Advances in the Understanding of Biological Sciences Using Next Generation Sequencing (NGS) Approaches

Sablok, Gaurav; Kumar, Sunil; Ueno, S.; Kuo, Jimmy; Varotto, Claudio

doi:10.1007/978-3-319-17157-9

Cited by 4 publications

(1 citation statement)

References 356 publications

(465 reference statements)

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“…In the wake of the human genetics research, plant structural variation has increasingly been recognized not only as a common feature and evolutionary force of genomes but also as a genetic mechanism regulating relevant adaptive traits (Zmieńko et al 2013;Francia et al 2015). CNVs are complementary to single nucleotide variants as a major source of genetic variability and could account for an important part of the missing heritability of complex traits (Manolio et al 2009).…”

Section: Introductionmentioning

confidence: 99%

Copy number variation at the HvCBF4–HvCBF2 genomic segment is a major component of frost resistance in barley

Francia

Morcia²,

Pasquariello

et al. 2016

Plant Mol Biol

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A family of CBF transcription factors plays a major role in reconfiguring the plant transcriptome in response to low-freezing temperature in temperate cereals. In barley, more than 13 HvCBF genes map coincident with the major QTL FR-H2 suggesting them as candidates to explain the function of the locus. Variation in copy number (CNV) of specific HvCBFs was assayed in a panel of 41 barley genotypes using RT-qPCR. Taking advantage of an accurate phenotyping that combined Fv/Fm and field survival, resistance-associated variants within FR-H2 were identified. Genotypes with an increased copy number of HvCBF4 and HvCBF2 (at least ten and eight copies, respectively) showed greater frost resistance. A CAPS marker able to distinguish the CBF2A, CBF2B and CBF2A/B forms was developed and showed that all the higher-ranking genotypes in term of resistance harbour only CBF2A, while other resistant winter genotypes harbour also CBF2B, although at a lower CNV. In addition to the major involvement of the HvCBF4-HvCBF2 genomic segment in the proximal cluster of CBF elements, a negative role of HvCBF3 in the distal cluster was identified. Multiple linear regression models taking into account allelic variation at FR-H1/VRN-H1 explained 0.434 and 0.550 (both at p < 0.001) of the phenotypic variation for Fv/Fm and field survival respectively, while no interaction effect between CNV at the HvCBFs and FR-H1/VRN-H1 was found. Altogether our data suggest a major involvement of the CBF genes located in the proximal cluster, with no apparent involvement of the central cluster contrary to what was reported for wheat

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Section: Introductionmentioning

confidence: 99%

Copy number variation at the HvCBF4–HvCBF2 genomic segment is a major component of frost resistance in barley

Francia

Morcia²,

Pasquariello

et al. 2016

Plant Mol Biol

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Glucosylation prevents plant defense activation in phloem-feeding insects

et al. 2020

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The Triticeae CBF Gene Cluster—To Frost Resistance and Beyond

Caccialupi,

Milc,

Caradonia

et al. 2023

Cells

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The pivotal role of CBF/DREB1 transcriptional factors in Triticeae crops involved in the abiotic stress response has been highlighted. The CBFs represent an important hub in the ICE-CBF-COR pathway, which is one of the most relevant mechanisms capable of activating the adaptive response to cold and drought in wheat, barley, and rye. Understanding the intricate mechanisms and regulation of the cluster of CBF genes harbored by the homoeologous chromosome group 5 entails significant potential for the genetic improvement of small grain cereals. Triticeae crops seem to share common mechanisms characterized, however, by some peculiar aspects of the response to stress, highlighting a combined landscape of single-nucleotide variants and copy number variation involving CBF members of subgroup IV. Moreover, while chromosome 5 ploidy appears to confer species-specific levels of resistance, an important involvement of the ICE factor might explain the greater tolerance of rye. By unraveling the genetic basis of abiotic stress tolerance, researchers can develop resilient varieties better equipped to withstand extreme environmental conditions. Hence, advancing our knowledge of CBFs and their interactions represents a promising avenue for improving crop resilience and food security.

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Advances in the Understanding of Biological Sciences Using Next Generation Sequencing (NGS) Approaches

Cited by 4 publications

References 356 publications

Copy number variation at the HvCBF4–HvCBF2 genomic segment is a major component of frost resistance in barley

Copy number variation at the HvCBF4–HvCBF2 genomic segment is a major component of frost resistance in barley

Glucosylation prevents plant defense activation in phloem-feeding insects

The Triticeae CBF Gene Cluster—To Frost Resistance and Beyond

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