Evaluation of homozygosity levels of onion (Allium cepa L.) inbred lines using molecular markers evenly distributed in a high-resolution linkage map

• Published in: Euphytica Vol. 219; no. 9; p. 96
• Main Authors: Moon, Jin Seong, Kim, Bongju, Kim, Sunggil
• Format: Journal Article
• Language: English
• Published: Dordrecht Springer Netherlands 01.09.2023; Springer; Springer Nature B.V
• Subjects: Allium cepa; Biomedical and Life Sciences; Biotechnology; Clustering; Cultivars; Genetic analysis; Genetic distance; Genetic diversity; Genotypes; Heterozygosity; High resolution; Homozygosity; Inbreeding; Inbreeding depression; Life Sciences; Mating; Onions; Phylogeny; Plant breeding; Plant Genetics and Genomics; Plant introductions; Plant Pathology; Plant Physiology; Plant Sciences; Pollination; Population genetics; Vegetables; L.; Inbreeding depression; High-resolution melting (HRM) marker; Homozygosity; Onion; Heterozygosity
• ISSN: 0014-2336; 1573-5060
• DOI: 10.1007/s10681-023-03226-w

Onion ( Allium cepa L.) is a cross-pollinated crop with severe inbreeding depression. Inbred breeding lines are thus commonly maintained through sib-mating or a combination of sib-mating and self-pollination. Therefore, the homozygosity levels of onion inbred lines are generally low compared with self-pollinated crops. To evaluate the homozygosity levels of inbred lines, 43 high-resolution melting markers that were evenly distributed throughout eight onion linkage groups were selected among 652 markers consisting of a high-resolution linkage map. Eight individual plants from 119 inbred lines collected from five onion-breeding institutes were analyzed using the 43 HRM markers, resulting in an average homozygosity level of 0.55. This indicates that almost half of the 43 markers were still segregating in those inbred lines. The homozygosity levels of inbred lines varied between the onion-breeding institutes but they were generally higher than those of the Plant Introduction (PI) accessions. Additionally, the average proportion of genotypes fixed as either homozygous or heterozygous was 0.46 in 12 F 1 cultivars, indicating that their parental lines had low homozygosity levels. Phylogenetic analyses based on the pairwise genetic distances of all entries did not show clear clustering of related entries. This lack of clear clustering patterns was attributed to the relatively large within-population variations and low genetic diversity of the analyzed entries. The observed heterozygosity of the 43 markers was generally higher than the expected heterozygosity. Moreover, one marker exhibited a marked increase in observed heterozygosity, suggesting the possible involvement of this genomic region in inbreeding depression.