title: Genome-Wide Sequence Variation Identification and Floral-Associated Trait Comparisons Based on the Re-sequencing of the 'Nagafu No. 2' and 'Qinguan' Varieties of Apple (Malus domestica Borkh.).
abstract: Apple (Malus domestica Borkh.) is a commercially important fruit worldwide. Detailed information on genomic DNA polymorphisms, which are important for understanding phenotypic traits, is lacking for the apple. We re-sequenced two elite apple varieties, 'Nagafu No. 2' and 'Qinguan,' which have different characteristics. We identified many genomic variations, including 2,771,129 single nucleotide polymorphisms (SNPs), 82,663 structural variations (SVs), and 1,572,803 insertion/deletions (INDELs) in 'Nagafu No. 2' and 2,262,888 SNPs, 63,764 SVs, and 1,294,060 INDELs in 'Qinguan.' The 'SNP,' 'INDEL,' and 'SV' distributions were non-random, with variation-rich or -poor regions throughout the genomes. In 'Nagafu No. 2' and 'Qinguan' there were 171,520 and 147,090 non-synonymous SNPs spanning 23,111 and 21,400 genes, respectively; 3,963 and 3,196 SVs in 3,431 and 2,815 genes, respectively; and 1,834 and 1,451 INDELs in 1,681 and 1,345 genes, respectively. Genetic linkage maps of 190 flowering genes associated with multiple flowering pathways in 'Nagafu No. 2,' 'Qinguan,' and 'Golden Delicious,' identified complex regulatory mechanisms involved in floral induction, flower bud formation, and flowering characteristics, which might reflect the genetic variation of the flowering genes. Expression profiling of key flowering genes in buds and leaves suggested that the photoperiod and autonomous flowering pathways are major contributors to the different floral-associated traits between 'Nagafu No. 2' and 'Qinguan.' The genome variation data provided a foundation for the further exploration of apple diversity and gene-phenotype relationships, and for future research on molecular breeding to improve apple and related species.
authors.affiliation: College of Horticulture, Northwest Agriculture and Forestry University Yangling, China.
authors.forename: Libo
authors.initials: L
authors.lastname: Xing
authors.affiliation: College of Horticulture, Northwest Agriculture and Forestry University Yangling, China.
authors.forename: Dong
authors.initials: D
authors.lastname: Zhang
authors.affiliation: College of Horticulture, Northwest Agriculture and Forestry University Yangling, China.
authors.forename: Xiaomin
authors.initials: X
authors.lastname: Song
authors.affiliation: College of Horticulture, Northwest Agriculture and Forestry University Yangling, China.
authors.forename: Kai
authors.initials: K
authors.lastname: Weng
authors.affiliation: College of Horticulture, Northwest Agriculture and Forestry University Yangling, China.
authors.forename: Yawen
authors.initials: Y
authors.lastname: Shen
authors.affiliation: College of Horticulture, Northwest Agriculture and Forestry University Yangling, China.
authors.forename: Youmei
authors.initials: Y
authors.lastname: Li
authors.affiliation: College of Horticulture, Northwest Agriculture and Forestry University Yangling, China.
authors.forename: Caiping
authors.initials: C
authors.lastname: Zhao
authors.affiliation: College of Horticulture, Northwest Agriculture and Forestry University Yangling, China.
authors.forename: Juanjuan
authors.initials: J
authors.lastname: Ma
authors.affiliation: College of Horticulture, Northwest Agriculture and Forestry University Yangling, China.
authors.forename: Na
authors.initials: N
authors.lastname: An
authors.affiliation: College of Horticulture, Northwest Agriculture and Forestry University Yangling, China.
authors.forename: Mingyu
authors.initials: M
authors.lastname: Han
keywords: INDELs; apple (Malus domestica Borkh.); flowering genes; genome variation; re-sequencing