marker-assisted selection in wheat - ictsd

Chapter 11 – Marker-assisted selection in poultry 189(Wang et al., 2005). The SNP map willfacilitate the development of genome-wideSNP assays, containing between 5 000 and20 000 SNPs per assay.For the study of gene expression, thereare various complementary DNA (cDNA)microarrays available, varying from targetedarrays (immune, neuroendocrine,embryo) to whole genome generic arrays.Recently, a whole-genome Affymetrixchip was developed in collaboration withthe chicken genomics community (www.affymetrix.com and www.chicken-genome.org/resources/affymetrix-faq1.htm).Altogether, this provides a very comprehensivetoolbox to study the functionalgenomics of chicken, whether this be anindividual gene or the entire genome.Current uptake of MAS in chickenImplementation of MAS requires knowledgeof marker-trait associations basedon QTL and candidate gene studies, andideally from studies of the underlyinggenetic mechanisms. There have been alarge number of QTL studies in chickencovering a wide range of traits includinggrowth, meat quality, egg production, diseaseresistance (both infectious diseasesand production diseases) and behaviour.These studies have recently been reviewed(Hocking, 2005). A total of 27 papersreported 114 genome-wide significant QTLfrom experimental crosses largely involvingWhite Leghorn and broiler lines. A summaryof the QTL that have been detected ispresented in Table 1. While the abundanceof QTL would indicate ample opportunityfor MAS in chicken, it must be notedthat nearly all studies were carried out inexperimental crosses and hence the resultsdo not reflect QTL within selected populations.However, these results do providea good starting point to search for QTLwithin commercial populations, as demonstratedfor growth and carcass traits wheremany published QTL also explained variationwithin a broiler dam line (de Koninget al., 2003; de Koning et al., 2004). To theauthors’ knowledge, there are no otherQTL studies within commercial lines ofpoultry in the public domain. Of the QTLfrom experimental crosses, only a smallnumber has been followed up by fine mappinganalyses and the responsible genemutation has only been described for somedisease resistance QTL (Liu et al., 2001a, b;Liu et al., 2003).A good example of how QTL mappingcombined with functional studies canidentify functional variants is for Marek’sdisease. Marek’s disease (MD) is an infec-Table 1Quantitative traits and chromosomal locations in experimental chicken crossesTrait Chromosome (number of QTL) Total QTL Number of papersBehaviour/fear 1,2(3),3,4(2),7,10,27, E22 11 5Body fat 1(2),3,5,7(2),15,28 8 3Body weight 1(7),2(4),3(4),4(5),5,8(2),11,12,13(2),27(3)Z(2) 32 9Carcass quality 1(2),2,3,4(2).5(2),6(2),7(3),8(2),9,13(2),27,Z(2) 21 1Disease resistance 1(4),2(2),3(2),4(2),5(5),6(2),7,8,14,18,27,Z 23 10Egg number 8,Z(2) 3 1Egg quality 2,11,Z 3 2Egg weight 1,2,3,4(3),14,23,Z 9 3Feed intake 1,4 2 2Sexual maturity Z(2) 2 2Source: Hocking, 2005.