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.
Highlights
The domesticated apple (Malus domestica Borkh.) is one of the most commercially important fruit worldwide, with over 60 million tons produced each year (Food and Agriculture Organization of the United Nations, 20131)
The re-sequencing data have been deposited in NCBI Sequence Read Archive (SRA12)
We speculated that some of the identified genetic variations might contribute to the phenotypic differences in floralassociated traits; we focused our analysis on single nucleotide polymorphisms (SNPs), structural variations (SVs), and INDELs associated with flowering genes in genic regions
Summary
The domesticated apple (Malus domestica Borkh.) is one of the most commercially important fruit worldwide, with over 60 million tons produced each year (Food and Agriculture Organization of the United Nations, 20131). There are more than 10,000 documented cultivars of apples (Hummer and Janick, 2009), resulting in a range of desired characteristics. China is the leading apple-producing country, with a planting area of 3.1 million hectares and production of 33 million tons annually. ‘Nagafu No 2’ apples have difficulty forming flower buds and have an alternate bearing problem, which results in unstable and low fruit production. ‘Nagafu No 2’ and ‘Qinguan’ are important materials for apple breeding and genetic research in China because of their different flowering and drought resistance characteristics. The genetic basis underlying these differences and the associated genomic information for these two varieties are poorly understood
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