Abstract
BackgroundApple (Malus ssp.), one of the most important temperate fruit crops, has a long cultivation history and is economically important. To identify the genetic relationships among the apple germplasm accessions, whole-genome structural variants identified between M. domestica cultivars ‘Jonathan’ and ‘Golden Delicious’ were used.ResultsA total of 25,924 insertions and deletions (InDels) were obtained, from which 102 InDel markers were developed. Using the InDel markers, we found that 942 (75.3%) of the 1251 Malus accessions from 35 species exhibited a unique identity signature due to their distinct genotype combinations. The 102 InDel markers could distinguish 16.7–71.4% of the 331 bud sports derived from ‘Fuji’, ‘Red Delicious’, ‘Gala’, ‘Golden Delicious’, and other cultivars. Five distinct genetic patterns were found in 1002 diploid accessions based on 78 bi-allele InDel markers. Genetic structure analysis indicated that M. domestica showed higher genetic diversity than the other species. Malus underwent a relatively high level of wild-to-crop or crop-to-wild gene flow. M. sieversii was closely related to both M. domestica and cultivated Chinese cultivars.ConclusionsThe identity signatures of Malus accessions can be used to determine distinctness, uniformity, and stability. The results of this study may also provide better insight into the genetic relationships among Malus species.
Highlights
Apple (Malus ssp.), one of the most important temperate fruit crops, has a long cultivation history and is economically important
Our results showed that Insertion and deletion (InDel) were more well-distributed on chromosomes than the other types of structural variant (SV) (Fig. 1c)
Of the 170 InDels chosen throughout the genome (10 per chromosome), 102 were validated for further analyses. These InDels were combined into nine fluorescence multiplex Polymerase chain reaction (PCR) groups; each group contained three to 24 InDel markers (Table S2)
Summary
Apple (Malus ssp.), one of the most important temperate fruit crops, has a long cultivation history and is economically important. To identify the genetic relationships among the apple germplasm accessions, wholegenome structural variants identified between M. domestica cultivars ‘Jonathan’ and ‘Golden Delicious’ were used. Apple (Malus ssp.), one of the most commonly cultivated fruit crops, supports many local economies in temperate zones. Malus is extremely rich in diversity, with 25 to 78 species in the genus depending on the taxonomic classifications [51, 56]. The genetic variability and allelic diversity in these accessions are usually examined to reveal their distinctness. The test for distinctness, uniformity, and stability (DUST) is a statutory requirement to release a new cultivar (International Union for the Protection of New Varieties of Plants (UPOV) Convention Articles 5–9, 991)[64]. It is necessary to develop an efficient marker-assisted DUST protocol in Malus plants
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