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Bud endodormancy in deciduous fruit trees is an adaptive trait evolved by selection for the capacity to survive unfavorable environmental conditions. Deciduous trees require a certain amount of winter chill named chilling requirement (CR) to promote bud endodormancy release. In recent decades, global warming has endangered the chill accumulation in deciduous fruit trees. Developing low-CR cultivars is a practical way to neutralize the effect of climate changes on the cultivation and distribution of deciduous fruit trees. In this review, we focus on the effect of chilling accumulation on bud endodormancy release and the genetic mechanisms underlying the chilling requirement in deciduous fruit trees. Additionally, we put forth a regulatory model for bud endodormancy and provide prospective directions for future research in deciduous fruit trees. [ABSTRACT FROM AUTHOR]

Apple is one of the most economically important and popular temperate fruit trees. The domestication of apple has resulted in substantial phenotypic differences, particularly between wild and cultivated varieties. However, the relationship between gene expression and phenotypic variations in apple remains poorly understood. Here, we present a comprehensive dataset featuring five distinct apple varieties, including two wild varieties and three representative cultivated varieties. The dataset comprises of both phenomics data, encompassing twelve fruit quality-related traits continuously measured over two years, and transcriptomic data obtained at different developmental stages with three biological replicates. We performed basic quality control process, gene expression normalization and differential gene expression analysis to demonstrate the utility and reliability of the dataset. Our findings indicate that gene expression strongly related with phenotypic variations in apple. This dataset serves as a valuable resource, encompassing phenomics and transcriptomic data in multiple formats, thereby facilitating further exploration of the relationships between gene expression and phenotypic traits in apple. [ABSTRACT FROM AUTHOR]

Key message: A candidate gene, designate PpRPH, in the D locus was identified to control fruit acidity in peach. Fruit acidity has a strong impact on organoleptic quality of fruit. Peach fruit acidity is controlled by a large-effect D locus on chromosome 5. In this study, the D locus was mapped to a 509-kb interval, with two markers, 5dC720 and 5C1019, co-segregating with the non-acid/acid trait of peach fruit. Within this interval, a candidate gene encoding a putative small protein, designated PpRPH, showed a consistency between gene expression and fruit acidity, with up- and down-regulation in non-acidic and acidic fruits, respectively. Transient ectopic expression of PpRPH in tobacco leaves caused an increase of pH by approximately 40% compared to the control transformed with empty vector. Whereas, the concentrations of citrate and malate decreased significantly by 22% and 37%, respectively, with respect to the empty vector control. All these results suggest that PpRPH is a strong candidate gene of the D locus. These findings contribute to our overall understanding of the complex mechanism underlying fruit acidity in peach as well as that in other fruit crops. [ABSTRACT FROM AUTHOR]

The present study synthesized Mo-doped δ-MnO2 powders with different doping ratios by implementing hydrothermal method. Various analyses, namely X-ray diffraction (XRD), scanning electron microscopy (SEM), transmission electron microscopy (TEM), the Brunauer–Emmett–Teller (BET) method, Raman spectroscopy, X-ray photoelectron spectroscopy (XPS), X-ray fluorescence spectrometer (XRF), and electrochemical measurements, were applied to characterize the dependence of the δ-MnO2 structure, morphology and electrochemical performance on Mo-doping. The experimental results indicated Mo6+ ions entered into the δ-MnO2 crystal lattice and occupied the Mn sites. Appropriate amount of Mo6+ ions doping decreases the charge transfer resistance and increases the Li+ ion diffusion coefficient, thus producing optimal electrochemical performance. The Mo 5% sample with Mo6+/Mn2+ molar ratio of 5:100 in the original solution presented a specific charge capacity of 476.8 mAh g−1 after 100 cycles at 1000 mA g−1 as well as capacity retention ratio of 112.7%. [ABSTRACT FROM AUTHOR]

