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Aghogho CI, Kayondo SI, Eleblu SJY, Ige A, Asante I, Offei SK, Parkes E, Egesi C, Mbanjo EGN, Shah T, Kulakow P, Rabbi IY. Genome-wide association study for yield and quality of granulated cassava processed product. THE PLANT GENOME 2024; 17:e20469. [PMID: 38880944 DOI: 10.1002/tpg2.20469] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 04/27/2024] [Accepted: 05/03/2024] [Indexed: 06/18/2024]
Abstract
The starchy storage roots of cassava are commonly processed into a variety of products, including cassava granulated processed products (gari). The commercial value of cassava roots depends on the yield and quality of processed products, directly influencing the acceptance of new varieties by farmers, processors, and consumers. This study aims to estimate genetic advance through phenotypic selection and identify genomic regions associated and candidate genes linked with gari yield and quality. Higher single nucleotide polymorphism (SNP)-based heritability estimates compared to broad-sense heritability estimates were observed for most traits highlighting the influence of genetic factors on observed variation. Using genome-wide association analysis of 188 clones, genotyped using 53,150 genome-wide SNPs, nine SNPs located on seven chromosomes were significantly associated with peel loss, gari yield, color parameters for gari and eba, bulk density, swelling index, and textural properties of eba. Future research will focus on validating and understanding the functions of identified genes and their influence on gari yield and quality traits.
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Affiliation(s)
- Cynthia Idhigu Aghogho
- West Africa Centre for Crop Improvement (WACCI), College of Basic and Applied Sciences, University of Ghana, Legon, Ghana
- International Institute of Tropical Agriculture (IITA), Ibadan, Nigeria
| | - Siraj Ismail Kayondo
- International Institute of Tropical Agriculture (IITA), Eastern Africa Hub, Dar es Salaam, Tanzania
| | - Saviour J Y Eleblu
- West Africa Centre for Crop Improvement (WACCI), College of Basic and Applied Sciences, University of Ghana, Legon, Ghana
| | - Adenike Ige
- Department of Agronomy and Plant Genetics, University of Minnesota, Minneapolis, Minnesota, USA
| | - Isaac Asante
- West Africa Centre for Crop Improvement (WACCI), College of Basic and Applied Sciences, University of Ghana, Legon, Ghana
| | - Samuel K Offei
- West Africa Centre for Crop Improvement (WACCI), College of Basic and Applied Sciences, University of Ghana, Legon, Ghana
| | - Elizabeth Parkes
- International Institute of Tropical Agriculture (IITA), Ibadan, Nigeria
| | - Chiedozie Egesi
- National Root Crops Research Institute, Umuahia, Nigeria
- Plant Breeding and Genetics Section, School of Integrative Plant Science, College of Agriculture and Life Sciences, Cornell University, Ithaca, New York, USA
| | | | - Trushar Shah
- International Institute of Tropical Agriculture (IITA), c/o ILRI, Nairobi, Kenya
| | - Peter Kulakow
- International Institute of Tropical Agriculture (IITA), Ibadan, Nigeria
| | - Ismail Y Rabbi
- International Institute of Tropical Agriculture (IITA), Ibadan, Nigeria
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Yang D, Li Y, Zhu M, Cui R, Gao J, Shu Y, Lu X, Zhang H, Zhang K. Genome-Wide Identification and Expression Analysis of the Cucumber FKBP Gene Family in Response to Abiotic and Biotic Stresses. Genes (Basel) 2023; 14:2006. [PMID: 38002948 PMCID: PMC10671320 DOI: 10.3390/genes14112006] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2023] [Revised: 10/20/2023] [Accepted: 10/24/2023] [Indexed: 11/26/2023] Open
Abstract
The FKBP (FK506-binding protein) gene family is an important member of the PPlase protease family and plays a vital role during the processes of plant growth and development. However, no studies of the FKBP gene family have been reported in cucumber. In this study, 19 FKBP genes were identified in cucumber, which were located on chromosomes 1, 3, 4, 6, and 7. Phylogenetic analysis divided the cucumber FKBP genes into three subgroups. The FKBP genes in the same subgroup exhibited similar structures and conserved motifs. The cis-acting elements analysis revealed that the promoters of cucumber FKBP genes contained hormone-, stress-, and development-related cis-acting elements. Synteny analysis of the FKBP genes among cucumber, Arabidopsis, and rice showed that 12 kinds of syntenic relationships were detected between cucumber and Arabidopsis FKBP genes, and 3 kinds of syntenic relationships were observed between cucumber and rice FKBP genes. The tissue-specific expression analysis showed that some FKBP genes were expressed in all tissues, while others were only highly expressed in part of the 10 types of tissues. The expression profile analysis of cucumber FKBP genes under 13 types of stresses showed that the CsaV3_1G007080 gene was differentially expressed under abiotic stresses (high temperature, NaCl, silicon, and photoperiod) and biotic stresses (downy mildew, green mottle mosaic virus, Fusarium wilt, phytophthora capsica, angular leaf spot, and root-knot nematode), which indicated that the CsaV3_1G007080 gene plays an important role in the growth and development of cucumber. The interaction protein analysis showed that most of the proteins in the FKBP gene family interacted with each other. The results of this study will lay the foundation for further research on the molecular biological functions of the cucumber FKBP gene family.
