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Wang B, Li W, Xu K, Lei Y, Zhao D, Li X, Zhang J, Zhang Z. A splice site mutation in the FvePHP gene is associated with leaf development and flowering time in woodland strawberry. HORTICULTURE RESEARCH 2022; 10:uhac249. [PMID: 36643753 PMCID: PMC9832950 DOI: 10.1093/hr/uhac249] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Accepted: 11/01/2022] [Indexed: 06/17/2023]
Abstract
Leaves and flowers are crucial for the growth and development of higher plants. In this study we identified a mutant with narrow leaflets and early flowering (nlef) in an ethyl methanesulfonate-mutagenized population of woodland strawberry (Fragaria vesca) and aimed to identify the candidate gene. Genetic analysis revealed that a single recessive gene, nlef, controlled the mutant phenotype. We found that FvH4_1g25470, which encodes a putative DNA polymerase α with a polymerase and histidinol phosphatase domain (PHP), might be the candidate gene, using bulked segregant analysis with whole-genome sequencing, molecular markers, and cloning analyses. A splice donor site mutation (C to T) at the 5' end of the second intron led to an erroneous splice event that reduced the expression level of the full-length transcript of FvePHP in mutant plants. FvePHP was localized in the nucleus and was highly expressed in leaves. Silencing of FvePHP using the virus-induced gene silencing method resulted in partial developmental defects in strawberry leaves. Overexpression of the FvePHP gene can largely restore the mutant phenotype. The expression levels of FveSEP1, FveSEP3, FveAP1, FveFUL, and FveFT were higher in the mutants than those in 'Yellow Wonder' plants, probably contributing to the early flowering phenotype in mutant plants. Our results indicate that mutation in FvePHP is associated with multiple developmental pathways. These results aid in understanding the role of DNA polymerase in strawberry development.
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Affiliation(s)
- Baotian Wang
- Liaoning Key Laboratory of Strawberry Breeding and Cultivation, College of Horticulture, Shenyang Agricultural University, Shenyang, 110866, China
- Laboratory of Protected Horticulture (Shenyang Agricultural University), Ministry of Education, Shenyang, People’s Republic of China
| | - Weijia Li
- Liaoning Key Laboratory of Strawberry Breeding and Cultivation, College of Horticulture, Shenyang Agricultural University, Shenyang, 110866, China
- Laboratory of Protected Horticulture (Shenyang Agricultural University), Ministry of Education, Shenyang, People’s Republic of China
- Institute of Carbon Materials Science, Shanxi Datong University, Datong, 037009, China
| | - Kexin Xu
- Liaoning Key Laboratory of Strawberry Breeding and Cultivation, College of Horticulture, Shenyang Agricultural University, Shenyang, 110866, China
- Laboratory of Protected Horticulture (Shenyang Agricultural University), Ministry of Education, Shenyang, People’s Republic of China
| | - Yingying Lei
- Liaoning Key Laboratory of Strawberry Breeding and Cultivation, College of Horticulture, Shenyang Agricultural University, Shenyang, 110866, China
- Laboratory of Protected Horticulture (Shenyang Agricultural University), Ministry of Education, Shenyang, People’s Republic of China
| | - Di Zhao
- Analytical and Testing Center, Shenyang Agricultural University, Shenyang, 110866, China
| | - Xue Li
- Liaoning Key Laboratory of Strawberry Breeding and Cultivation, College of Horticulture, Shenyang Agricultural University, Shenyang, 110866, China
- Laboratory of Protected Horticulture (Shenyang Agricultural University), Ministry of Education, Shenyang, People’s Republic of China
| | - Junxiang Zhang
- Correspondence: Zhihong Zhang, E-mail: ; Tel: +86 024 88487143; Fax: +86 024 88487143. Junxiang Zhang, E-mail: ; Tel: +86 024 88487143; Fax: +86 024 88487143
| | - Zhihong Zhang
- Correspondence: Zhihong Zhang, E-mail: ; Tel: +86 024 88487143; Fax: +86 024 88487143. Junxiang Zhang, E-mail: ; Tel: +86 024 88487143; Fax: +86 024 88487143
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Cui Z, Luo J, Qi C, Ruan Y, Li J, Zhang A, Yang X, He Y. Genome-wide association study (GWAS) reveals the genetic architecture of four husk traits in maize. BMC Genomics 2016; 17:946. [PMID: 27871222 PMCID: PMC5117540 DOI: 10.1186/s12864-016-3229-6] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2016] [Accepted: 11/01/2016] [Indexed: 12/21/2022] Open
Abstract
