Genetic Dissection of Spike Productivity Traits in the Siberian Collection of Spring Barley

Overview

Journal Biomolecules

Publisher MDPI

Specialties Biochemistry
Molecular Biology

Date 2023 Jun 28

PMID 37371489

Authors

Irina V Rozanova

Yuriy N Grigoriev

Vadim M Efimov

Alexander V Igoshin

Elena K Khlestkina

Affiliations

Soon will be listed here.

Abstract

Barley ( L.) is one of the most commonly cultivated cereals worldwide. Its local varieties can represent a valuable source of unique genetic variants useful for crop improvement. The aim of this study was to reveal loci contributing to spike productivity traits in Siberian spring barley and to develop diagnostic DNA markers for marker-assisted breeding programs. For this purpose we conducted a genome-wide association study using a panel of 94 barley varieties. In total, 64 SNPs significantly associated with productivity traits were revealed. Twenty-three SNP markers were validated by genotyping in an independent sample set using competitive allele-specific PCR (KASP). Finally, fourteen markers associated with spike productivity traits on chromosomes 2H, 4H and 5H can be suggested for use in breeding programs.

Citing Articles

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References

Jackson D, Turner R . Power analysis for random-effects meta-analysis. Res Synth Methods. 2017; 8(3):290-302. PMC: 5590730. DOI: 10.1002/jrsm.1240. View

Coleman A, Maroschek J, Raasch L, Takken F, Ranf S, Huckelhoven R . The Arabidopsis leucine-rich repeat receptor-like kinase MIK2 is a crucial component of early immune responses to a fungal-derived elicitor. New Phytol. 2020; 229(6):3453-3466. DOI: 10.1111/nph.17122. View

van Esse G, Walla A, Finke A, Koornneef M, Pecinka A, von Korff M . Six-Rowed Spike3 (VRS3) Is a Histone Demethylase That Controls Lateral Spikelet Development in Barley. Plant Physiol. 2017; 174(4):2397-2408. PMC: 5543938. DOI: 10.1104/pp.17.00108. View

Mou S, Meng Q, Gao F, Zhang T, He W, Guan D . A cysteine-rich receptor-like protein kinase CaCKR5 modulates immune response against Ralstonia solanacearum infection in pepper. BMC Plant Biol. 2021; 21(1):382. PMC: 8375189. DOI: 10.1186/s12870-021-03150-y. View

Bayer M, Rapazote-Flores P, Ganal M, Hedley P, Macaulay M, Plieske J . Development and Evaluation of a Barley 50k iSelect SNP Array. Front Plant Sci. 2017; 8:1792. PMC: 5651081. DOI: 10.3389/fpls.2017.01792. View

Monat C, Padmarasu S, Lux T, Wicker T, Gundlach H, Himmelbach A . TRITEX: chromosome-scale sequence assembly of Triticeae genomes with open-source tools. Genome Biol. 2019; 20(1):284. PMC: 6918601. DOI: 10.1186/s13059-019-1899-5. View

Koppolu R, Anwar N, Sakuma S, Tagiri A, Lundqvist U, Pourkheirandish M . Six-rowed spike4 (Vrs4) controls spikelet determinacy and row-type in barley. Proc Natl Acad Sci U S A. 2013; 110(32):13198-203. PMC: 3740847. DOI: 10.1073/pnas.1221950110. View

Chaumont F, Moshelion M, Daniels M . Regulation of plant aquaporin activity. Biol Cell. 2005; 97(10):749-64. DOI: 10.1042/BC20040133. View

Mehdi S, Derkacheva M, Ramstrom M, Kralemann L, Bergquist J, Hennig L . The WD40 Domain Protein MSI1 Functions in a Histone Deacetylase Complex to Fine-Tune Abscisic Acid Signaling. Plant Cell. 2015; 28(1):42-54. PMC: 4746680. DOI: 10.1105/tpc.15.00763. View

10.

Zwirek M, Waugh R, McKim S . Interaction between row-type genes in barley controls meristem determinacy and reveals novel routes to improved grain. New Phytol. 2018; 221(4):1950-1965. PMC: 6492131. DOI: 10.1111/nph.15548. View

11.

Tanno K, Taketa S, Takeda K, Komatsuda T . A DNA marker closely linked to the vrs1 locus (row-type gene) indicates multiple origins of six-rowed cultivated barley ( Hordeum vulgare L.). Theor Appl Genet. 2003; 104(1):54-60. DOI: 10.1007/s001220200006. View

12.

Sobota R, Shriner D, Kodaman N, Goodloe R, Zheng W, Gao Y . Addressing population-specific multiple testing burdens in genetic association studies. Ann Hum Genet. 2015; 79(2):136-47. PMC: 4334751. DOI: 10.1111/ahg.12095. View

13.

Mrizova K, Holaskova E, Oz M, Jiskrova E, Frebort I, Galuszka P . Transgenic barley: a prospective tool for biotechnology and agriculture. Biotechnol Adv. 2013; 32(1):137-57. DOI: 10.1016/j.biotechadv.2013.09.011. View

14.

Youssef H, Eggert K, Koppolu R, Alqudah A, Poursarebani N, Fazeli A . VRS2 regulates hormone-mediated inflorescence patterning in barley. Nat Genet. 2016; 49(1):157-161. DOI: 10.1038/ng.3717. View

15.

Fang Y, Zhang X, Zhang X, Tong T, Zhang Z, Wu G . A High-Density Genetic Linkage Map of SLAFs and QTL Analysis of Grain Size and Weight in Barley ( L.). Front Plant Sci. 2021; 11:620922. PMC: 7793689. DOI: 10.3389/fpls.2020.620922. View

16.

Bull H, Casao M, Zwirek M, Flavell A, Thomas W, Guo W . Barley SIX-ROWED SPIKE3 encodes a putative Jumonji C-type H3K9me2/me3 demethylase that represses lateral spikelet fertility. Nat Commun. 2017; 8(1):936. PMC: 5643332. DOI: 10.1038/s41467-017-00940-7. View

17.

Bykova I, Lashina N, Efimov V, Afanasenko O, Khlestkina E . Identification of 50 K Illumina-chip SNPs associated with resistance to spot blotch in barley. BMC Plant Biol. 2018; 17(Suppl 2):250. PMC: 5751810. DOI: 10.1186/s12870-017-1198-9. View

18.

Thabet S, Moursi Y, Karam M, Borner A, Alqudah A . Natural Variation Uncovers Candidate Genes for Barley Spikelet Number and Grain Yield under Drought Stress. Genes (Basel). 2020; 11(5). PMC: 7290517. DOI: 10.3390/genes11050533. View

19.

Liu C, Lu F, Cui X, Cao X . Histone methylation in higher plants. Annu Rev Plant Biol. 2010; 61:395-420. DOI: 10.1146/annurev.arplant.043008.091939. View

20.

Thirulogachandar V, Alqudah A, Koppolu R, Rutten T, Graner A, Hensel G . Leaf primordium size specifies leaf width and vein number among row-type classes in barley. Plant J. 2017; 91(4):601-612. DOI: 10.1111/tpj.13590. View