**5. Conclusion and perspectives**

**Locus Primer sequences, 5′–3′ PCR product References**

**Table 5.** Important HWM and LMW glutenin loci, their chromosomal location and primer sequences for detection of

**Primer sequences, 5′–3′ PCR product References**

FAM: *Glu-A1a* or *Glu-A1b* VIC: *Glu-A1c*

*Glu-B1al*: 447 bp Others: 0 bp

FAM: *Glu-D1a* or

*Glu-A3b*: 894 bp Others: 0 bp

*Glu-A3d:* 967 bp Others: 0 bp

**Glu-B3b***:* 1549 bp Others: 0 bp

*Glu-B3d*: 662 bp Others: 0 bp

*Glu-B3g*: 853 bp Others: 0 bp

others VIC: *Glu-D1d* [84, 97]

[98]

[84, 99]

[86, 87]

[88]

*Gli-B1.1***:** 369 bp *Gli-B1.2* or 1BL.1RS: 0 bp

*Gli-B1.2***:** 397 bp *Gli-B1.1* or 1BL.1RS: 0 bp

**Rht-D1b***:* 237 bp *Rht-D1a:* 0 bp

*Gpc-B1*: 122 bp No *Gpc-B1*: 126 bp

961 bp Others: 0 bp

**High** *wbm* **expression**:

[96]

[106]

[103]

[105]

F: TGATCTGGCCACAAAGGGA R: CATTGGCCACCAATTCCTGT

F: TGATCTGGCCACAAAGGGC R: CATTGGCCACCAATTCCTGT

R: CATCCCCATGGCCATCTCGAGCTA

R: TTATGGATCTCTTTATGTCTGTGT

R: TTCCTCTACCCATGAATCTAGCA

*Rht-D1* F: GGTAGGGAGGCGAGAGGCGAG

*wbm* F: CCGTCACAAGATTTACAGGGTTG

*Gpc-B1* F: TCTCCAAGAGGGGAGAGACA

**Table 6.** Additional loci influencing wheat quality traits.

Favourable alleles are marked in bold.

*Gli-B1 (1BL.1RS)*

**Locus Chr. arm**

12 Next Generation Plant Breeding

*Glu-A1* 1AL FAM: AAGTGTAACTTCTCCGCAACA

*Glu-B1* 1BL F: ACGTGTCCAAGCTTTGGTTC

*Glu-A3* 1AS F: TTCAGATGCAGCCAAACAA

*Glu-B3* 1BS F: ATCAGGTGTAAAAGTGATAG

Favourable alleles are marked in bold.

alleles with positive effects on wheat quality.

VIC: AAGTGTAACTTCTCCGCAACG Common: GGCCTGGATAGTATGAAACC

R: GATTGGTGGGTGGATACAGG

VIC: ATAGTATGAAACCTGCTGCGGAC

R: GCTGTGCTTGGATGATACTCTA

F: TTCAGATGCAGCCAAACAA R: TGGGGTTGGGAGACACATA

R: TGCTACATCGACATATCCA

R: GTTGGGGTTGGGAAACA

F: CACCATGAAGACCTTCCTCA R: CACCATGAAGACCTTCCTCA

F: CCAAGAAATACTAGTTAACACTAGTC

Common: TACTAAAAAGGTATTACCCAAGTGTAACTT

*Glu-D1* 1DL FAM: ATAGTATGAAACCTGCTGCGGAG

Trait-linked DNA markers have been identified for numerous traits in wheat, including disease resistance and grain quality. Employing such markers in MAS offers several advantages to wheat breeding compared to conventional phenotypic selection and laborious analysis of grain quality. These advantages include the fixation of desirable traits at an early stage of the breeding program and marker-assisted backcrossing in order to transfer agronomically important genes from wild relatives to cultivated wheat.

In addition, DNA markers are neutral to both environment and tissue type. Thus, they can be employed at any plant developmental stage and independent on environmental conditions during selection. This is particularly relevant for selection for disease resistance. DNA markers further offer the possibility for targeted pyramiding of several resistance genes, a task impossible by phenotypic selection due to complex host-pathogen interactions. To secure durable resistance, it is important to combine qualitative and quantitative resistance in a given line. Here, molecular markers can be used to combine both resistances.

