1
|
Marzario S, Sica R, Taranto F, Fania F, Esposito S, De Vita P, Gioia T, Logozzo G. Phenotypic evolution in durum wheat ( Triticum durum Desf.) based on SNPs, morphological traits, UPOV descriptors and kernel-related traits. FRONTIERS IN PLANT SCIENCE 2023; 14:1206560. [PMID: 37701808 PMCID: PMC10493298 DOI: 10.3389/fpls.2023.1206560] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2023] [Accepted: 07/21/2023] [Indexed: 09/14/2023]
Abstract
Durum wheat is a worldwide staple crop cultivated mainly in the Mediterranean basin. Progress in durum wheat breeding requires the exploitation of genetic variation among the gene pool enclosed in landraces, old cultivars and modern cultivars. The aim of this study was to provide a more comprehensive view of the genetic architecture evolution among 123 durum wheat accessions (41 landraces, 41 old cultivars and 41 modern cultivars), grown in replicated randomized complete block in two areas, Metaponto (Basilicata) and Foggia (Apulia), using the Illumina iSelect 15K wheat SNP array and 33 plant and kernel traits including the International Union for the Protection of new Varieties of Plants (UPOV) descriptors. Through DAPC and Bayesian population structure five groups were identified according to type of material data and reflecting the genetic basis and breeding strategies involved in their development. Phenotypic and genotypic coefficient of variation were low for kernel width (6.43%) and for grain protein content (1.03%). Highly significant differences between environments, genotypes and GEI (Genotype x Environment Interaction) were detected by mixed ANOVAs for agro-morphological-quality traits. Number of kernels per spike (h2 = 0.02) and grain protein content (h2 = 0.03) were not a heritability character and highly influenced by the environment. Nested ANOVAs revealed highly significant differences between DAPC clusters within environments for all traits except kernel roundness. Ten UPOV traits showed significant diversity for their frequencies in the two environments. By PCAmix multivariate analysis, plant height, heading time, spike length, weight of kernels per spike, thousand kernel weight, and the seed related traits had heavy weight on the differentiation of the groups, while UPOV traits discriminated moderately or to a little extent. The data collected in this study provide useful resources to facilitate management and use of wheat genetic diversity that has been lost due to selection in the last decades.
Collapse
Affiliation(s)
- Stefania Marzario
- School of Agricultural, Forestry, Food and Environmental Sciences, University of Basilicata, Potenza, Italy
| | - Rita Sica
- School of Agricultural, Forestry, Food and Environmental Sciences, University of Basilicata, Potenza, Italy
| | | | - Fabio Fania
- Department of Agriculture, Food, Natural Resources, and Engineering (DAFNE) - University of Foggia, Foggia, Italy
| | | | - Pasquale De Vita
- Council for Agricultural Research and Economics (CREA), Research Centre for Cereal and Industrial Crops (CREA-CI), Foggia, Italy
| | - Tania Gioia
- School of Agricultural, Forestry, Food and Environmental Sciences, University of Basilicata, Potenza, Italy
| | - Giuseppina Logozzo
- School of Agricultural, Forestry, Food and Environmental Sciences, University of Basilicata, Potenza, Italy
| |
Collapse
|
2
|
Long Z, Tu M, Xu Y, Pak H, Zhu Y, Dong J, Lu Y, Jiang L. Genome-wide-association study and transcriptome analysis reveal the genetic basis controlling the formation of leaf wax in Brassica napus. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:2726-2739. [PMID: 36724105 DOI: 10.1093/jxb/erad047] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Accepted: 02/01/2023] [Indexed: 06/06/2023]
Abstract
Cuticular wax protects plants from various biotic and abiotic stresses. However, the genetic network of wax biosynthesis and the environmental factors influencing leaf wax production in rapeseed (Brassica napus) remains unclear. Here, we demonstrated the role of leaf wax in the resistance to Sclerotinia infection in rapeseed. We found that leaves grown under high light intensity had higher expression of genes involved in wax biosynthesis, and produced more wax on the leaf surface, compared with those grown under low light conditions. Genome-wide association study (GWAS) identified 89 single nucleotide polymorphisms significantly associated with leaf wax coverage. A cross-analysis between GWAS and differentially expressed genes (DEGs) in the leaf epidermis of the accessions with contrasting differences in wax content revealed 17 candidate genes that control this variation in rapeseed. Selective sweep analysis combined with DEG analysis unveiled 510 candidate genes with significant selective signatures. From the candidate genes, we selected BnaA02.LOX4, a putative lipoxygenase, and BnaCnn.CER1, BnaA02.CER3, BnaC02.CER3, and BnaA01.CER4 (ECERIFERUM1-4) that were putatively responsible for wax biosynthesis, to analyse the allelic forms and haplotypes corresponding to high or low leaf wax coverage. These data enrich our knowledge about wax formation, and provide a gene pool for breeding an ideal leaf wax content in rapeseed.
