New Study Provides Insights into the Genetic Determination of Fruit Traits of Pe

Posted by Ilsa Miller on April 1st, 2021

Pear is a typical self-incompatible species with a high degree of genomic heterozygosity, and the cycle of selecting and breeding new varieties by traditional hybridization methods is long and the efficiency is low.

On February 18, Nature Communications published online the latest cooperation results between Nanjing Agricultural University and Cornell University. In this study, genome-wide association analysis of 312 sand pear variety resources revealed the process of pear domestication and improvement, and identified new genes that regulate pear stone cell formation.

“The discovery of new genes demonstrates that in a highly heterozygous species, key genes can also be sought by means of genome-wide association analysis, and our method is feasible.” Wu Jun, co-corresponding author of the paper and professor at Nanjing Agricultural University, said in an interview with the Chinese Journal of Science that the results will provide a very valuable reference for the development of molecular breeding techniques for perennial fruit trees and the analysis of regulatory mechanisms of complex traits, helping scientists understand crop genomes with a high degree of heterozygosity.

In order to find the genetic loci or genes required for breeding to control important traits in the genome of pear, scientists generally use the means of population genetic research.

The object of population genetic analysis is natural population, that is, different populations of a species. Through genome sequencing of these different populations, a large number of single nucleotide polymorphism markers were found from a genome-wide scale, and then analysis of population genetic evolution, phylogeny, and germplasm resource identification was carried out.

Fei Zhangjun, co-corresponding author of the paper and professor at Cornell University, told the Chinese Journal of Science that diversity-rich resources contain varieties with various trait differences, so relevant regions on the genome also show differences. Trait differences as well as genetic differences are an essential basis for studying plant domestication, improvement, as well as genome-wide association analysis.

"The more natural populations and genetic diversity are studied in population genetics, the more variation is, the more traits are different between varieties, and the more single nucleotide polymorphism markers are found, the greater the probability of discovering new genetic loci and genes. Therefore, doing population genetic research should try to target populations with rich genetic diversity." Dr. Mingyue Zhang, co-first author of the paper, said.

In this study, genome-wide genetic variation analysis was performed on the natural population of 312 sand pear varieties, and a total of 2.15 T resequencing data were obtained to identify more than 3.4 million single nucleotide polymorphisms.

Wu Jun said, through the population analysis of local pear varieties and artificially selected varieties, it was found that the stone cell, sugar, acid and other traits of pear fruit were continuously selected during domestication and improvement, while the fruit size and other traits were only selected during domestication.

Fei explained that pear breeding can be divided into two stages: domestication and improvement, of which domestication refers to the process from wild species to landraces, while improvement refers to the process from landraces to modern cultivated species.

At the domestication stage, fruits become significantly larger, so fruit size is under selection, which affects regions or genes within the genome that are associated with fruit size; at the improvement stage, fruit size does not change. Other traits, such as stone cells, sugars, and acids, changed significantly at both stages.

"This also shows that in the improvement stage of pear, people are no longer very concerned about fruit size, but mainly to further improve the quality of fruit." Fei Zhangjun said.

According to Zhang Mingyue, the research team further carried out genome-wide association analysis on 8 quality traits, including fruit weight, color, stone cell, and 3 phenological phase traits, including fruit development days, and obtained 42 association intervals, including known functional genes. And coincide with the location of known quantitative trait sites for some traits.

Zhang Shaoling said this is also the first successful genome-wide association analysis of this highly heterozygous fruit of pears. Due to the high degree of heterozygosity of the pear genome, many traits are complex traits, that is, traits controlled by multiple genes, and these genes are often distributed on different chromosomes, which makes it difficult to find key genes.

For example, in the pear genome, there are about 100 sugar-related genes, involving sugar transformation, synthesis, transportation, storage, etc., of which there are still many unclear molecular mechanisms.

"The main purpose of genome-wide association analysis is to find out the loci closely associated with these important fruit traits in the pear genome, so as to further identify candidate genes that regulate these traits, provide important information for molecular breeding of pears to improve fruit quality, and can also help us further understand the molecular regulatory mechanism of important pear fruit traits." Fei Zhangjun said.

Wu Jun believes that by mining functional genes, it provides important gene resources for the improvement of target traits in pear breeding, and can also be used for crossbreeding by further screening parents with these important functional genes to breed better varieties.

Usually, the fruit quality traits concerned by scientists include color, sweetness, acidity, etc., and stone cells are a special trait affecting the taste of pear fruits.

Plants all contain lignin, which is usually found in shoots. Zhang Shaoling introduced that the fruit of pears is different from other fruits, and their cell walls will slowly accumulate lignin, and when lignin precipitates too much, thin-walled cells die, and they aggregate in a pile and make people taste rough, like stone grains, so they are called stone cells.

When the content of stone cells in fruit is high, it will produce sand sensation, and the flesh quality of fruit is relatively coarse. However, the presence of this lignin can in turn promote gastrointestinal peristalsis and digestion and absorption. Scientists hope that the fruit contains a certain amount of stone cells, both to maintain healthy and beneficial qualities and to bring a pleasant taste.

Fei Zhangjun believes that reducing the content of stone cells in pulp should be a major goal in pear breeding now.

Therefore, the team focused on genetic loci related to stone cells.

Dr. Xue Cheng, co-first author of the paper, introduced that they carried out gene function validation, combined with phenotypic data, transcriptome, phylogenetic relationship and other analyses, to lock a new gene, PbrSTONE.

Through the transient transformation system of pear fruit and the stable transformation system of Arabidopsis thaliana, they confirmed that this gene can regulate the formation of lignin in pear fruit stone cells and major components, and clarified that it has an interaction relationship with PbrC3H, a key gene in the lignin synthesis pathway, thereby synergistically regulating the synthesis mechanism of lignin in stone cell components.

Although lignin-related genes have been studied in model plants in the past, new genes suggest that there are special genes and molecular mechanisms in pear fruit that regulate lignin synthesis in plants, Zhang said. The discovery of new genes lays a foundation for creating new excellent germplasm, screening excellent parents for hybrid breeding, and improving pear quality.

Wu Jun believes that the discovery of this new gene can help us to further understand the regulatory network of stone cell generation in pear fruit, provide direct information for modern molecular breeding of pear, and provide direct target genes for the future use of new biotechnology to improve the fruit quality of pear.

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