As DNA markers have been correlated to numerous traits, they can be employed to combine, e.g., resistance and grain quality in the early generations. Consequently, DNA markers are being employed in early generations to select for several traits, in turn reducing the number of lines entering replicated, multi-location trials. Similarly, the number of samples for laboratory analysis of grain quality can be reduced. In effect, the application of MAS can lead to an optimisation of resources demanded by any given breeding program, allowing the breeder to focus phenotypic selection on highly multi-genic traits, difficult to handle with MAS, e.g., yield.

[7] Brown J, Chartrain L, Lasserre-Zuber P, Saintenac C. Genetics of resistance to Zymoseptoria tritici and applications to wheat breeding. Fungal Genetics and Biology. 2015;**79**:

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[8] Adhikari TB, Yang X, Cavaletto JR, Hu X, Buechley G, Ohm HW, et al. Molecular mapping of Stb1, a potentially durable gene for resistance to septoria tritici blotch in wheat. Theoretical and Applied Genetics. 2004;**109**(5):944-953. Available from: http://www.ncbi.

[9] Liu Y, Zhang L, Thompson IA, Goodwin SB, Ohm HW. Molecular mapping re-locates the Stb2 gene for resistance to Septoria tritici blotch derived from cultivar Veranopolis on wheat chromosome 1BS. Euphytica [Internet]. 2012;**190**(1):145-156. Available from:

[10] Arraiano LS, Chartrain L, Bossolini E, Slatter HN, Keller B, JKM B.A gene in European wheat cultivars for resistance to an African isolate of Mycosphaerella graminicola. Plant Pathology

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[11] Goodwin SB, Cavaletto JR, Hale IL, Thompson I, Xu SS, Adhikari TB, et al. A new map location of gene *Stb3* for resistance to Septoria tritici blotch in wheat. Crop Science [Internet]. 2015;**55**(1):35-43. Available from: https://www.crops.org/publications/cs/abstracts/55/1/35

[12] Brading P, Verstappen E, Kema G, Brown J.A gene-for-gene relationship between wheat and mycosphaerella graminicola, the septoria tritici blotch pathogen. Phytopathology [Internet]. 2002;**92**(4):439-445. Available from http://www.ncbi.nlm.nih.gov/pubmed/18942957

[13] Flor HH. Current status of the gene-for-gene concept. Annual Review of Phytopathology.

[14] Arraiano LS, Brown J. Identification of isolate-specific and partial resistance to septoria tritici blotch in 238 European wheat cultivars and breeding lines. Plant Pathology.

[15] Vagndorf N, Nielsen NH, Edriss V, Andersen JR, Orabi J, Jørgensen LN, et al. Genomewide association study reveals novel quantitative trait loci associated with resistance towards Septoria tritici blotch in North European winter wheat. Plant Breeding. 2017;**136**:474-482

[16] Adhikari TB, Cavaletto JR, Dubcovsky J, Gieco JO, Schlatter AR, Goodwin SB. Molecular mapping of the Stb4 gene for resistance to septoria tritici blotch in wheat. Phytopathology [Internet]. 2004;**94**(11):1198-1206. Available from: http://www.ncbi.nlm.nih.gov/pubmed/

[17] Arraiano LS, Worland AJ, Ellerbrook C, Brown JKM. Chromosomal location of a gene for resistance to septoria tritici blotch (*Mycosphaerella graminicola*) in the hexaploid wheat

[18] McCartney CA, Brûlé-Babel AL, Lamari L, Somers DJ. Chromosomal location of a racespecific resistance gene to Mycosphaerella graminicola in the spring wheat ST6. Theoretical and Applied Genetics [Internet]. 2003;**107**(7):1181-1186. Available from: http://www.ncbi.

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http://link.springer.com/10.1007/s10681-012-0796-8

Following developments in technologies and statistical genetics, the application of DNA markers in breeding is rapidly changing. While MAS has been employed to select for traits controlled by one/few genes, genomic selection will allow accurate selection for traits affected by numerous genes.

Once genomic selection has been validated in breeding programs, it can be implemented in combination with MAS. This will further improve selection efficiency and accuracy for disease resistance and quality parameters as well as for multi-genic traits such as yield.