Background Maize (Zea mays) husk referring to the leafy outer enclosing the ear, plays an important role in grain production by directly contributing photosynthate and protecting ear from pathogen infection. Although the physiological functions related to husk have been extensively studied, little is known about its morphological variation and genetic basis in natural population. Results Here we utilized a maize association panel including 508 inbred lines with tropical, subtropical and temperate backgrounds to decipher the genetic architecture attributed to four husk traits, i.e. number of layers, length, width and thickness. Evaluating the phenotypic diversity at two different environments showed that four traits exhibit broadly natural variations and moderate levels of heritability with 0.64, 0.74, 0.49 and 0.75 for number, length, width and thickness, respectively. Diversity analysis indicated that different traits have dissimilar responses to subpopulation effects. A series of significantly positive or negative correlations between husk phenotypes and other agronomic traits were identified, indicating that husk growth is coordinated with other developmental processes. Combining husk traits with about half of a million of single nucleotide polymorphisms (SNPs) via genome-wide association study revealed a total of 9 variants significantly associated with traits at P < 1.04 × 10-5, which are implicated in multiple functional categories, such as cellular trafficking, transcriptional regulation and metabolism. Conclusions These results provide instrumental information for understanding the genetic basis of husk development, and further studies on identified candidate genes facilitate to illuminate molecular pathways regulating maize husk growth. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-3229-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Zhenhai Cui
- National Maize Improvement Center of China, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100094, China.,College of Biological Science and Technology, Shenyang Agricultural University, Shenyang, 110866, China
| | - Jinhong Luo
- National Maize Improvement Center of China, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100094, China
| | - Chuangye Qi
- National Maize Improvement Center of China, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100094, China
| | - Yanye Ruan
- College of Biological Science and Technology, Shenyang Agricultural University, Shenyang, 110866, China
| | - Jing Li
- National Maize Improvement Center of China, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100094, China
| | - Ao Zhang
- National Maize Improvement Center of China, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100094, China.,College of Agronomy, Shenyang Agricultural University, Shenyang, 110866, China
| | - Xiaohong Yang
- National Maize Improvement Center of China, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100094, China.
| | - Yan He
- National Maize Improvement Center of China, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100094, China.
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Digel B, Tavakol E, Verderio G, Tondelli A, Xu X, Cattivelli L, Rossini L, von Korff M. Photoperiod-H1 (Ppd-H1) Controls Leaf Size. PLANT PHYSIOLOGY 2016; 172:405-15. [PMID: 27457126 PMCID: PMC5074620 DOI: 10.1104/pp.16.00977] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2016] [Accepted: 07/22/2016] [Indexed: 05/18/2023]
Abstract
Leaf size is a major determinant of plant photosynthetic activity and biomass; however, it is poorly understood how leaf size is genetically controlled in cereal crop plants like barley (Hordeum vulgare). We conducted a genome-wide association scan for flowering time, leaf width, and leaf length in a diverse panel of European winter cultivars grown in the field and genotyped with a single-nucleotide polymorphism array. The genome-wide association scan identified PHOTOPERIOD-H1 (Ppd-H1) as a candidate gene underlying the major quantitative trait loci for flowering time and leaf size in the barley population. Microscopic phenotyping of three independent introgression lines confirmed the effect of Ppd-H1 on leaf size. Differences in the duration of leaf growth and consequent variation in leaf cell number were responsible for the leaf size differences between the Ppd-H1 variants. The Ppd-H1-dependent induction of the BARLEY MADS BOX genes BM3 and BM8 in the leaf correlated with reductions in leaf size and leaf number. Our results indicate that leaf size is controlled by the Ppd-H1- and photoperiod-dependent progression of plant development. The coordination of leaf growth with flowering may be part of a reproductive strategy to optimize resource allocation to the developing inflorescences and seeds.
