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This assumption was validated by Wenzl et al. [12] through genetic mapping of over 2000 DArT markers in many mapping populations of barley, where fewer than 2% of the markers mapped to more than one locus in the genome.
Studies using many mapping populations derived from a diverse array of accessions will enable progress towards an understanding of the global genetic architecture of complex traits (Tonsor et al., 2005).
Another challenge for milling yield analysis is that many mapping populations for milling yield had varied kernel shape among the individual lines and heterogeneity in grain dimensions confounds the assessment of genetic effects [ 9, 24, 26- 31].
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Although quite small for linkage map generation, this population is typical of many cacao mapping populations, which are often studied in regions where resources are limited.
Thus, many different mapping populations may be needed to represent the allelic diversity of the genes contributing to the character under study in the tested species.
The seed protein QTL mapped to soybean linkage group I (LG I) is of particular interest due to the large additive effect that accounts for its consistent detection in many soybean mapping populations [ 22, 24, 25] and across multiple environments [ 26].
Combined with the large land requirements of tree breeding and the need to maintain trees for many years, cacao mapping populations seldom have more than a hundred individuals, although a few exceptions exist at larger cacao research stations.
Although in many studies, immortal mapping populations such as doubled haploid and recombinant inbred lines are used, in our present study, we used F3 families for three consecutive years to detect QTL, as F3 families represent the comprehensive genetic information of heterozygous and homozygous plants and their interacting effects on phenotype.
Mapping the Ty-1 and Ty-3 loci was time-consuming and required large mapping populations over many generations of selection [ 21].
To obtain an integrated map of a cross pollinated population, individual parental maps were generally constructed and then integrated to produce a consensus map of the population by estimation of the average recombination frequency of the loci in the two parents, as has been used for other pseudo-test cross mapping populations in many tree species [ 38- 40].
Sn79 is avirulent on wheat and produces no apparent effectors when infiltrated onto many cultivars and mapping population parents.
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