Collapse
Affiliation(s)
- Zhengbiao Long
- Institute of Crop Science, Zhejiang University, Yu-Hang-Tang Road 866, 310058, Hangzhou, China
| | - Mengxin Tu
- Institute of Crop Science, Zhejiang University, Yu-Hang-Tang Road 866, 310058, Hangzhou, China
| | - Ying Xu
- Institute of Crop Science, Zhejiang University, Yu-Hang-Tang Road 866, 310058, Hangzhou, China
| | - Haksong Pak
- Institute of Crop Science, Zhejiang University, Yu-Hang-Tang Road 866, 310058, Hangzhou, China
| | - Yang Zhu
- Institute of Crop Science, Zhejiang University, Yu-Hang-Tang Road 866, 310058, Hangzhou, China
| | - Jie Dong
- Institute of Crop Science, Zhejiang University, Yu-Hang-Tang Road 866, 310058, Hangzhou, China
| | - Yunhai Lu
- Institute of Crop Science, Zhejiang University, Yu-Hang-Tang Road 866, 310058, Hangzhou, China
| | - Lixi Jiang
- Institute of Crop Science, Zhejiang University, Yu-Hang-Tang Road 866, 310058, Hangzhou, China
| |
Collapse
|
3
|
Assessing the role of glaucousness in imparting tolerance to moisture and heat stress in wheat. Biologia (Bratisl) 2022. [DOI: 10.1007/s11756-022-01177-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
|
4
|
Zheng J, Yang C, Zheng X, Yan S, Qu F, Zhao J, Pei Y. Lipidomic, Transcriptomic, and BSA-660K Single Nucleotide Polymorphisms Profiling Reveal Characteristics of the Cuticular Wax in Wheat. FRONTIERS IN PLANT SCIENCE 2021; 12:794878. [PMID: 34899814 PMCID: PMC8652291 DOI: 10.3389/fpls.2021.794878] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Accepted: 10/26/2021] [Indexed: 05/15/2023]
Abstract
Plant epidermal wax helps protect plants from adverse environmental conditions, maintains the function of tissues and organs, and ensures normal plant development. However, the constituents of epidermal wax and the regulatory mechanism of their biosynthesis in wheat have not been fully understood. Wheat varieties with different wax content, Jinmai47 and Jinmai84, were selected to comparatively analyze their waxy components and genetic characteristics, using a combination of lipidomic, transcriptomic, and BSA-Wheat 660K chip analysis. Through lipidomic analysis, 1287 lipid molecules were identified representing 31 lipid subclasses. Among these, Diacylglycerols (DG), (O-acyl)-ω-hydroxy fatty acids (OAHFA), wax ester (WE), Triacylglycerols (TG), and Monoradylglycerols (MG) accounted for 96.4% of the total lipids in Jinmai84 and 94.5% in Jinmai47. DG, OAHFA, and WE were higher in Jinmai84 than in Jinmai47 with the content of OAHFA 2.88-fold greater and DG 1.66-fold greater. Transcriptome sequence and bioinformatics analysis revealed 63 differentially expressed genes related to wax biosynthesis. Differentially expressed genes (DEGs) were found to be involved with the OAHFA, DG, and MG of synthesis pathways, which enriched the wax metabolism pathway. Non-glaucous and glaucous bulks from a mapping population were used to identify single nucleotide polymorphisms (SNP) via 660K chip analysis. Two loci centered on chromosomes 2D and 4B were detected and the locus on 4B is likely novel. These data improve understanding of complex lipid metabolism for cuticular wax biosynthesis in wheat and lay the foundation for future detailed investigation of mechanisms regulating wax metabolism.
