Extensive genetic and DNA methylation variation contribute to heterosis in triploid loquat hybrids

Abstract

We aim to overcome the unclear origin of the loquat and elucidate the heterosis mechanism of the triploid loquat. Here we investigated the genetic and epigenetic variations between the triploid plant and its parental lines using amplified fragment length polymorphism (AFLP) and methylation-sensitive amplified fragment length polymorphism (MSAP) analyses. We show that in addition to genetic variations, extensive DNA methylation variation occurred during the formation process of triploid loquat, with the triploid hybrid having increased DNA methylation compared to the parents. Furthermore, a correlation existed between genetic variation and DNA methylation remodeling, suggesting that genome instability may lead to DNA methylation variation or vice versa. Sequence analysis of the MSAP bands revealed that over 53% of them overlap with protein-coding genes, which may indicate a functional role of the differential DNA methylation in gene regulation and hence heterosis phenotypes. Consistent with this, the genetic and epigenetic alterations were associated closely to the heterosis phenotypes of triploid loquat, and this association varied for different traits. Our results suggested that the formation of triploid is accompanied by extensive genetic and DNA methylation variation, and these changes contribute to the heterosis phenotypes of the triploid loquats from the two cross lines.

Functional Identification of EjGIF1 in Arabidopsis and Preliminary Analysis of Its Regulatory Mechanisms in the Formation of Triploid Loquat Leaf Heterosis

“…Triploid loquat breeding provides a new way to solve the problem of low edible rate of diploid loquats. Previous studies in our lab found that triploid loquats are not only seedless, but also have a variety of excellent traits that diploid and tetraploid loquats do not have, such as larger and greener loquat leaves, showing an obvious heterosis (Liu et al, 2018b(Liu et al, , 2019. Liu et al (2018a,b) have studied the mechanisms of triploid loquat heterosis by using several triploid loquats with clear genetic relationship and found that extensive genetic variation and DNA methylation remodeling after the formation of triploid loquat may change the gene expression patterns in triploid loquats, and these further promoted the formation of triploid loquat heterosis.…”

“…In this study, we have investigated the expression level of one specific leaf development-related gene EjGIF1 in triploid loquats and their parents based on the results of our previous research that the leaf morphologies (length and width) of triploid loquats exhibited pronounced heterosis. Based on the results of EjGIF1 ectopic expression in Arabidopsis, we further investigated the expression level of EjGIF1 in triploid loquats (Liu et al, 2018b). These suggested that high expression of EjGIF1 in triploid hybrids played a critical role in the leaf size heterosis formation.…”

“…The T2 homozygous progenies and WT plants were grown in the growth chamber for about 1 month and their leaf morphology traits were recorded individually. The methods for leaf length and width measuring were the same as Liu et al (2018b), and the leaf size was measured by using the ImageJ software.…”

“…The amplification products were also sequenced as the same as described above, and for each CpG island, 15 randomly chosen clones per genotype were sequenced. The methylation levels were counted as described by Liu et al (2018b).…”

Single-molecule real-time sequencing of the full-length transcriptome of loquat under low-temperature stress

“…Freezing injury has severely jeopardized the economic benefits of farmers and has become a major restricting factor for sustainable development in many production areas worldwide. Current research on loquat has mainly focused on cell genetics [6,7], physiology and biochemistry [8,9], molecular markers [10], molecular clones [11,12], etc. Several transcriptome studies in loquat focused on flower bud differentiation [13], fruit development and ripening [14,15], and postharvest storage [16], research on transcriptome in cold stress of loquat is limited [17], little is known about its cold tolerance mechanisms.…”