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Exome-wide variation in a diverse barley panel reveals genetic associations with ten agronomic traits in Eastern landraces. J Genet Genomics 2022; 50:241-252. [PMID: 36566016 DOI: 10.1016/j.jgg.2022.12.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 12/08/2022] [Accepted: 12/09/2022] [Indexed: 12/24/2022]
Abstract
Barley (Hordeum vulgare ssp. vulgare) was one of the first crops to be domesticated and is adapted to a wide range of environments. Worldwide barley germplasm collections possess valuable allelic variations that could further improve barley productivity. Although barley genomics has offered a global picture of allelic variation among varieties and its association with various agronomic traits, polymorphisms from East Asian varieties remain scarce. In this study, we analyzed exome polymorphisms in a panel of 274 barley varieties collected worldwide, including 137 varieties from East Asian countries and Ethiopia. We revealed the underlying population structure and conducted genome-wide association studies for ten agronomic traits. Moreover, we examined genome-wide associations for traits related to grain size such as awn length and glume length. Our results demonstrate the value of diverse barley germplasm panels containing Eastern varieties, highlighting their distinct genomic signatures relative to Western subpopulations.
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Mizuno N, Matsunaka H, Yanaka M, Nakata M, Nakamura K, Nakamaru A, Kiribuchi-Otobe C, Ishikawa G, Chono M, Hatta K, Fujita M, Kobayashi F. Allelic variations of Vrn-1 and Ppd-1 genes in Japanese wheat varieties reveal the genotype-environment interaction for heading time. BREEDING SCIENCE 2022; 72:343-354. [PMID: 36776445 PMCID: PMC9895800 DOI: 10.1270/jsbbs.22017] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Accepted: 08/07/2022] [Indexed: 05/31/2023]
Abstract
The timing of heading is largely affected by environmental conditions. In wheat, Vrn-1 and Ppd-1 have been identified as the major genes involved in vernalization requirement and photoperiod sensitivity, respectively. To compare the effects of Vrn-1 and Ppd-1 alleles on heading time under different environments, we genotyped Vrn-1 and Ppd-1 homoeologues and measured the heading time at Morioka, Tsukuba and Chikugo in Japan for two growing seasons. A total of 128 Japanese and six foreign varieties, classified into four populations based on the 519 genome-wide SNPs, were used for analysis. Varieties with the spring alleles (Vrn-D1a or Vrn-D1b) at the Vrn-D1 locus and insensitive allele (Hapl-I) at the Ppd-D1 locus were found in earlier heading varieties. The effects of Vrn-D1 and Ppd-D1 on heading time were stronger than those of the other Vrn-1 and Ppd-1 homoeologues. Analysis of variance revealed that heading time was significantly affected by the genotype-environment interactions. Some Vrn-1 and Ppd-1 alleles conferred earlier or later heading in specific environments, indicating that the effect of both alleles on the timing of heading depends on the environment. Information on Vrn-1 and Ppd-1 alleles, together with heading time in various environments, provide useful information for wheat breeding.
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Affiliation(s)
- Nobuyuki Mizuno
- Institute of Crop Science, National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518, Japan
| | - Hitoshi Matsunaka
- Kyusyu Okinawa Agricultural Research Center, National Agriculture and Food Research Organization, 496 Izumi, Chikugo, Fukuoka 833-0041, Japan
- Hokkaido Agricultural Research Center, National Agriculture and Food Research Organization, 9-4 Shinsei-minami, Memuro, Kasai, Hokkaido 082-0081, Japan
| | - Mikiko Yanaka
- Kyusyu Okinawa Agricultural Research Center, National Agriculture and Food Research Organization, 496 Izumi, Chikugo, Fukuoka 833-0041, Japan
| | - Masaru Nakata
- Kyusyu Okinawa Agricultural Research Center, National Agriculture and Food Research Organization, 496 Izumi, Chikugo, Fukuoka 833-0041, Japan
| | - Kazuhiro Nakamura
- Kyusyu Okinawa Agricultural Research Center, National Agriculture and Food Research Organization, 496 Izumi, Chikugo, Fukuoka 833-0041, Japan
| | - Akiko Nakamaru
- Tohoku Agricultural Research Center, National Agriculture and Food Research Organization, 4 Akahira, Shimo-kuriyagawa, Morioka, Iwate 020-0198, Japan
| | - Chikako Kiribuchi-Otobe
- Institute of Crop Science, National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518, Japan
| | - Goro Ishikawa
- Institute of Crop Science, National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518, Japan
| | - Makiko Chono
- Institute of Crop Science, National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518, Japan
| | - Koichi Hatta
- Institute of Crop Science, National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518, Japan
- Hokkaido Agricultural Research Center, National Agriculture and Food Research Organization, 9-4 Shinsei-minami, Memuro, Kasai, Hokkaido 082-0081, Japan
| | - Masaya Fujita
- Institute of Crop Science, National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518, Japan
| | - Fuminori Kobayashi
- Institute of Crop Science, National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518, Japan
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Fernández-Calleja M, Casas AM, Igartua E. Major flowering time genes of barley: allelic diversity, effects, and comparison with wheat. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2021; 134:1867-1897. [PMID: 33969431 PMCID: PMC8263424 DOI: 10.1007/s00122-021-03824-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Accepted: 03/24/2021] [Indexed: 05/10/2023]
Abstract
This review summarizes the allelic series, effects, interactions between genes and with the environment, for the major flowering time genes that drive phenological adaptation of barley. The optimization of phenology is a major goal of plant breeding addressing the production of high-yielding varieties adapted to changing climatic conditions. Flowering time in cereals is regulated by genetic networks that respond predominately to day length and temperature. Allelic diversity at these genes is at the basis of barley wide adaptation. Detailed knowledge of their effects, and genetic and environmental interactions will facilitate plant breeders manipulating flowering time in cereal germplasm enhancement, by exploiting appropriate gene combinations. This review describes a catalogue of alleles found in QTL studies by barley geneticists, corresponding to the genetic diversity at major flowering time genes, the main drivers of barley phenological adaptation: VRN-H1 (HvBM5A), VRN-H2 (HvZCCTa-c), VRN-H3 (HvFT1), PPD-H1 (HvPRR37), PPD-H2 (HvFT3), and eam6/eps2 (HvCEN). For each gene, allelic series, size and direction of QTL effects, interactions between genes and with the environment are presented. Pleiotropic effects on agronomically important traits such as grain yield are also discussed. The review includes brief comments on additional genes with large effects on phenology that became relevant in modern barley breeding. The parallelisms between flowering time allelic variation between the two most cultivated Triticeae species (barley and wheat) are also outlined. This work is mostly based on previously published data, although we added some new data and hypothesis supported by a number of studies. This review shows the wide variety of allelic effects that provide enormous plasticity in barley flowering behavior, which opens new avenues to breeders for fine-tuning phenology of the barley crop.
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Affiliation(s)
- Miriam Fernández-Calleja
- Department of Genetics and Plant Production, Aula Dei Experimental Station, EEAD-CSIC, Avenida Montañana, 1005, 50059, Zaragoza, Spain
| | - Ana M Casas
- Department of Genetics and Plant Production, Aula Dei Experimental Station, EEAD-CSIC, Avenida Montañana, 1005, 50059, Zaragoza, Spain
| | - Ernesto Igartua
- Department of Genetics and Plant Production, Aula Dei Experimental Station, EEAD-CSIC, Avenida Montañana, 1005, 50059, Zaragoza, Spain.
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