Collapse
Affiliation(s)
- Jun Zheng
- State Key Laboratory of Sustainable Dryland Agriculture, Institute of Wheat Research, Shanxi Agricultural University, Linfen, China
- College of Life Science, Shanxi University, Taiyuan, China
| | - Chenkang Yang
- College of Life Science, Shanxi University, Taiyuan, China
| | - Xingwei Zheng
- State Key Laboratory of Sustainable Dryland Agriculture, Institute of Wheat Research, Shanxi Agricultural University, Linfen, China
| | - Suxian Yan
- State Key Laboratory of Sustainable Dryland Agriculture, Institute of Wheat Research, Shanxi Agricultural University, Linfen, China
| | - Fei Qu
- State Key Laboratory of Sustainable Dryland Agriculture, Institute of Wheat Research, Shanxi Agricultural University, Linfen, China
| | - Jiajia Zhao
- State Key Laboratory of Sustainable Dryland Agriculture, Institute of Wheat Research, Shanxi Agricultural University, Linfen, China
| | - Yanxi Pei
- College of Life Science, Shanxi University, Taiyuan, China
| |
Collapse
|
5
|
Barraj Barraj R, Segado P, Moreno-González R, Heredia A, Fernández-Muñoz R, Domínguez E. Genome-wide QTL analysis of tomato fruit cuticle deposition and composition. HORTICULTURE RESEARCH 2021; 8:113. [PMID: 33931622 PMCID: PMC8087829 DOI: 10.1038/s41438-021-00548-5] [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: 11/23/2020] [Revised: 03/22/2021] [Accepted: 04/01/2021] [Indexed: 05/24/2023]
Abstract
Genetics of traits related to fruit cuticle deposition and composition was studied in two red-fruited tomato species. Two mapping populations derived from the cross between the cultivated tomato (Solanum lycopersicum L.) and its closest relative wild species Solanum pimpinellifolium L. were employed to conduct a QTL analysis. A combination of fruit cuticle deposition, components and anatomical traits were investigated and the individual effect of each QTL evaluated. A total of 70 QTLs were identified, indicating that all the cuticle traits analyzed have a complex polygenic nature. A combination of additive and epistatic interactions was observed for all the traits, with positive contribution of both parental lines to most of them. Colocalization of QTLs for various traits uncovered novel genomic regions producing extensive changes in the cuticle. Cuticle density emerges as an important trait since it can modulate cuticle thickness and invagination thus providing a strategy for sustaining mechanical strength without compromising palatability. Two genomic regions, located in chromosomes 1 and 12, are responsible for the negative interaction between cuticle waxes and phenolics identified in tomato fruit. Several candidate genes, including transcription factors and structural genes, are postulated and their expression analyzed throughout development.
