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Mitsuhashi S. Genetic diversity among maize (Zea mays L.) inbred lines adapted to Japanese climates. PLoS One 2024; 19:e0297549. [PMID: 38271395 PMCID: PMC10810424 DOI: 10.1371/journal.pone.0297549] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Accepted: 01/08/2024] [Indexed: 01/27/2024] Open
Abstract
Understanding the genetic diversity of inbred lines is vital for development of superior F1 varieties. The present study aimed to analyze Japanese maize parental inbred lines and determine their genetic diversity for future breeding. Genetic analyses were conducted using multiple methods. Principal component analysis (PCA), phylogenetic trees, and Bayesian clustering reflected borders between heterotic groups according to the derivation of each inbred line. A self-pollinated line derived from a classic F1 variety and another line from an open-pollinated population from the same derivation were classified as separate components by PCA and Bayesian clustering. The result suggests that open pollination could be essential in modern breeding. Of those classified as dent or flint based on their derivation, some had a combination of all components or clusters. Therefore, the classification of inbred lines should be based on their derivation and DNA markers. The findings will be valuable for breeding and genetic studies in Japan. Additionally, these techniques may be used to obtain a more significant number of SNPs and related phenotypic data.
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Affiliation(s)
- Shohei Mitsuhashi
- Institute of Livestock and Grassland Science, NARO, Nasushiobara, Tochigi, Japan
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Mastrangelo AM, Hartings H, Lanzanova C, Balconi C, Locatelli S, Cassol H, Valoti P, Petruzzino G, Pecchioni N. Genetic Diversity within a Collection of Italian Maize Inbred Lines: A Resource for Maize Genomics and Breeding. PLANTS (BASEL, SWITZERLAND) 2024; 13:336. [PMID: 38337869 PMCID: PMC10857507 DOI: 10.3390/plants13030336] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Revised: 01/16/2024] [Accepted: 01/17/2024] [Indexed: 02/12/2024]
Abstract
Genetic diversity is fundamental for studying the complex architecture of the traits of agronomic importance, controlled by major and minor loci. Moreover, well-characterized germplasm collections are essential tools for dissecting and analyzing genetic and phenotypic diversity in crops. A panel of 360 entries, a subset of a larger collection maintained within the GenBank at CREA Bergamo, which includes the inbreds derived from traditional Italian maize open-pollinated (OP) varieties and advanced breeding ones (Elite Inbreds), was analyzed to identify SNP markers using the tGBS® genotyping-by-sequencing technology. A total of 797,368 SNPs were found during the initial analysis. Imputation and filtering processes were carried out based on the percentage of missing data, redundant markers, and rarest allele frequencies, resulting in a final dataset of 15,872 SNP markers for which a physical map position was identified. Using this dataset, the inbred panel was characterized for linkage disequilibrium (LD), genetic diversity, population structure, and genetic relationships. LD decay at a genome-wide level indicates that the collection is a suitable resource for association mapping. Population structure analyses, which were carried out with different clustering methods, showed stable grouping statistics for four groups, broadly corresponding to 'Insubria', 'Microsperma', and 'Scagliolino' genotypes, with a fourth group composed prevalently of elite accessions derived from Italian and US breeding programs. Based on these results, the CREA Italian maize collection, genetically characterized in this study, can be considered an important tool for the mapping and characterization of useful traits and associated loci/alleles, to be used in maize breeding programs.
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Affiliation(s)
- Anna Maria Mastrangelo
- CREA-Centro di Ricerca Cerealicoltura e Colture Industriali/Research Centre for Cereal and Industrial Crops, SS 673 Metri 25200, 71122 Foggia, Italy; (G.P.); (N.P.)
| | - Hans Hartings
- CREA-Centro di Ricerca Cerealicoltura e Colture Industriali/Research Centre for Cereal and Industrial Crops, Via Stezzano 24, 24126 Bergamo, Italy; (H.H.); (C.L.); (C.B.); (S.L.); (H.C.); (P.V.)
| | - Chiara Lanzanova
- CREA-Centro di Ricerca Cerealicoltura e Colture Industriali/Research Centre for Cereal and Industrial Crops, Via Stezzano 24, 24126 Bergamo, Italy; (H.H.); (C.L.); (C.B.); (S.L.); (H.C.); (P.V.)
| | - Carlotta Balconi
- CREA-Centro di Ricerca Cerealicoltura e Colture Industriali/Research Centre for Cereal and Industrial Crops, Via Stezzano 24, 24126 Bergamo, Italy; (H.H.); (C.L.); (C.B.); (S.L.); (H.C.); (P.V.)
| | - Sabrina Locatelli
- CREA-Centro di Ricerca Cerealicoltura e Colture Industriali/Research Centre for Cereal and Industrial Crops, Via Stezzano 24, 24126 Bergamo, Italy; (H.H.); (C.L.); (C.B.); (S.L.); (H.C.); (P.V.)
| | - Helga Cassol
- CREA-Centro di Ricerca Cerealicoltura e Colture Industriali/Research Centre for Cereal and Industrial Crops, Via Stezzano 24, 24126 Bergamo, Italy; (H.H.); (C.L.); (C.B.); (S.L.); (H.C.); (P.V.)
| | - Paolo Valoti
- CREA-Centro di Ricerca Cerealicoltura e Colture Industriali/Research Centre for Cereal and Industrial Crops, Via Stezzano 24, 24126 Bergamo, Italy; (H.H.); (C.L.); (C.B.); (S.L.); (H.C.); (P.V.)
| | - Giuseppe Petruzzino
- CREA-Centro di Ricerca Cerealicoltura e Colture Industriali/Research Centre for Cereal and Industrial Crops, SS 673 Metri 25200, 71122 Foggia, Italy; (G.P.); (N.P.)
| | - Nicola Pecchioni
- CREA-Centro di Ricerca Cerealicoltura e Colture Industriali/Research Centre for Cereal and Industrial Crops, SS 673 Metri 25200, 71122 Foggia, Italy; (G.P.); (N.P.)
- CREA-Centro di Ricerca Cerealicoltura e Colture Industriali/Research Centre for Cereal and Industrial Crops, Via Stezzano 24, 24126 Bergamo, Italy; (H.H.); (C.L.); (C.B.); (S.L.); (H.C.); (P.V.)
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