Recently, research group from China Agricultural University published a paper in Nature Communications, revealing the regulatory mechanism of intron variations on fruit coloration.  

 

By constructing pan-genomes of 13 Malus species, the study discovered that structural variations in intron regions influence the expression of the key gene MMK2, thereby affecting fruit peel coloration. Specifically, wild apple species with non-colored fruit contain LTR/Gypsy TE insertions in the fourth intron of MMK2, which weakens the promoting effect of the non-coding RNA encoding this gene, leading to decreased MMK2 expression and consequently impacting peel coloration. This finding elucidates how intron variations mildly participated in the domestication and breeding of apples.

 

Through pan-genome analysis, the study also identified a series of genetic variation sites that concurrently act on stress resistance and fruit quality traits, providing gene resources for breeding selection. This research not only deepens the understanding of the genetic regulation mechanisms of fruit coloration, but also provides references for genetic variation studies in other crops.