Population genetics analysis is crucial for understanding the degree of linkage disequilibrium in a germplasm collection for association mapping and breeding strategies. Here, we report population structure patterns and genetic differentiation of coffee germplasm collections in China using 19 ISSR markers. A total of 129 unique alleles were detected, with an average of 6.8 alleles per ISSR. The estimated average Nei's gene diversity (He) index for all tested accessions was 0.49. A clustering pattern correlating with predefined species origin, rather than isolation by distance, was observed for all the tested accessions. C. arabica is highly differentiated from C. liberica and C. canephora, with Fst values of 0.33 and 0.21, respectively. By contrast, C. liberica and C. excelsa Chevalier showed a close genetic association, with the Fst value of 0.04. Significant differentiation was also detected within C. arabica accessions, which were separated in three genetic subgroups supported by pairwise (Fst) index and Nei's standard genetic distance tests. The Fst outlier test for deviation from expected distribution between Fst and expected heterozygosity identified five putative ISSRs under selection, with two, UBC864 and UBC842, showing signals of positive selection. Our study provides useful information for identifying core collections for genetics studies, breeding programs, and development of future germplasm management strategies. [ABSTRACT FROM AUTHOR]

R2R3-MYB genes play a pivotal role in regulating anthocyanin accumulation. Here, we report two tandemly duplicated R2R3-MYB genes in peach, PpMYB10.1 and PpMYB10.2, with the latter showing lower ability to induce anthocyanin accumulation than the former. Site-directed mutation assay revealed two amino acid changes in the R3 repeat, Arg/Lys66 and Gly/Arg93, responsible for functional divergence between these two PpMYB10 genes. Anthocyanin-promoting activity of PpMYB10.2 was significantly increased by a single amino acid replacement of Arg93 with Gly93. However, either the Gly93 → Arg93 or Arg66 → Lys66 substitutions alone showed little impact on anthocyanin-promoting activity of PpMYB10.1, but simultaneous substitutions caused a significant decrease. Reciprocal substitution of Arg/Gly93 could significantly alter binding affinity to PpbHLH3, while the Arg66 → Lys66 substitution is predicted to affect the folding of the MYB DNA-binding domain, instead of PpbHLH3-binding affinity. Overall, the change of anthocyanin-promoting activity was accompanied with that of bHLH-binding affinity, suggesting that DNA-binding affinity of R2R3-MYBs depends on their bHLH partners. Our study is helpful for understanding of functional evolution of R2R3-MYBs and their interaction with DNA targets. [ABSTRACT FROM AUTHOR]

Amygdalus mira (Koehne) Ricker (Basionym: Prunus mira Koehne) is a wild relative species of peach belonging to Rosaceae family. It is likely the oldest progenitor of peach and considered threatened or even on the verge of extinction, which requires urgent conservation attention. To contribute to such efforts, complete chloroplast genome of A. mira was assembled using Illumina Hiseq 2500 platform. The cpDNA genome is 157,330 bp in length and has a GC content of 36.80%, with a typical circular quadripartite structure comprising a pair of inverted repeats (IRA and IRB) separated by two single-copy regions. The cpDNA genome consisted of 88 coding sequences (CDS), 37 tRNAs and 8 rRNAs genes. 583 simple sequence repeat (SSR) motifs were identified, where hexa-nucleotide was the most common (27.7% of all SSRs). The complete cpDNA genome of A. mira will be of valuable data for the upcoming research on comparative population genomics of peach. [ABSTRACT FROM AUTHOR]

Gelatinization temperature (GT), an important parameter for rice cooking quality, is mainly regulated by the ALK gene encoding starch synthase IIa. Here, we reported the nucleotide diversity of the ALK gene in 122 cultivated accessions and 199 wild rice accessions that were collected around the Pearl River Basin in China. A total of 93 single nucleotide ploymorphisms (SNPs) were identified, with an average of one SNP per 40 bp. Tajima D statistics revealed that the DNA sequences covering the last exon have probably evolved under balancing selection. Based on two functional SNPs (an A to G substitution at 4198 bp and a GC to TT dinucleotide substitution at 4330/4331 bp), three haplotypes, G/GC, G/TT, and A/GC, were identified in both wild and cultivated accessions, with the G/GC haplotype being predominant. Interestingly, the A/GC haplotype was exclusively found in the wild accessions from Guangdong province, while the G/TT haplotype was only present in the wild accessions from Jiangxi province and Hainan Island. This suggests that the G/TT and A/GC variants may have arisen independently and undergone balancing selection on separate haplotypes in multiple populations. Our result supports earlier hypothesis that cultivated rice was independently domesticated from multiple domestication events in China. Our study aids in the understanding of the domestication process that led to the improvement of rice grain quality. [ABSTRACT FROM AUTHOR]

