Molecular Marker Assisted Selection: A Vital Tool For Wheat Breeding

Molecular Marker Assisted Selection: A Vital Tool For Wheat Breeding

Wheat (Triticum spp.) is a cereal grain, cultivated worldwide. It is the second most-produced cereal after maize. The importance of bread wheat for human food requires continuous improvement of wheat quality and productivity. Genetic complexity impedes breeders to identify, map and trace useful genes associated with excellent traits for crop breeding. However, it gives potential opportunity to create diversity by introducing alien genes or chromosome segments. Molecular marker as assisted selection method here provide vital role in screening and mapping genes and traits of interest in populations. Both advantages and disadvantages of molecular markers for wheat breeding are discussed.

Wheat (Triticum spp.) is a cereal grain, originally from the Levant region of the Near East and Ethiopian Highlands, but now cultivated worldwide. In 2007 world production of wheat was 607 million tons, making it the third most-produced cereal behind maize (784 million tons) and rice (651 million tons) (FAO, 2007). In 2009, world production of wheat was 682 million tons, making it the second most-produced cereal after maize (817 million tons), and with rice as close third (679 million tons) (FAO, 2009). As one of the first grains to be domesticated, modern wheats developed from cultivation starting in the middle east about 9-11,000 years ago in the fertile crescent of the middle east (Wroot et al., 2001). Wheat's domestication produced larger grains and a more productive crop, which could not have survived in the wild and required continued intervention of farmers intentionally planting it. By 4,000 BC the expanding geographical range of farming resulted in bread wheat becoming a common staple from England to China. Although rice was more important to the development of East Asian cultures, wheat was the nutritional foundation for cultures in Europe, the middle east and western Asia (Wroot et al., 2001).

Wheat genetics is more complicated than that of most other domesticated species. The wheat species mainly includes diploid, tetraploid and hexaploid. Bread wheat (T. aestivum), an allohexaploid species, consists of A, B and D genomes, each of which contains seven pairs of homologous chromosomes. By extensive studies of the identification and evolution of hexaploid wheat’s ancestral genomes, T. aestivum has come to one of the best characterized examples of genome evolution. B, D and A genomes was diverged gradually from an ancestral diploid species. Sitopsis section containing S genomes probably contributed B genome to T. aestivum was diverged in 2.5-4.5 MYA, and then the divergence time of D genome donor (Ae. tauschii) of common wheat was 1-2.5 MYA, and last T. urartu as A genome contributor appeared less than 1 MYA (Huang et al., 2002). In accepted view, hexaploid wheat arose from the hybridization of a tetraploid wheat (T. turgidum, AABB) with a diploid (Ae. tauschii) progenitor less than 8000 YA (Huang et al., 2002). The tetraploid wheat originated from the hybridization of two diploid ancestors during 0.5-3 MYA, T. urartu (AuAu) and an unconfirmed species (BB) relative to Aegilops speltoides (SsSs) (Huang et al., 2002).

Tetraploid wheat (T. durum, AABB) is widely used in European daily table while hexaploid wheat (T. aestivum, AABBDD) is popular in Asia. Most breads, even rye and oat breads, are made with at least a portion of wheat flour because of two main quality characteristics of wheat that improve the breads - its gluten, and its alpha-amylase activity. High gluten flours offer elasticity in the dough, allowing for it to rise without developing large air pockets. Tender pastries, like pie crusts and biscuits, are best with low gluten flours. All wheat flours are best with low alpha-amylase activity, because alpha amylase turns starch to sugar and prevents development of proper dough characteristics. Many flours are carefully blended mixtures of both hard and soft wheats designed precisely for a specific purpose.

For wheat breeding, quality, productivity and resistance are the most important characteristics of common wheat that breeders concern. In past decades, common wheat has been improved for breeding work mainly by transgenes and chromosome engineering. Brunner et al., (2011) transformed Pm3b gene, a powdery mildew resistant gene in wheat, and found it expressed 5 to 600 fold than endogenous Pm3b gene. The transgenic plant shows significantly improvement of resistance to powdery mildew in both greenhouse and field (Brunner et al., 2011). Improvement by chromosome engineering is widely achieved in the past years. Because relatives of common wheat provide a number of desirable genes, such as those for resistance to biotic, abiotic stresses and disease resistances, breeders apply the traditional cross method between common wheat and its relatives to transfer alien chromosome and/or chromosome segments from relatives into cultivated wheats. Wheat-Secale introgression is one of the successful example that has been cultivated for decades with continuously excellent performance (Yang et al., 2008).

With improvement of desired traits, breeders, therefore, want to keep those trails in the field for following years as well as select well performed strains that carry target genes or chromosome segments. Molecular marker assisted selection was risen, which refers to a process whereby a marker (morphological, biochemical or one based on DNA/RNA variation) is used for indirect selection of a genetic determinant or determinants of a trait of interest, not based on the trait itself, but on a marker linked to it. After the first wheat RFLP (Restriction Fragment Length Polymorphism) maps were published in 1995, a considerable amount of molecular markers have been extensively used in wheat genome mapping and targeting different traits, such as RAPD (Random Amplified Polymorphic DNAs), STS (Sequence-Tagged Site), DAF (DNA Amplification Fingerprinting), AFLP (Amplified Fragment Length Polymorphism) and STMS (Microsatellites) as well as other markers including EST (Expressed Sequence Tags) and SNPs (Single Nucleotide Polymorphisms). The use of molecular markers include 1) characterization of the parental lines with markers in order to select the best parental combinations. For instance, markers can give information on the origin of disease resistance in breeding germplasm , the number of genes involved, and the resistance mechanisms and identifying the number of major genes segregating in any particular cross can also help to define the optimal size of the breeding population; 2) pyramid gene combinations in segregating progenies by selecting for or against both dominant and recessive alleles, which can be done in very early generations; 3) introgression of genes via backcross strategy. Marker assisted backcrossing allows the rapid introgression of a target trait, which can be recessive , in conjunction with recovery of the recurrent parent background.