Collapse
Affiliation(s)
- Rida Barraj Barraj
- Instituto de Hortofruticultura Subtropical y Mediterránea La Mayora, Universidad de Málaga-Consejo Superior de Investigaciones Científicas, Departamento de Mejora Genética y Biotecnología, Estación Experimental La Mayora, Algarrobo-Costa, E-29750, Málaga, Spain
| | - Patricia Segado
- Instituto de Hortofruticultura Subtropical y Mediterránea La Mayora, Universidad de Málaga-Consejo Superior de Investigaciones Científicas, Departamento de Biología Molecular y Bioquímica, Universidad de Málaga, E-29071, Málaga, Spain
| | - Rocío Moreno-González
- Instituto de Hortofruticultura Subtropical y Mediterránea La Mayora, Universidad de Málaga-Consejo Superior de Investigaciones Científicas, Departamento de Biología Molecular y Bioquímica, Universidad de Málaga, E-29071, Málaga, Spain
- Departament de Bioquímica i Fisiologia and Institut de Recerca en Nutrició i Seguretat Alimentària (INSA-UB), Universitat de Barcelona (UB), E-08028, Barcelona, Spain
| | - Antonio Heredia
- Instituto de Hortofruticultura Subtropical y Mediterránea La Mayora, Universidad de Málaga-Consejo Superior de Investigaciones Científicas, Departamento de Biología Molecular y Bioquímica, Universidad de Málaga, E-29071, Málaga, Spain
| | - Rafael Fernández-Muñoz
- Instituto de Hortofruticultura Subtropical y Mediterránea La Mayora, Universidad de Málaga-Consejo Superior de Investigaciones Científicas, Departamento de Mejora Genética y Biotecnología, Estación Experimental La Mayora, Algarrobo-Costa, E-29750, Málaga, Spain
| | - Eva Domínguez
- Instituto de Hortofruticultura Subtropical y Mediterránea La Mayora, Universidad de Málaga-Consejo Superior de Investigaciones Científicas, Departamento de Mejora Genética y Biotecnología, Estación Experimental La Mayora, Algarrobo-Costa, E-29750, Málaga, Spain.
| |
Collapse
|
6
|
Góralska M, Bińkowski J, Lenarczyk N, Bienias A, Grądzielewska A, Czyczyło-Mysza I, Kapłoniak K, Stojałowski S, Myśków B. How Machine Learning Methods Helped Find Putative Rye Wax Genes Among GBS Data. Int J Mol Sci 2020; 21:E7501. [PMID: 33053706 PMCID: PMC7593958 DOI: 10.3390/ijms21207501] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Revised: 09/23/2020] [Accepted: 10/07/2020] [Indexed: 11/17/2022] Open
Abstract
The standard approach to genetic mapping was supplemented by machine learning (ML) to establish the location of the rye gene associated with epicuticular wax formation (glaucous phenotype). Over 180 plants of the biparental F2 population were genotyped with the DArTseq (sequencing-based diversity array technology). A maximum likelihood (MLH) algorithm (JoinMap 5.0) and three ML algorithms: logistic regression (LR), random forest and extreme gradient boosted trees (XGBoost), were used to select markers closely linked to the gene encoding wax layer. The allele conditioning the nonglaucous appearance of plants, derived from the cultivar Karlikovaja Zelenostebelnaja, was mapped at the chromosome 2R, which is the first report on this localization. The DNA sequence of DArT-Silico 3585843, closely linked to wax segregation detected by using ML methods, was indicated as one of the candidates controlling the studied trait. The putative gene encodes the ABCG11 transporter.
Collapse
Affiliation(s)
- Magdalena Góralska
- Department of Plant Genetics, Breeding and Biotechnology, West-Pomeranian University of Technology, Szczecin, ul. Słowackiego 17, 71–434 Szczecin, Poland; (M.G.); (J.B.); (N.L.); (A.B.); (S.S.)
| | - Jan Bińkowski
- Department of Plant Genetics, Breeding and Biotechnology, West-Pomeranian University of Technology, Szczecin, ul. Słowackiego 17, 71–434 Szczecin, Poland; (M.G.); (J.B.); (N.L.); (A.B.); (S.S.)
| | - Natalia Lenarczyk
- Department of Plant Genetics, Breeding and Biotechnology, West-Pomeranian University of Technology, Szczecin, ul. Słowackiego 17, 71–434 Szczecin, Poland; (M.G.); (J.B.); (N.L.); (A.B.); (S.S.)