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Affiliation(s)
- Dekun Yang
- College of Agriculture, Anhui Science and Technology University, Fengyang 233100, China; (D.Y.); (M.Z.); (R.C.); (J.G.); (Y.S.); (X.L.)
| | - Yahui Li
- School of Life Science, Huaibei Normal University, Huaibei 235000, China;
| | - Mengdi Zhu
- College of Agriculture, Anhui Science and Technology University, Fengyang 233100, China; (D.Y.); (M.Z.); (R.C.); (J.G.); (Y.S.); (X.L.)
| | - Rongjing Cui
- College of Agriculture, Anhui Science and Technology University, Fengyang 233100, China; (D.Y.); (M.Z.); (R.C.); (J.G.); (Y.S.); (X.L.)
| | - Jiong Gao
- College of Agriculture, Anhui Science and Technology University, Fengyang 233100, China; (D.Y.); (M.Z.); (R.C.); (J.G.); (Y.S.); (X.L.)
| | - Yingjie Shu
- College of Agriculture, Anhui Science and Technology University, Fengyang 233100, China; (D.Y.); (M.Z.); (R.C.); (J.G.); (Y.S.); (X.L.)
| | - Xiaomin Lu
- College of Agriculture, Anhui Science and Technology University, Fengyang 233100, China; (D.Y.); (M.Z.); (R.C.); (J.G.); (Y.S.); (X.L.)
| | - Huijun Zhang
- School of Life Science, Huaibei Normal University, Huaibei 235000, China;
| | - Kaijing Zhang
- College of Agriculture, Anhui Science and Technology University, Fengyang 233100, China; (D.Y.); (M.Z.); (R.C.); (J.G.); (Y.S.); (X.L.)
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Nian L, Zhang X, Liu X, Li X, Liu X, Yang Y, Haider FU, Zhu X, Ma B, Mao Z, Xue Z. Characterization of B-box family genes and their expression profiles under abiotic stresses in the Melilotus albus. FRONTIERS IN PLANT SCIENCE 2022; 13:990929. [PMID: 36247587 PMCID: PMC9559383 DOI: 10.3389/fpls.2022.990929] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Accepted: 08/25/2022] [Indexed: 06/16/2023]
Abstract
B-box (BBX) proteins are one of the zinc-finger transcription factor that plays a critical role in plant development, growth, and multiple stress responses. Although BBX genes have been reported in many model organisms, no comprehensive study has yet been conducted on the BBX genes in Melilotus albus, and the biological functions of this family remain unknown. In this study, a total of 20 BBX (MaBBX) genes were identified in M. albus and were phylogenetically divided into five clades. BBX members within the same clade showed similar conserved domain, suggesting similarity of potential biological function. Analysis of MaBBX conserved motifs showed that every subfamily contained two common motifs. Distribution mapping shows that BBX proteins are nonrandomly localized in eight chromosomes. The synteny showed that most homologous gene pairs of the MaBBX gene family were amplified by segmental replication, which meant segmental replication was the main way for the MaBBX gene family to evolve. Additionally, the cis-element analysis predicted light-responsive, various hormone and stress-related elements in the promoter regions of MaBBXs. Furthermore, the expression levels of all 20 MaBBX genes were detected by qRT-PCR under salt, cold, and dark stresses in M. albus. Moreover, it was observed that 16 genes had higher expression levels after 3 h of salt treatment, 10 genes were significantly upregulated after 3 h of cold treatment, and all genes were up regulated after 3 h of dark treatment, and then appeared to decline. In addition, it was also noticed that MaBBX13 may be an important candidate for improving tolerance to abiotic stress. The prediction of protein tertiary structure showed that the tertiary structures of members of the same subfamily of MaBBX proteins were highly similar. The hypothesis exhibited that most of the MaBBX proteins were predicted to be localized to the nucleus and cytoplasm and was validated by transient expression assays of MaBBX15 in tobacco leaf epidermal cells. This study provides useful information for further investigating and researching the regulatory mechanisms of BBX family genes in response to abiotic stresses in M. albus.
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Affiliation(s)
- Lili Nian
- College of Forestry, Gansu Agricultural University, Lanzhou, China
| | - Xiaoning Zhang
- College of Forestry, Gansu Agricultural University, Lanzhou, China
| | - Xingyu Liu
- College of Forestry, Gansu Agricultural University, Lanzhou, China
| | - Xiaodan Li
- College of Management, Gansu Agricultural University, Lanzhou, China
| | - Xuelu Liu
- College of Resources and Environmental Sciences, Gansu Agricultural University, Lanzhou, China
| | - Yingbo Yang
- College of Resources and Environmental Sciences, Gansu Agricultural University, Lanzhou, China
| | - Fasih Ullah Haider
- College of Resources and Environmental Sciences, Gansu Agricultural University, Lanzhou, China
| | - Xiaolin Zhu
- College of Agronomy, Gansu Agricultural University, Lanzhou, China
| | - Biao Ma
- College of Resources and Environmental Sciences, Gansu Agricultural University, Lanzhou, China
| | - Zixuan Mao
- College of Resources and Environmental Sciences, Gansu Agricultural University, Lanzhou, China
| | - Zongyang Xue
- College of Resources and Environmental Sciences, Gansu Agricultural University, Lanzhou, China
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