally, we provided a set of effective, polymorphic, and reliable EST-SSR markers sufficient for accelerating the discovery of metabolic and pathway-specific functional genes for genetic improvement and increased commercial productivity.
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Affiliation(s)
- Wei Chen
- State Key Laboratory of Plant Breeding and Genetics, Sichuan Agricultural University, Chengdu 611130, China
| | - Huai Yang
- State Key Laboratory of Plant Breeding and Genetics, Sichuan Agricultural University, Chengdu 611130, China
| | - Shengfu Zhong
- State Key Laboratory of Plant Breeding and Genetics, Sichuan Agricultural University, Chengdu 611130, China
| | - Jun Zhu
- State Key Laboratory of Plant Breeding and Genetics, Sichuan Agricultural University, Chengdu 611130, China
| | - Qiuyi Zhang
- State Key Laboratory of Plant Breeding and Genetics, Sichuan Agricultural University, Chengdu 611130, China
| | - Zhi Li
- State Key Laboratory of Plant Breeding and Genetics, Sichuan Agricultural University, Chengdu 611130, China
| | - Tianheng Ren
- State Key Laboratory of Plant Breeding and Genetics, Sichuan Agricultural University, Chengdu 611130, China
| | - Feiquan Tan
- State Key Laboratory of Plant Breeding and Genetics, Sichuan Agricultural University, Chengdu 611130, China
| | - Jinliang Shen
- College of Forestry, Sichuan Agricultural University, Chengdu 611130, China
| | - Qing Li
- Department of Biology and Chemistry, Chongqing Industry and Trade Polytechnic, Chongqing 408000, China
| | - Peigao Luo
- State Key Laboratory of Plant Breeding and Genetics, Sichuan Agricultural University, Chengdu 611130, China
- Correspondence:
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