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Furthermore, the SNM likely overestimates the number of rare alleles that would be observed in a fully re-sequenced maize data set, due to the effect of the domestication bottleneck.
In this example, we evaluated the ability of estimating GEBV across clusters in a highly structured Maize data set.
For the maize data set, with a large number of markers, the moderate decay of singular values causes a low level of ill-conditioning.
The decay pattern of singular values and the noise in the wheat data set were different from those found in the maize data set.
The entries of the maize data set represent world-wide genetic diversity, whereas the genetic materials of rapeseed, potato, and sugar beet were sampled from commercial plant breeding programs.
For the approaches BLUP, RRWA, RMLA, BL, and HEM, the correlation between predicted and observed phenotypic values ranged between 0.31 for flowering time in the maize data set and 0.86 for molasses loss in the sugar beet data set (Table 3).
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Models BIR1 and BIR2 had the lowest PMSE in 16 of the 21 maize data sets.
At a percentile value α=15%, SVC-lin achieved the best RE in 13 of the 14 maize data sets and in 9 of the 16 wheat data sets.
When applying our method to other maize data sets, High- C0 t derived sequences showed the greatest enrichment for low-copy sequences.
For the 21 maize data sets, the X matrix had a rank equal to n with moderate decay in singular values, indicating moderate ill-conditioning.
The 21 maize data sets and the 17 wheat data sets, as well as the R scripts developed to fit the predictive statistical models BIRR, BAI, BIR1, and BIR2 used in this study, are deposited at http://repository.cimmyt.org/xmlui/handle/10883/4036.org/xmlui/handle/10883/4036
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