Genetic Architecture of Main Effect QTL for Heading Date in European Winter Wheat

Overview

Journal Front Plant Sci

Date 2014 Jun 7

PMID 24904613

Citations 47

Authors

Christine Zanke

Jie Ling

Jorg Plieske

Sonja Kollers

Erhard Ebmeyer

Viktor Korzun

Odile Argillier

Gunther Stiewe

Maike Hinze

Sebastian Beier

Martin W Ganal

Marion S Roder

Affiliations

Soon will be listed here.

Abstract

A genome-wide association study (GWAS) for heading date (HD) was performed with a panel of 358 European winter wheat (Triticum aestivum L.) varieties and 14 spring wheat varieties through the phenotypic evaluation of HD in field tests in eight environments. Genotyping data consisted of 770 mapped microsatellite loci and 7934 mapped SNP markers derived from the 90K iSelect wheat chip. Best linear unbiased estimations (BLUEs) were calculated across all trials and ranged from 142.5 to 159.6 days after the 1st of January with an average value of 151.4 days. Considering only associations with a -log10 (P-value) ≥ 3.0, a total of 340 SSR and 2983 SNP marker-trait associations (MTAs) were detected. After Bonferroni correction for multiple testing, a total of 72 SSR and 438 SNP marker-trait associations remained significant. Highly significant MTAs were detected for the photoperiodism gene Ppd-D1, which was genotyped in all varieties. Consistent associations were found on all chromosomes with the highest number of MTAs on chromosome 5B. Linear regression showed a clear dependence of the HD score BLUEs on the number of favorable alleles (decreasing HD) and unfavorable alleles (increasing HD) per variety meaning that genotypes with a higher number of favorable or a low number of unfavorable alleles showed lower HD and therefore flowered earlier. For the vernalization gene Vrn-A2 co-locating MTAs on chromosome 5A, as well as for the photoperiodism genes Ppd-A1 and Ppd-B1 on chromosomes 2A and 2B were detected. After the construction of an integrated map of the SSR and SNP markers and by exploiting the synteny to sequenced species, such as rice and Brachypodium distachyon, we were able to demonstrate that a marker locus on wheat chromosome 5BL with homology to the rice photoperiodism gene Hd6 played a significant role in the determination of the heading date in wheat.

Citing Articles

Genetic dissection of value-added quality traits and agronomic parameters through genome-wide association mapping in bread wheat ( L.).

Vishwakarma M, Bhati P, Kumar U, Singh R, Kumar S, Govindan V Front Plant Sci. 2024; 15:1419227.

PMID: 39228836 PMC: 11368860. DOI: 10.3389/fpls.2024.1419227.

Fungal Disease Tolerance with a Focus on Wheat: A Review.

Maulenbay A, Rsaliyev A J Fungi (Basel). 2024; 10(7).

PMID: 39057367 PMC: 11277790. DOI: 10.3390/jof10070482.

High-throughput field phenotyping reveals that selection in breeding has affected the phenology and temperature response of wheat in the stem elongation phase.

Roth L, Kronenberg L, Aasen H, Walter A, Hartung J, van Eeuwijk F J Exp Bot. 2023; 75(7):2084-2099.

PMID: 38134290 PMC: 10967243. DOI: 10.1093/jxb/erad481.

Genetic control and prospects of predictive breeding for European winter wheat's Zeleny sedimentation values and Hagberg-Perten falling number.

Muqaddasi Q, Muqaddasi R, Ebmeyer E, Korzun V, Argillier O, Mirdita V Theor Appl Genet. 2023; 136(11):229.

PMID: 37874400 PMC: 10598174. DOI: 10.1007/s00122-023-04450-7.

Genome-wide association study of lipase and esterase in wholegrain wheat flour (Triticum aestivum L.).

Wei C, Yates S, Zhu D, Hund A, Studer B, Nystrom L PLoS One. 2023; 18(3):e0282510.

PMID: 36893202 PMC: 9997868. DOI: 10.1371/journal.pone.0282510.

References

Reif J, Maurer H, Korzun V, Ebmeyer E, Miedaner T, Wurschum T . Mapping QTLs with main and epistatic effects underlying grain yield and heading time in soft winter wheat. Theor Appl Genet. 2011; 123(2):283-92. DOI: 10.1007/s00122-011-1583-y. View

Yu L, Morgounov A, Wanyera R, Keser M, Singh S, Sorrells M . Identification of Ug99 stem rust resistance loci in winter wheat germplasm using genome-wide association analysis. Theor Appl Genet. 2012; 125(4):749-58. DOI: 10.1007/s00122-012-1867-x. View

Salse J, Abrouk M, Bolot S, Guilhot N, Courcelle E, Faraut T . Reconstruction of monocotelydoneous proto-chromosomes reveals faster evolution in plants than in animals. Proc Natl Acad Sci U S A. 2009; 106(35):14908-13. PMC: 2736418. DOI: 10.1073/pnas.0902350106. View

