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ARS Home » Northeast Area » Geneva, New York » Grape Genetics Research Unit (GGRU) » Research » Publications at this Location » Publication #371578

Research Project: Grapevine Genetics, Genomics and Molecular Breeding for Disease Resistance, Abiotic Stress Tolerance, and Improved Fruit Quality

Location: Grape Genetics Research Unit (GGRU)

Title: Phased diploid and pan-genomes of cultivated and wild apples unravel genetic basis of apple domestication

item SUN, XUEPENG - Boyce Thompson Institute
item JIAO, CHEN - Boyce Thompson Institute
item SCHWANINGER, HEIDI - US Department Of Agriculture (USDA)
item CHAO, THOMAS - US Department Of Agriculture (USDA)
item MA, YUMIN - Shandong Academy Of Agricultural Sciences
item DUAN, NAIBIN - Shandong Academy Of Agricultural Sciences
item KHAN, AWAIS - Cornell University
item XU, KENONG - Cornell University
item CHENG, LAILIANG - Cornell University
item Zhong, Gan-Yuan
item FEI, ZHANGJUN - Boyce Thompson Institute

Submitted to: Nature Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 9/22/2020
Publication Date: 11/2/2020
Citation: Sun, X., Jiao, C., Schwaninger, H., Chao, T., Ma, Y., Duan, N., Khan, A., Xu, K., Cheng, L., Zhong, G., Fei, Z. 2020. Phased diploid and pan-genomes of cultivated and wild apples unravel genetic basis of apple domestication. Nature Genetics.

Interpretive Summary: Apple is an important fruit worldwide. It was originated through hybridization of different wild apple species, among which Malus sieversii and Malus sylvestris are the major progenitors. Today, thousands of apple varieties are grown worldwide and they display tremendous morphological variations, which together underlie great diversity in their genomes (genetic codes). To help improve apples through breeding we need to understand apple genomes. Two such genomes were previously sequenced and assembled, but their quality was limited due to the availability of technologies at the time. In this study, we used cutting-edge technologies to assembly reference-grade, phased diploid genomes for the cultivated apple Gala, a top cultivar grown worldwide, and two major wild progenitors, M. sieversii and M. sylvestris. We also constructed pan-genome for each of the three Malus species. This work significantly improves our current knowledge of apple domestication history and genome diversity.

Technical Abstract: Apple genomes are highly heterozygous by nature. Here, we report the haplotype-resolved genomes of cultivated apple (Malus domestica cv. Gala) and its two major wild progenitors, M. sieversii and M. sylvestris. Substantial variations are identified between the two haplotypes of each genome. Analysis of these genomes reveals repeated bursts of long terminal repeat retrotransposons that may have contributed to apple genome evolution and population diversification. Origins of genomic regions in cultivated apples from wild progenitors are inferred; in Gala, ~15% of the genome comprises alleles from both progenitors. Deep sequencing of 91 accessions identifies selective sweeps in cultivated apples that originated from either of the two progenitors and are associated with important domestication traits. Finally, analysis of pangenomes constructed for the three Malus species uncover thousands of new genes and detects hundreds of genes that have been selected from one of the progenitors and become largely fixed in cultivated apples.