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Affiliation(s)
- Benedikt Digel
- Max Planck Institute for Plant Breeding Research, D-50829 Cologne, Germany (B.D., M.v.K.);Institute of Plant Genetics, Heinrich-Heine-University, 40225 Duesseldorf, Germany (B.D., M.v.K.);Cluster of Excellence on Plant Sciences "From Complex Traits Towards Synthetic Modules," 40225 Duesseldorf, Germany (B.D., M.v.K.);Università degli Studi di Milano-DiSAA, 20133 Milan, Italy (E.T., G.V., L.R.);Department of Crop Production and Plant Breeding, College of Agriculture, Shiraz University, 7144165186 Shiraz, Iran (E.T.);Council for Agricultural Research and Economics, Genomics Research Centre, 29017 Fiorenzuola d'Arda, Italy (A.T., L.C.);Hubei Provincial Key Laboratory for Protection and Application of Special Plants in Wu Ling Area of China, Key Laboratory of State Ethnic Affairs Commission for Biologica Technology, College of Life Science, South-Central University for Nationalities, Wuhan 430074, China (X.X.); andParco Tecnologico Padano, Loc. Cascina Codazza, 26900 Lodi, Italy (L.R.)
| | - Elahe Tavakol
- Max Planck Institute for Plant Breeding Research, D-50829 Cologne, Germany (B.D., M.v.K.);Institute of Plant Genetics, Heinrich-Heine-University, 40225 Duesseldorf, Germany (B.D., M.v.K.);Cluster of Excellence on Plant Sciences "From Complex Traits Towards Synthetic Modules," 40225 Duesseldorf, Germany (B.D., M.v.K.);Università degli Studi di Milano-DiSAA, 20133 Milan, Italy (E.T., G.V., L.R.);Department of Crop Production and Plant Breeding, College of Agriculture, Shiraz University, 7144165186 Shiraz, Iran (E.T.);Council for Agricultural Research and Economics, Genomics Research Centre, 29017 Fiorenzuola d'Arda, Italy (A.T., L.C.);Hubei Provincial Key Laboratory for Protection and Application of Special Plants in Wu Ling Area of China, Key Laboratory of State Ethnic Affairs Commission for Biologica Technology, College of Life Science, South-Central University for Nationalities, Wuhan 430074, China (X.X.); andParco Tecnologico Padano, Loc. Cascina Codazza, 26900 Lodi, Italy (L.R.)
| | - Gabriele Verderio
- Max Planck Institute for Plant Breeding Research, D-50829 Cologne, Germany (B.D., M.v.K.);Institute of Plant Genetics, Heinrich-Heine-University, 40225 Duesseldorf, Germany (B.D., M.v.K.);Cluster of Excellence on Plant Sciences "From Complex Traits Towards Synthetic Modules," 40225 Duesseldorf, Germany (B.D., M.v.K.);Università degli Studi di Milano-DiSAA, 20133 Milan, Italy (E.T., G.V., L.R.);Department of Crop Production and Plant Breeding, College of Agriculture, Shiraz University, 7144165186 Shiraz, Iran (E.T.);Council for Agricultural Research and Economics, Genomics Research Centre, 29017 Fiorenzuola d'Arda, Italy (A.T., L.C.);Hubei Provincial Key Laboratory for Protection and Application of Special Plants in Wu Ling Area of China, Key Laboratory of State Ethnic Affairs Commission for Biologica Technology, College of Life Science, South-Central University for Nationalities, Wuhan 430074, China (X.X.); andParco Tecnologico Padano, Loc. Cascina Codazza, 26900 Lodi, Italy (L.R.)
| | - Alessandro Tondelli
- Max Planck Institute for Plant Breeding Research, D-50829 Cologne, Germany (B.D., M.v.K.);Institute of Plant Genetics, Heinrich-Heine-University, 40225 Duesseldorf, Germany (B.D., M.v.K.);Cluster of Excellence on Plant Sciences "From Complex Traits Towards Synthetic Modules," 40225 Duesseldorf, Germany (B.D., M.v.K.);Università degli Studi di Milano-DiSAA, 20133 Milan, Italy (E.T., G.V., L.R.);Department of Crop Production and Plant Breeding, College of Agriculture, Shiraz University, 7144165186 Shiraz, Iran (E.T.);Council for Agricultural Research and Economics, Genomics Research Centre, 29017 Fiorenzuola d'Arda, Italy (A.T., L.C.);Hubei Provincial Key Laboratory for Protection and Application of Special Plants in Wu Ling Area of China, Key Laboratory of State Ethnic Affairs Commission for Biologica Technology, College of Life Science, South-Central University for Nationalities, Wuhan 430074, China (X.X.); andParco Tecnologico Padano, Loc. Cascina Codazza, 26900 Lodi, Italy (L.R.)
