Identification of Novel Loci Precisely Modulating Pre-Harvest Sprouting Resistance and Red Color Components of the Seed Coat in T. aestivum L.

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Identification of Novel Loci Precisely Modulating Pre-Harvest Sprouting Resistance and Red Color Components of the Seed Coat in T. aestivum L. / Afonnikova, Svetlana D.; Kiseleva, Antonina A.; Fedyaeva, Anna V. et al.

In: Plants, Vol. 13, No. 10, 1309, 05.2024.

Research output: Contribution to journal › Article › peer-review

BibTeX

@article{1ece53ca768f4b758f2fd5f18bd240dd,

title = "Identification of Novel Loci Precisely Modulating Pre-Harvest Sprouting Resistance and Red Color Components of the Seed Coat in T. aestivum L.",

abstract = "The association between pre-harvest sprouting (PHS) and seed coat color has long been recognized. Red-grained wheats generally exhibit greater PHS resistance compared to white-grained wheat, although variability in PHS resistance exists within red-grained varieties. Here, we conducted a genome-wide association study on a panel consisting of red-grained wheat varieties, aimed at uncovering genes that modulate PHS resistance and red color components of seed coat using digital image processing. Twelve loci associated with PHS traits were identified, nine of which were described for the first time. Genetic loci marked by SNPs AX-95172164 (chromosome 1B) and AX-158544327 (chromosome 7D) explained approximately 25% of germination index variance, highlighting their value for breeding PHS-resistant varieties. The most promising candidate gene for PHS resistance was TraesCS6B02G147900, encoding a protein involved in aleurone layer morphogenesis. Twenty-six SNPs were significantly associated with grain color, independently of the known Tamyb10 gene. Most of them were related to multiple color characteristics. Prioritization of genes within the revealed loci identified TraesCS1D03G0758600 and TraesCS7B03G1296800, involved in the regulation of pigment biosynthesis and in controlling pigment accumulation. In conclusion, our study identifies new loci associated with grain color and germination index, providing insights into the genetic mechanisms underlying these traits.",

keywords = "Tamyb10, association analysis, image analysis, pre-harvest sprouting, red-grained wheat, seed coat color, winter wheat",

author = "Afonnikova, {Svetlana D.} and Kiseleva, {Antonina A.} and Fedyaeva, {Anna V.} and Komyshev, {Evgenii G.} and Koval, {Vasily S.} and Afonnikov, {Dmitry A.} and Salina, {Elena A.}",

note = "The author(s) declare financial support was received for the research, authorship, and/or publication of this article. This work was supported by the Russian Science Foundation project No. 22-74-00122 (grain color trait phenotyping and analysis) and project No. 21-76-30003 (genetic data analysis).",

year = "2024",

month = may,

doi = "10.3390/plants13101309",

language = "English",

volume = "13",

journal = "Plants",

issn = "2223-7747",

publisher = "Multidisciplinary Digital Publishing Institute (MDPI)",

number = "10",

}

RIS

TY - JOUR

T1 - Identification of Novel Loci Precisely Modulating Pre-Harvest Sprouting Resistance and Red Color Components of the Seed Coat in T. aestivum L.

AU - Afonnikova, Svetlana D.

AU - Kiseleva, Antonina A.

AU - Fedyaeva, Anna V.

AU - Komyshev, Evgenii G.

AU - Koval, Vasily S.

AU - Afonnikov, Dmitry A.

AU - Salina, Elena A.

N1 - The author(s) declare financial support was received for the research, authorship, and/or publication of this article. This work was supported by the Russian Science Foundation project No. 22-74-00122 (grain color trait phenotyping and analysis) and project No. 21-76-30003 (genetic data analysis).

PY - 2024/5

Y1 - 2024/5

N2 - The association between pre-harvest sprouting (PHS) and seed coat color has long been recognized. Red-grained wheats generally exhibit greater PHS resistance compared to white-grained wheat, although variability in PHS resistance exists within red-grained varieties. Here, we conducted a genome-wide association study on a panel consisting of red-grained wheat varieties, aimed at uncovering genes that modulate PHS resistance and red color components of seed coat using digital image processing. Twelve loci associated with PHS traits were identified, nine of which were described for the first time. Genetic loci marked by SNPs AX-95172164 (chromosome 1B) and AX-158544327 (chromosome 7D) explained approximately 25% of germination index variance, highlighting their value for breeding PHS-resistant varieties. The most promising candidate gene for PHS resistance was TraesCS6B02G147900, encoding a protein involved in aleurone layer morphogenesis. Twenty-six SNPs were significantly associated with grain color, independently of the known Tamyb10 gene. Most of them were related to multiple color characteristics. Prioritization of genes within the revealed loci identified TraesCS1D03G0758600 and TraesCS7B03G1296800, involved in the regulation of pigment biosynthesis and in controlling pigment accumulation. In conclusion, our study identifies new loci associated with grain color and germination index, providing insights into the genetic mechanisms underlying these traits.

AB - The association between pre-harvest sprouting (PHS) and seed coat color has long been recognized. Red-grained wheats generally exhibit greater PHS resistance compared to white-grained wheat, although variability in PHS resistance exists within red-grained varieties. Here, we conducted a genome-wide association study on a panel consisting of red-grained wheat varieties, aimed at uncovering genes that modulate PHS resistance and red color components of seed coat using digital image processing. Twelve loci associated with PHS traits were identified, nine of which were described for the first time. Genetic loci marked by SNPs AX-95172164 (chromosome 1B) and AX-158544327 (chromosome 7D) explained approximately 25% of germination index variance, highlighting their value for breeding PHS-resistant varieties. The most promising candidate gene for PHS resistance was TraesCS6B02G147900, encoding a protein involved in aleurone layer morphogenesis. Twenty-six SNPs were significantly associated with grain color, independently of the known Tamyb10 gene. Most of them were related to multiple color characteristics. Prioritization of genes within the revealed loci identified TraesCS1D03G0758600 and TraesCS7B03G1296800, involved in the regulation of pigment biosynthesis and in controlling pigment accumulation. In conclusion, our study identifies new loci associated with grain color and germination index, providing insights into the genetic mechanisms underlying these traits.

KW - Tamyb10

KW - association analysis

KW - image analysis

KW - pre-harvest sprouting

KW - red-grained wheat

KW - seed coat color

KW - winter wheat

UR - https://www.scopus.com/record/display.uri?eid=2-s2.0-85194046955&origin=inward&txGid=6adda1f813ac5dc259b542a9e247d37f

UR - https://www.mendeley.com/catalogue/6d6a9caf-f201-35ca-a02e-aaba16b3b589/

U2 - 10.3390/plants13101309

DO - 10.3390/plants13101309

M3 - Article

C2 - 38794380

VL - 13

JO - Plants

JF - Plants

SN - 2223-7747

IS - 10

M1 - 1309

ER -

ID: 61043390