RFLPs were first developed for human genome mapping (Botstein et al., 1980). Later, these markers were adopted for mapping plant genomes, especially including those of bread wheat (Chao et al., 1989, Liu and Tsunewaki, 1991, Xie et al., 1993) and Aegilops tauschii (Gill, K. S. et al., 1991). However, RFLP analysis has some limitations compared to other markers. It is time-consuming and labour-intensive. Moreover, this approach has been relatively less useful in wheat, because of the low frequency of RFLPs.

Compared to RFLPs, PCR-based molecular markers provide the potential to reduce the time, effort and expense required for molecular mapping and trait targeting. RAPDs have been used for a variety of purposes containing the construction of genetic linkage maps (Reiter et al., 1992), gene tagging, identification of cultivars (Yang et al., 2008), assessment of genetic variation in populations (Chalmers et al., 1992) and phylogenetics relationships among species in wheat. Further, this molecular marker has been developed to be species-specific (Yang et al., 2008), genome-specific and chromosome-specific marker. Although RAPD has proved useful for many crops, it shows low level of polymorphism in wheat as RFLPs. Due to the random amplification of 6 nucleotides primer, it is lack of reproducibility of results.

EST is a DNA segment representing the sequence from a cDNA clone. It has been shown that ESTs are 150-400 bp in length and useful in searching for similarity and for mapping. According to the property of EST sequence, molecular markers based on EST could be employed to target genes that are associated with traits under certain treatments or conditions. In the most recent release (April 16, 2012) of the EST database from the National Center for Biotechnology Information (NCBI), more than 1285900 hexaploid wheat ESTs are listed, which offers huge information for gene mapping and targeting.

By the development of modern biotechnology, probably next 5 years other techniques might take the place of molecular markers, such as sequencing the whole genome of interest plant which could give accurate and comprehensive results, when the cost of sequencing is low enough. However, so far, molecular markers coupled with cytogenetic approach, for instance Fluorescence in situ hybridization (FISH), provide a quick and cheap but powerful method for breeders to screen targets in large populations and to map relatively accurate genes of interest.

Reference:
Botstein, D., R. L. White, M. Skolnick, and R. W. Davis, 1980: Construction of a genetic linkage map in man using restriction fragment length polymorphisms. Am. J. Hum. Genet. 32: 314-331.

Brunner S., Hurni S., Herren G., Kalinina O., Burg S. V., Zeller S. L., Schmid B., Winzeler M., and Keller B.. 2011: Transgenic Pm3b wheat lines show resistance to powdery mildew in the field. Plant Biotechnology Journal. 9: 897-910.

Chao, S. P., P. J. Sharp, A. J. Worland, E. J. Warham, R. M. D. Koebner, and M. D. Gale, 1989: RFLP-based genetic maps of wheat homologous group 7 chromosomes. TAG. 78: 493-504.

Chalmers, K. J., R. Waugh, J. I. Sprent, A. J. Simons, and W. Powell, 1992: Detection of genetic variation between and within populations of Gliricidia sepium and G. maculata using RAPD markers. Heredity. 69: 465-472.

“Faostat”. 2007. Retrieved 2009-05-05.

Gill, K. S., E. L. Lubberts, B. S. Gill, W. J. Raupp, and T. S. Cox, 1991: A genetic linkage map of Triticum tauschii (DD) and its relationship to the D genome of bread wheat (AABBDD). Genome. 34: 362-374.

Huang S., Sirikhachornkit A., Su X., Faris J., Gill B., Haselkorn R. and Gornicki P. 2002: Genes encoding plastid acetyl-CoA carboxylase and3-phosphoglycerate kinase of the Triticum/Aegilops complex and the evolutionary history of polyploid wheat. PNAS. 99:8133-8138.

Liu, Y. G., and K. Tsunewak, 1991: Restriction fragment length polymorphism (RFLP) analysis in wheat. II. Linkage maps of the RFLP sites in common wheat. Jpn. J. Genet. 66: 617-633.

Reiter R. S., Williams J. G. K., Feldmann K. A., Rafalski J. A., Tingey S. V., and Scolnik P. A., 1922: Global and local genome mapping in Arabidopsis thaliana by using recombinant inbred lines and random amplied polymorphic DNAs. Proc. Natl. Acad. Sci. USA. 89: 1477-1481.

“World Wheat, Corn and Rice”. Oklahoma State University, FAOSTAT.

Wroot, S., Pinkersgall, D., and "Oz", (2001). The History of Wheat.

Xie, D. X., K. M. Devos, G. Moore, and M. D. Gale, 1993: RFLP-based genetic maps of the homoeologous group 4 chromosomes of bread wheat (Triticum aestivum L.). Theor. Appl. Genet. 87: 70-74.

Yang Z. J., Li G. R., Jia J. Q., Zeng X., Lei M. P., Zeng Z. X., Zhang T., and Ren Z. L. 2009: Molecular cytogenetic characterization of wheat–Secale africanum amphiploids and derived introgression lines with stripe rust resistance. Euphytica. 167:197–202.