| | - Anna Bienias
- Department of Plant Genetics, Breeding and Biotechnology, West-Pomeranian University of Technology, Szczecin, ul. Słowackiego 17, 71–434 Szczecin, Poland; (M.G.); (J.B.); (N.L.); (A.B.); (S.S.)
| | - Agnieszka Grądzielewska
- Institute of Plant Genetics, Breeding and Biotechnology, University of Life Sciences in Lublin, ul. Akademicka, 20–950 Lublin, Poland;
| | - Ilona Czyczyło-Mysza
- Polish Academy of Sciences, The Franciszek Górski Institute of Plant Physiology, Niezapominajek 21, 30–239 Kraków, Poland; (I.C.-M.); (K.K.)
| | - Kamila Kapłoniak
- Polish Academy of Sciences, The Franciszek Górski Institute of Plant Physiology, Niezapominajek 21, 30–239 Kraków, Poland; (I.C.-M.); (K.K.)
| | - Stefan Stojałowski
- Department of Plant Genetics, Breeding and Biotechnology, West-Pomeranian University of Technology, Szczecin, ul. Słowackiego 17, 71–434 Szczecin, Poland; (M.G.); (J.B.); (N.L.); (A.B.); (S.S.)
| | - Beata Myśków
- Department of Plant Genetics, Breeding and Biotechnology, West-Pomeranian University of Technology, Szczecin, ul. Słowackiego 17, 71–434 Szczecin, Poland; (M.G.); (J.B.); (N.L.); (A.B.); (S.S.)
| |
Collapse
|
7
|
Würschum T, Leiser WL, Langer SM, Tucker MR, Miedaner T. Genetic Architecture of Cereal Leaf Beetle Resistance in Wheat. PLANTS (BASEL, SWITZERLAND) 2020; 9:plants9091117. [PMID: 32872389 PMCID: PMC7570205 DOI: 10.3390/plants9091117] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Revised: 08/24/2020] [Accepted: 08/25/2020] [Indexed: 06/11/2023]
Abstract
Wheat production can be severely damaged by endemic and invasive insect pests. Here, we investigated resistance to cereal leaf beetle in a panel of 876 winter wheat cultivars, and dissected the genetic architecture underlying this insect resistance by association mapping. We observed an effect of heading date on cereal leaf beetle infestation, with earlier heading cultivars being more heavily infested. Flag leaf glaucousness was also found to be correlated with resistance. In line with the strong effect of heading time, we identified Ppd-D1 as a major quantitative trait locus (QTL), explaining 35% of the genotypic variance of cereal leaf beetle resistance. The other identified putative QTL explained much less of the genotypic variance, suggesting a genetic architecture with many small-effect QTL, which was corroborated by a genomic prediction approach. Collectively, our results add to our understanding of the genetic control underlying insect resistances in small-grain cereals.
Collapse
Affiliation(s)
- Tobias Würschum
- Institute of Plant Breeding, Seed Science and Population Genetics, University of Hohenheim, 70593 Stuttgart, Germany
| | - Willmar L. Leiser
- State Plant Breeding Institute, University of Hohenheim, 70593 Stuttgart, Germany; (W.L.L.); (S.M.L.); (T.M.)
| | - Simon M. Langer
- State Plant Breeding Institute, University of Hohenheim, 70593 Stuttgart, Germany; (W.L.L.); (S.M.L.); (T.M.)
- BASF Agricultural Solutions GmbH, 67063 Ludwigshafen, Germany
| | - Matthew R. Tucker
- School of Agriculture, Food and Wine, Waite Campus, University of Adelaide, 5064 Urrbrae, Australia
| | - Thomas Miedaner
- State Plant Breeding Institute, University of Hohenheim, 70593 Stuttgart, Germany; (W.L.L.); (S.M.L.); (T.M.)
| |
Collapse
|