Transposable elements account for approximately 30 % of the Prunus genome; however, their evolutionary origin and functionality remain largely unclear. In this study, we identified a hAT transposon family, termed Moshan, in Prunus. The Moshan elements consist of three types, aMoshan, tMoshan, and mMoshan. The aMoshan and tMoshan types contain intact or truncated transposase genes, respectively, while the mMoshan type is miniature inverted-repeat transposable element (MITE). The Moshan transposons are unique to Rosaceae, and the copy numbers of different Moshan types are significantly correlated. Sequence homology analysis reveals that the mMoshan MITEs are direct deletion derivatives of the tMoshan progenitors, and one kind of mMoshan containing a MuDR-derived fragment were amplified predominately in the peach genome. The mMoshan sequences contain cis-regulatory elements that can enhance gene expression up to 100-fold. The mMoshan MITEs can serve as potential sources of micro and long noncoding RNAs. Whole-genome re-sequencing analysis indicates that mMoshan elements are highly active, and an insertion into S- haplotype- specific F- box gene was reported to cause the breakdown of self-incompatibility in sour cherry. Taken together, all these results suggest that the mMoshan elements play important roles in regulating gene expression and driving genomic structural variation in Prunus. [ABSTRACT FROM AUTHOR]

Soluble sugars and organic acids have a strong impact on the overall organoleptic quality of fruits. In this study, we report the identification of quantitative trait loci (QTLs) for individual sugars and organic acids in apple. A high density linkage map of apple was constructed using the 1536 EST-derived SNP GoldenGate genotyping platform. The linkage map consists of 601 molecular markers, including 540 single nucleotide polymorphisms (SNPs) and 61 simple sequence repeats (SSRs), spanning 1368.4 cM with an average of 2.28 cM per marker. The contents of soluble sugars, including sucrose, glucose, fructose, sorbitol, and organic acids, including malic acid and citric acid, were used as the phenotypic data in QTL analysis. Two QTLs for malic acid content were detected on linkage groups (LGs) 8 and 16, while no QTL was found for citric acid content. Four QTLs for the glucose, sucrose, fructose, and sorbitol content were found to be clustered in one region on LG 3. Moreover, an additional QTL for glucose content was detected on the LG 4. Our study not only expands our understanding of the genetic basis for fruit organoleptic quality but it also provides molecular markers that will aid in marker-assisted selection for fruit quality in apple breeding programs. [ABSTRACT FROM AUTHOR]

A segregating mapping population of 'Co-op 17' × 'Co-op 16' was used to identify quantitative trait loci (QTLs) associated with various fruit quality traits in apple. Phenotypic data were collected over 2 years for fruit circumference (in centimeter), diameter at midpoint (in centimeter), length (in centimeter), weight (in gram), total soluble solids (in degree Brix), and total titratable acids (in percent) for the segregating population. The phenotypic data along with a previously constructed genetic map, based on simple sequence repeat markers derived from expressed sequence tag and bacterial artificial chromosome end sequence databases, were used in marker-trait association analysis. Interval mapping identified two QTLs linked to fruit size components on linkage groups 03 and 05 with limit of detection scores of 3.27-4.06 and 3.29-4.02 along with phenotypic variation accounting for 15.4-46.4 and 18.3-21.9 %, respectively. [ABSTRACT FROM AUTHOR]

Yellow fruit flesh color, resulting from the accumulation of carotenoids, is one of the most important commercial traits of peach. Yellow flesh is controlled by a single locus ( Y), with white flesh dominant over yellow flesh. In this study, the Y locus was narrowed to a 2.6-cM interval flanked by two markers, SSRy and W2691. SSRy, which is located on the first exon of a gene encoding carotenoid cleavage dioxygenase (CCD4), was cosegregated with the Y locus in two peach F populations. RNA-Seq and qRT-PCR analysis revealed transcript level of CCD4 was consistent with carotenoid degradation in peach fruits. All these results suggest that CCD4 is responsible for white and yellow coloration of peach fruit flesh. In fruits of white-fleshed peach, carotenoids are synthesized but subsequently degraded into colorless compounds, leading to the formation of white color. CCD4 is likely to utilize β-carotene as the substrate in peach. Interestingly, CCD4 also controls white and yellow coloration of leaf midveins of peach. Moreover, LCYE was highly expressed in peach leaves, whereas its transcript was not detectable in fruits. This suggests the difference of carotenoid biosynthesis between peach fruits and leaves. Our study not only shows for the first time the pleiotropic effects of CCD4 gene in peach but also provides a morphological marker for easy selection of new peach cultivars with desirable white or yellow flesh colors. [ABSTRACT FROM AUTHOR]

