Characterization and management of long runs of homozygosity in parental nucleus lines and their associated crossbred progeny

Table 5 Average (±SD) difference for multiple genome-wide diversity metrics between the parents and their associated progeny across different mate allocation scenarios

Breed	Diversity parameter^a	Relationship used to constrain parental relationships^b
Breed	Diversity parameter^a	Random	A	SNPRM	ROHRM
LW	Pedigree inbreeding	0.011 (0.001)	−0.001 (0.001)	0.004 (0.001)	0.004 (0.001)
	Heterozygosity	−0.007 (0.001)	−0.004 (0.001)	0.004 (0.001)	0.004 (0.001)
	ROH5 inbreeding	0.012 (0.002)	0.003 (0.002)	−0.012 (0.002)	−0.014 (0.002)
LA	Pedigree inbreeding	0.008 (0.001)	−0.003 (0.002)	0.001 (0.001)	0.001 (0.001)
	Heterozygosity	−0.003 (0.001)	0.001 (0.002)	0.006 (0.002)	0.005 (0.002)
	ROH5 inbreeding	0.006 (0.003)	−0.003 (0.003)	−0.013 (0.003)	−0.015 (0.003)
DU	Pedigree inbreeding	0.007 (0.001)	−0.007 (0.001)	−0.001 (0.001)	−0.002 (0.001)
	Heterozygosity	−0.003 (0.001)	0.001 (0.001)	0.008 (0.001)	0.006 (0.001)
	ROH5 inbreeding	0.003 (0.003)	−0.006 (0.002)	−0.017 (0.002)	−0.019 (0.002)

DU Duroc, LW Large White, LA Landrace
^aPedigree inbreeding: refers to diagonals of the pedigree-based relationship matrix; heterozygosity (%): proportion of SNPs that are heterozygous; ROH5 inbreeding (%): proportion of the genome that is in a ROH of at least 5 Mb
^bRandom refers to random mating; A refers to minimizing pedigree-based parent relationships; SNPRM refers to minimizing SNP-bySNP based parent relationships; ROHRM refers to minimizing ROH-based parent relationships

ISSN: 1297-9686