Genetic variation and association analyses identify genes linked to fruit set-related traits in grapevine

Dynamic temporal transcriptome analysis reveals grape VlMYB59-VlCKX4 regulatory module controls fruit set

Fruit set is a key stage in determining yield potential and guaranteeing quality formation and regulation. N-(2-chloro-4-pyridyl)-N'-phenylurea (CPPU) has been widely applied in grape production, the most iconic of which is the promotion of grape fruit set. However, current studies still lack the molecular mechanism of CPPU-induced grape fruit set. Here, the dynamic, high-resolution stage-specific transcriptome profiles were generated based on two different treatments and five developmental periods during fruit set in 'Kyoho' grape (Vitis vinifera L. × V. labrusca L.). Pairwise comparison and functional category analysis showed that phytohormone action cytokinin was significantly enriched during the CPPU-induced grape fruit set, but not the natural one. Value differentially expressed gene (VDEG) was a newly proposed analysis strategy for mining genes related to the grape fruit set. Notably, the cytokinin metabolic process was significantly enriched among up-regulated VDEGs. Of importance, a key VDEG VlCKX4 related to the cytokinin metabolic process was identified as related to the grape fruit set. Overexpression of VlCKX4 gene promoted the Arabidopsis plants that produce more and heavier siliques. The transcription factor VlMYB59 directly bound to the promoter of VlCKX4 and activated its expression. Moreover, overexpression of VlMYB59 gene also promoted the Arabidopsis fruit set. Overall, VlMYB59 responded to CPPU treatment and directly activated the expression of VlCKX4, thus promoting the fruit set. A regulatory pathway of the VlMYB59-VlCKX4 module in the fruit set was uncovered, which provides important insights into the molecular mechanisms of the fruit set and good genetic resources for high fruit set rate breeding.

Biography of Vitis genomics: recent advances and prospective

The grape genome is the basis for grape studies and breeding, and is also important for grape industries. In the last two decades, more than 44 grape genomes have been sequenced. Based on these genomes, researchers have made substantial progress in understanding the mechanism of biotic and abiotic resistance, berry quality formation, and breeding strategies. In addition, this work has provided essential data for future pangenome analyses. Apart from de novo assembled genomes, more than six whole-genome sequencing projects have provided datasets comprising almost 5000 accessions. Based on these datasets, researchers have explored the domestication and origins of the grape and clarified the gene flow that occurred during its dispersed history. Moreover, genome-wide association studies and other methods have been used to identify more than 900 genes related to resistance, quality, and developmental phases of grape. These findings have benefited grape studies and provide some basis for smart genomic selection breeding. Moreover, the grape genome has played a great role in grape studies and the grape industry, and the importance of genomics will increase sharply in the future.

Crop Landraces and Indigenous Varieties: A Valuable Source of Genes for Plant Breeding

Landraces and indigenous varieties comprise valuable sources of crop species diversity. Their utilization in plant breeding may lead to increased yield and enhanced quality traits, as well as resilience to various abiotic and biotic stresses. Recently, new approaches based on the rapid advancement of genomic technologies such as deciphering of pangenomes, multi-omics tools, marker-assisted selection (MAS), genome-wide association studies (GWAS), and CRISPR/Cas9 gene editing greatly facilitated the exploitation of landraces in modern plant breeding. In this paper, we present a comprehensive overview of the implementation of new genomic technologies and highlight their importance in pinpointing the genetic basis of desirable traits in landraces and indigenous varieties of annual, perennial herbaceous, and woody crop species cultivated in the Mediterranean region. The need for further employment of advanced -omic technologies to unravel the full potential of landraces and indigenous varieties underutilized genetic diversity is also indicated. Ultimately, the large amount of genomic data emerging from the investigation of landraces and indigenous varieties reveals their potential as a source of valuable genes and traits for breeding. The role of landraces and indigenous varieties in mitigating the ongoing risks posed by climate change in agriculture and food security is also highlighted.

