A key ‘foxy’ aroma gene is regulated by homology-induced promoter indels in the iconic juice grape ‘Concord’

Authors: Yang, Yingzhen; CUENCA, JOSE - Instituto Valenciano De Investigaciones Agrarias; WANG, NIAN - Huazhong Agricultural University; LIANG, ZHENCHANG - Chinese Academy Of Sciences; SUN, HONGHE - Boyce Thompson Institute; Gutierrez, Benjamin; XI, XIAOJUN - Shanghai Academy Of Agricultural Sciences; ARRO, JIE - Oak Ridge Institute For Science And Education (ORISE); WANG, YI - Chinese Academy Of Sciences; FAN, PEIGE - Chinese Academy Of Sciences; Londo, Jason; COUSINS, PETER - E & J Gallo Winery; LI, SHAOHUA - Chinese Academy Of Sciences; FEI, ZHANGJUN - Boyce Thompson Institute; Zhong, Gan-Yuan

Submitted to: Horticulture Research
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 3/30/2020
Publication Date: 4/18/2020
Citation: Yang, Y., Cuenca, J., Wang, N., Liang, Z., Sun, H., Gutierrez, B.L., Xi, X., Arro, J., Wang, Y., Fan, P., Londo, J.P., Cousins, P., Li, S., Fei, Z., Zhong, G. 2020. A key ‘foxy’ aroma gene is regulated by homology-induced promoter indels in the iconic juice grape ‘Concord’. Horticulture Research. 7(67). https://doi.org/10.1038/s41438-020-0304-6.
DOI: https://doi.org/10.1038/s41438-020-0304-6

Interpretive Summary: Concord’ is the most well-known juice grape cultivar with a special aroma, 'foxy flavor'. It is this ‘foxiness’ that makes ‘Concord’ grape very popular for the production of non-fermented juice and jellies. The 'foxy' aroma is also very much favored by table grape consumers. However, the odor is too strong for the production of wines and, understandably, ‘foxy’ aroma is not noticeable in the major wine grape species Vitis vinifera. ‘Foxy’ aroma is predominantly resulted from the accumulation of a chemical compound named as methyl anthranilate (MA) in berries. People don't know why 'Concord' and other cultivars with a parentage of the North American grape species V. labrusca have this special aroma, but popular wine grape species V. vinifera does not have it. In this study, we compared V. labrusca with V. vinifera and several other grape species and found that V. labrusca differed from other grape species in their MA synthesis gene, AMAT. In non-V. labrusca species, there were two major DNA sequences inserted into their AMAT promoter regions. The inserted changes reduced the levels of AMAT expression and MA accumulation, thus the levels of 'foxy' aroma in these non-V. labrusca grapes. We further confirmed the functions of these two major DNA sequence changes using several different approaches. The elucidation of the AMAT genetic regulation advances our understanding of the ‘foxy’ aroma trait and makes it more genetically trackable and amenable in grapevine breeding.

Technical Abstract: Concord’, the most well-known juice grape with a parentage of the North American grape species Vitis labrusca L., possesses a special ‘foxy’ aroma predominantly resulted from the accumulation of methyl anthranilate (MA) in berries. This aroma, however, is often perceived as an undesirable attribute by wine consumers and rarely noticeable in the common table and wine grape species V. vinifera. Here we discovered homology-induced promoter indels as a major genetic mechanism for species-specific regulation of a key ‘foxy’ aroma gene, anthraniloyl-CoA:methanol acyltransferase (AMAT), that is responsible for MA biosynthesis. We found the absence of a 426-bp and/or a 42-bp sequence in AMAT promoters highly associated with high levels of AMAT expression and MA accumulation in ‘Concord’ and other V. labrusca-derived grapes. These promoter variants, all with direct and inverted repeats, were further confirmed in more than 1,300 Vitis germplasm. Moreover, functional impact of these indels was validated in transgenic Arabidopsis. Superimposed on the promoter regulation, large structural changes including exonic insertion of a retrotransposon were present at the AMAT locus in some V. vinifera grapes. Elucidation of the AMAT genetic regulation advances our understanding of the ‘foxy’ aroma trait and makes it genetically trackable and amenable in grapevine breeding.