| | - Xin Xu
- Max Planck Institute for Plant Breeding Research, D-50829 Cologne, Germany (B.D., M.v.K.);Institute of Plant Genetics, Heinrich-Heine-University, 40225 Duesseldorf, Germany (B.D., M.v.K.);Cluster of Excellence on Plant Sciences "From Complex Traits Towards Synthetic Modules," 40225 Duesseldorf, Germany (B.D., M.v.K.);Università degli Studi di Milano-DiSAA, 20133 Milan, Italy (E.T., G.V., L.R.);Department of Crop Production and Plant Breeding, College of Agriculture, Shiraz University, 7144165186 Shiraz, Iran (E.T.);Council for Agricultural Research and Economics, Genomics Research Centre, 29017 Fiorenzuola d'Arda, Italy (A.T., L.C.);Hubei Provincial Key Laboratory for Protection and Application of Special Plants in Wu Ling Area of China, Key Laboratory of State Ethnic Affairs Commission for Biologica Technology, College of Life Science, South-Central University for Nationalities, Wuhan 430074, China (X.X.); andParco Tecnologico Padano, Loc. Cascina Codazza, 26900 Lodi, Italy (L.R.)
| | - Luigi Cattivelli
- Max Planck Institute for Plant Breeding Research, D-50829 Cologne, Germany (B.D., M.v.K.);Institute of Plant Genetics, Heinrich-Heine-University, 40225 Duesseldorf, Germany (B.D., M.v.K.);Cluster of Excellence on Plant Sciences "From Complex Traits Towards Synthetic Modules," 40225 Duesseldorf, Germany (B.D., M.v.K.);Università degli Studi di Milano-DiSAA, 20133 Milan, Italy (E.T., G.V., L.R.);Department of Crop Production and Plant Breeding, College of Agriculture, Shiraz University, 7144165186 Shiraz, Iran (E.T.);Council for Agricultural Research and Economics, Genomics Research Centre, 29017 Fiorenzuola d'Arda, Italy (A.T., L.C.);Hubei Provincial Key Laboratory for Protection and Application of Special Plants in Wu Ling Area of China, Key Laboratory of State Ethnic Affairs Commission for Biologica Technology, College of Life Science, South-Central University for Nationalities, Wuhan 430074, China (X.X.); andParco Tecnologico Padano, Loc. Cascina Codazza, 26900 Lodi, Italy (L.R.)
| | - Laura Rossini
- Max Planck Institute for Plant Breeding Research, D-50829 Cologne, Germany (B.D., M.v.K.);Institute of Plant Genetics, Heinrich-Heine-University, 40225 Duesseldorf, Germany (B.D., M.v.K.);Cluster of Excellence on Plant Sciences "From Complex Traits Towards Synthetic Modules," 40225 Duesseldorf, Germany (B.D., M.v.K.);Università degli Studi di Milano-DiSAA, 20133 Milan, Italy (E.T., G.V., L.R.);Department of Crop Production and Plant Breeding, College of Agriculture, Shiraz University, 7144165186 Shiraz, Iran (E.T.);Council for Agricultural Research and Economics, Genomics Research Centre, 29017 Fiorenzuola d'Arda, Italy (A.T., L.C.);Hubei Provincial Key Laboratory for Protection and Application of Special Plants in Wu Ling Area of China, Key Laboratory of State Ethnic Affairs Commission for Biologica Technology, College of Life Science, South-Central University for Nationalities, Wuhan 430074, China (X.X.); andParco Tecnologico Padano, Loc. Cascina Codazza, 26900 Lodi, Italy (L.R.)
| | - Maria von Korff
- Max Planck Institute for Plant Breeding Research, D-50829 Cologne, Germany (B.D., M.v.K.);Institute of Plant Genetics, Heinrich-Heine-University, 40225 Duesseldorf, Germany (B.D., M.v.K.);Cluster of Excellence on Plant Sciences "From Complex Traits Towards Synthetic Modules," 40225 Duesseldorf, Germany (B.D., M.v.K.);Università degli Studi di Milano-DiSAA, 20133 Milan, Italy (E.T., G.V., L.R.);Department of Crop Production and Plant Breeding, College of Agriculture, Shiraz University, 7144165186 Shiraz, Iran (E.T.);Council for Agricultural Research and Economics, Genomics Research Centre, 29017 Fiorenzuola d'Arda, Italy (A.T., L.C.);Hubei Provincial Key Laboratory for Protection and Application of Special Plants in Wu Ling Area of China, Key Laboratory of State Ethnic Affairs Commission for Biologica Technology, College of Life Science, South-Central University for Nationalities, Wuhan 430074, China (X.X.); andParco Tecnologico Padano, Loc. Cascina Codazza, 26900 Lodi, Italy (L.R.)
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