Genetic analysis of grapevine root system architecture and loci associated gene networks

Own-rooted grapevines and grapevine rootstocks are vegetatively propagated from cuttings and have an adventitious root system. Unraveling the genetic underpinnings of the adventitious root system architecture (RSA) is important for improving own-rooted and grafted grapevine sustainability for a changing climate. Grapevine RSA genetic analysis was conducted in an Vitis sp. 'VRS-F2' population. Nine root morphology, three total root system morphology, and two biomass traits that contribute to root anchorage and water and nutrient uptake were phenotyped. Quantitative trait loci (QTL) analysis was performed using a high density integrated GBS and rhAmpSeq genetic map. Thirty-one QTL were detected for eleven of the RSA traits (surface area, root volume, total root length, fresh weight, number of tips, forks or links, longest root and average root diameter, link length, and link surface area) revealing many small effects. Several QTL were colocated on chromosomes 1, 9, 13, 18, and 19. QTL with identical peak positions on chromosomes 1 or 13 were enriched for AP2-EREBP, AS2, C2C2-CO, HMG, and MYB transcription factors, and QTL on chromosomes 9 or 13 were enriched for the ALFIN-LIKE transcription factor and regulation of autophagy pathways. QTL modeling for individual root traits identified eight models explaining 13.2 to 31.8% of the phenotypic variation. 'Seyval blanc' was the grandparent contributing to the allele models that included a greater surface area, total root length, and branching (number of forks and links) traits promoting a greater root density. In contrast, V. riparia 'Manitoba 37' contributed the allele for greater average branch length (link length) and diameter, promoting a less dense elongated root system with thicker roots. LATERAL ORGAN BOUNDARY DOMAIN (LBD or AS2/LOB) and the PROTODERMAL FACTOR (PFD2 and ANL2) were identified as important candidate genes in the enriched pathways underlying the hotspots for grapevine adventitious RSA. The combined QTL hotspot and trait modeling identified transcription factors, cell cycle and circadian rhythm genes with a known role in root cell and epidermal layer differentiation, lateral root development and cortex thickness. These genes are candidates for tailoring grapevine root system texture, density and length in breeding programs.

Is Tempranillo Blanco Grapevine Different from Tempranillo Tinto Only in the Color of the Grapes? An Updated Review

Tempranillo Blanco is a somatic variant of Tempranillo Tinto that appeared as a natural, spontaneous mutation in 1988 in a single shoot of a single plant in an old vineyard. It was vegetatively propagated, and currently wines from Tempranillo Blanco are commercially available. The mutation that originated Tempranillo Blanco comprised single-nucleotide variations, chromosomal deletions, and reorganizations, losing hundreds of genes and putatively affecting the functioning and regulation of many others. The most evident, visual change in Tempranillo Blanco is the anthocyanin lost, producing this grapevine variety bunches of colorless grapes. This review aims to summarize from the available literature differences found between Tempranillo Blanco and Tinto in addition to the color of the grapes, in a climate change context and using fruit-bearing cuttings grown in temperature-gradient greenhouses as research-oriented greenhouses. The differences found include changes in growth, water use, bunch mass, grape quality (both technological and phenolic maturity), and some aspects of their photosynthetic response when grown in an atmosphere of elevated CO2 concentration and temperature, and low water availability. Under field conditions, Tempranillo Blanco yields less than Tempranillo Tinto, the lower weight of their bunches being related to a lower pollen viability and berry and seed setting.

Risk of sudden coronary death based on genetic background in Chinese Han population

Associations between gene variations and sudden cardiac arrest or coronary artery disease have been reported by genome-wide association studies. However, the implication of the genetic status in cases of sudden coronary death (SCD) from the Chinese Han population has remained to be investigated. The present study established a mini-sequencing system to examine putative death-causing single nucleotide polymorphisms (SNPs) using multiplex PCR, single base extension reaction and capillary electrophoresis techniques. A total of 198 samples from the Chinese Han population (age range, 34-71 years; mean age, 53.86 years) were examined using this method. Samples were classified into three groups: Coronary heart disease (CHD, n=70), SCD (n=53) and control (n=75) group. Significant associations were identified for 10, 4 and 6 SNPs in CHD, SCD and sudden death from CHD, respectively, using the χ² test. The SNPs obtained by binary logistic regression may be used to assess and predict the risk of disease. The predictive accuracy of the SNPs in each prediction model and their area under the receiver operating characteristic curve (AUC) values were determined. The AUC of the four SNPs (rs12429889, rs10829156, rs16942421 and rs12155623) to predict CHD was 0.928, the AUC of the six SNPs (rs2389202, rs2982694, rs10183640, rs597503, rs16942421 and rs12155623) to predict SCD was 0.922 and the AUC of the four SNPs (rs16866933, rs4621553, rs10829156 and rs12155623) to predict sudden death from CHD was 0.912. The multifactor dimensionality reduction values were as follows: 0.8690 (prediction model of CHD), 0.7601 (prediction model of SCD) and 0.7628 (prediction model of sudden death from CHD). Taken together, the results of the present study suggested that these SNPs have considerable potential for application in genetic tests to predict CHD or SCD. However, further studies are required to investigate the putative functions of these SNPs.