Genetic Factors Associated with Heading Responses Revealed by Field Evaluation of 274 Barley Accessions for 20 Seasons

Sato, Kazuhiro; Ishii, Makoto; Takahagi, Kotaro; Inoue, Komaki; Shimizu, Minami; Uehara‐Yamaguchi, Yukiko; Nishii, Ryuei; Mochida, Keiichi

doi:10.1016/j.isci.2020.101146

Cited by 7 publications

(2 citation statements)

References 38 publications

(43 reference statements)

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“…Interestingly, an early PHYC-e allele was selected in barley cultivars from Japan, where it may provide a selective advantage (Pankin et al 2014). Several population analysis studies support the role of HvPHYC in flowering time variation (Mikołajczak et al 2016;Ibrahim et al 2018;Hu et al 2019;Hill et al 2019;Sato et al 2020), as well as its effect in other agronomic traits, including yield (Tesso Obsa et al 2016;Gong et al 2016;Hill et al 2019). In the same pathway, mutations at HvELF3 (Mat-a or eam8) within recessive ppd-H1 stocks, were identified as a major earliness factor facilitating adaptation of barley to very short seasons, at high latitudes (Zakhrabekova et al 2012;Faure et al 2012).…”

Section: Other Genes Affecting Flowering Time Used In Modern Barley Breedingmentioning

confidence: 99%

Major flowering time genes of barley: allelic diversity, effects, and comparison with wheat

2021

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Key message 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. Abstract 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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Section: Other Genes Affecting Flowering Time Used In Modern Barley Breedingmentioning

confidence: 99%

Major flowering time genes of barley: allelic diversity, effects, and comparison with wheat

2021

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“…In barley, Vrn-H1 and Ppd-H1 were identified as the major stabilizing genes of the heading response for regional adaptation (Sato et al 2020). Vrn-1 and Ppd-1 genes have been frequently identified as the major quantitative trait loci for heading time in wheat (Guedira et al 2016, Iehisa et al 2014, Mizuno et al 2021, Nguyen et al 2013.…”

Section: Introductionmentioning

confidence: 99%

Allelic variations of <i>Vrn-1</i> and <i>Ppd-1</i> genes in Japanese wheat varieties reveal the genotype-environment interaction for heading time

et al. 2022

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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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Local haplotyping reveals insights into the genetic control of flowering time variation in wild and domesticated soybean

Mohamedikbal,

Al‐Mamun,

Marsh

et al. 2024

The Plant Genome

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The timing of flowering in soybean [Glycine max (L.) Merr.], a key legume crop, is influenced by many factors, including daylight length or photoperiodic sensitivity, that affect crop yield, productivity, and geographical adaptation. Despite its importance, a comprehensive understanding of the local linkage landscape and allelic diversity within regions of the genome influencing flowering and contributing to phenotypic variation in subpopulations has been limited. This study addresses these gaps by conducting an in‐depth trait association and linkage analysis coupled with local haplotyping using advanced bioinformatics tools, including crosshap, to characterize genomic variation using a pangenome dataset representing 915 domesticated and wild‐type individuals. The association analysis identified eight significant loci on seven chromosomes. Moving beyond traditional association analysis, local haplotyping of targeted regions on chromosomes 6 and 20 identified distinct haplotype structures, variation patterns, and genomic candidates influencing flowering in subpopulations. These results suggest the action of a network of genomic candidates influencing flowering time and an untapped reservoir of genomic variation for this trait in wild germplasm. Notably, GlymaLee.20G147200 on chromosome 20 was identified as a candidate gene that may cause delayed flowering in soybean, potentially through histone modifications of floral repressor loci as seen in Arabidopsis thaliana (L.) Heynh. These findings support future functional validation of haplotype‐based alleles for marker‐assisted breeding and genomic selection to enhance latitude adaptability of soybean without compromising yield.

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Genetic Factors Associated with Heading Responses Revealed by Field Evaluation of 274 Barley Accessions for 20 Seasons

Cited by 7 publications

References 38 publications

Major flowering time genes of barley: allelic diversity, effects, and comparison with wheat

Major flowering time genes of barley: allelic diversity, effects, and comparison with wheat

Allelic variations of <i>Vrn-1</i> and <i>Ppd-1</i> genes in Japanese wheat varieties reveal the genotype-environment interaction for heading time

Local haplotyping reveals insights into the genetic control of flowering time variation in wild and domesticated soybean

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