Trevaskis B, Hemming M, Dennis E, Peacock W . The molecular basis of vernalization-induced flowering in cereals. Trends Plant Sci. 2007; 12(8):352-7. DOI: 10.1016/j.tplants.2007.06.010. View

Bonnin I, Rousset M, Madur D, Sourdille P, Dupuits C, Brunel D . FT genome A and D polymorphisms are associated with the variation of earliness components in hexaploid wheat. Theor Appl Genet. 2007; 116(3):383-94. DOI: 10.1007/s00122-007-0676-0. View

Sorrells M, Gustafson J, Somers D, Chao S, Benscher D, Guedira-Brown G . Reconstruction of the synthetic W7984 x Opata M85 wheat reference population. Genome. 2011; 54(11):875-82. DOI: 10.1139/g11-054. View

Yan L, Loukoianov A, Tranquilli G, Helguera M, Fahima T, Dubcovsky J . Positional cloning of the wheat vernalization gene VRN1. Proc Natl Acad Sci U S A. 2003; 100(10):6263-8. PMC: 156360. DOI: 10.1073/pnas.0937399100. View

Sourdille P, Snape J, Cadalen T, Charmet G, Nakata N, Bernard S . Detection of QTLs for heading time and photoperiod response in wheat using a doubled-haploid population. Genome. 2000; 43(3):487-94. View

Hanocq E, Laperche A, Jaminon O, Laine A, Le Gouis J . Most significant genome regions involved in the control of earliness traits in bread wheat, as revealed by QTL meta-analysis. Theor Appl Genet. 2006; 114(3):569-84. DOI: 10.1007/s00122-006-0459-z. View

10.

Yan L, Loukoianov A, Blechl A, Tranquilli G, Ramakrishna W, SanMiguel P . The wheat VRN2 gene is a flowering repressor down-regulated by vernalization. Science. 2004; 303(5664):1640-4. PMC: 4737501. DOI: 10.1126/science.1094305. View

11.

Yan L, Fu D, Li C, Blechl A, Tranquilli G, Bonafede M . The wheat and barley vernalization gene VRN3 is an orthologue of FT. Proc Natl Acad Sci U S A. 2006; 103(51):19581-6. PMC: 1748268. DOI: 10.1073/pnas.0607142103. View

12.

Pestsova E, Roder M . Microsatellite analysis of wheat chromosome 2D allows the reconstruction of chromosomal inheritance in pedigrees of breeding programmes. Theor Appl Genet. 2003; 106(1):84-91. DOI: 10.1007/s00122-002-0998-x. View

13.

. The map-based sequence of the rice genome. Nature. 2005; 436(7052):793-800. DOI: 10.1038/nature03895. View

14.

Pin P, Zhang W, Vogt S, Dally N, Buttner B, Schulze-Buxloh G . The role of a pseudo-response regulator gene in life cycle adaptation and domestication of beet. Curr Biol. 2012; 22(12):1095-101. DOI: 10.1016/j.cub.2012.04.007. View

15.

Hanocq E, Niarquin M, Heumez E, Rousset M, Le Gouis J . Detection and mapping of QTL for earliness components in a bread wheat recombinant inbred lines population. Theor Appl Genet. 2004; 110(1):106-15. DOI: 10.1007/s00122-004-1799-1. View

16.

Lewis S, Faricelli M, Appendino M, Valarik M, Dubcovsky J . The chromosome region including the earliness per se locus Eps-Am1 affects the duration of early developmental phases and spikelet number in diploid wheat. J Exp Bot. 2008; 59(13):3595-607. PMC: 2561150. DOI: 10.1093/jxb/ern209. View

17.

Andres F, Coupland G . The genetic basis of flowering responses to seasonal cues. Nat Rev Genet. 2012; 13(9):627-39. DOI: 10.1038/nrg3291. View

18.

Somers D, Isaac P, Edwards K . A high-density microsatellite consensus map for bread wheat (Triticum aestivum L.). Theor Appl Genet. 2004; 109(6):1105-14. DOI: 10.1007/s00122-004-1740-7. View

19.

Yoshida T, Nishida H, Zhu J, Nitcher R, Distelfeld A, Akashi Y . Vrn-D4 is a vernalization gene located on the centromeric region of chromosome 5D in hexaploid wheat. Theor Appl Genet. 2009; 120(3):543-52. DOI: 10.1007/s00122-009-1174-3. View

20.

Letta T, Maccaferri M, Badebo A, Ammar K, Ricci A, Crossa J . Searching for novel sources of field resistance to Ug99 and Ethiopian stem rust races in durum wheat via association mapping. Theor Appl Genet. 2013; 126(5):1237-56. DOI: 10.1007/s00122-013-2050-8. View