Peach ( Prunus persica) is one of the most important of deciduous fruit trees worldwide. To facilitate isolation of genes controlling important horticultural traits of peach, transcriptome sequencing was conducted in this study. A total of 133 million pair-end RNA-Seq reads were generated from leaf, flower, and fruit, and 90 % of reads were mapped to the peach draft genome. Sequence assembly revealed 1,162 transcription factors and 2,140 novel transcribed regions (NTRs). Of these 2,140 NTRs, 723 contain an open reading frame, while the rest 1,417 are non-coding RNAs. A total of 9,587 SNPs were identified across six peach genotypes, with an average density of one SNP per ~5.7 kb. The top of chromosome 2 has higher density of expressed SNPs than the rest of the peach genome. The average density of SSR is 312.5/Mb, with tri-nucleotide repeats being the most abundant. Most of the detected SSRs are AT-rich repeats and the most common di-nucleotide repeat is CT/TC. The predominant type of alternative splicing (AS) events in peach is exon-skipping isoforms, which account for 43 % of all the observed AS events. In addition, the most active transcribed regions in peach genome were also analyzed. Our study reveals for the first time the complexity of the peach transcriptome, and our results will be helpful for functional genomics research in peach. [ABSTRACT FROM AUTHOR]

Starch is one of the main components of lotus rhizome and seed, and has a high potential influence on their eating and processing quality. However, little is known about the molecular mechanism underlying starch synthesis in lotus plants. Here, we report a genomewide identification and characterization of genes encoding granule-bound starch synthase in sacred lotus. Two GBSS genes, designated NnGBSSII-1 and NnGBSSII-2, have been identified in the genome of lotus variety 'China Antique.' NnGBSSII-1 is expressed in all tested tissues, including leaf, flower, leafstalk, rhizome, and seed, whereas NnGBSSII-2 is a pseudogene and its transcripts have not been detected in any tissues. Overall, the expression level of NnGBSSII-1 gene is positively correlated with amylose accumulation in lotus rhizome and seed. Moreover, a phylogenetic analysis shows that GBSS genes from N. nucifera and N. lutea are clustered together, and they have a closer relationship with GBSS genes from Proteaceae. This result supports the hypothesis that Nelumbo is taxonomically placed in the lotus family, Nelumbonaceae, under the order Proteales. Our results will be helpful for future genetic improvement of starch quality in rhizome and lotus seed. [ABSTRACT FROM AUTHOR]

Sugar content is a key feature of grape quality. The sugar content of grapes has been significantly improved after nearly a thousand years of artificial selection. However, the mechanism underlying the changes in the grape sugar content during the process of artificial selection remains largely unknown although several genes involved in sugar metabolism and transportation in grape have been identified. In this study, the genomes of 13 wild Vitis species and 14 cultivated Vitis vinifera accessions were resequenced to 2-5 X depth using the Illumina Hiseq2000 platform. Genetic variation of 138 genes involved in sugar biosynthesis and transport was investigated, and 7,690 and 12,717 single nucleotide polymorphisms/insertions and deletions (SNPs/InDel) were identified within the cultivated V. vinifera and wild Vitis species, respectively. The percentages of SNPs/InDels were 0.93 and 1.54 % in cultivated and wild species, respectively, and the wild Vitis species had 1.65-fold more SNPs/InDels than the cultivated V. vinifera. Moreover, the distribution of SNPs/InDels in gene regions was also investigated. Eight genes (HT4, PPFTK4, PPFTK6, PMT3, SPS1, HT8, HT15, SUSy1) showed low level of allelic diversity in cultivated species, suggesting they might have undergone purifying selection during the domestication process of grapes. Our genome DNA resequencing data provided a valuable resource for analyzing the effects of artificial selection on trait-related pathways in grape. The result that eight genes showed lower level of DNA variation in cultivated species than in wild species will be very helpful in understanding sugar accumulation in grapes. [ABSTRACT FROM AUTHOR]

Simple sequence repeats (SSRs) were used to assess genetic diversity and study genetic relatedness in a large collection of Malus germplasm. A total of 164 accessions from the Malus core collection, maintained at the University of Illinois, were genotyped using apple SSR markers. Each of the accessions was genotyped using a single robust SSR marker from each of the 17 different linkage groups in Malus. Data were subjected to principal component analysis, and a dendrogram was constructed to establish genetic relatedness. As expected, this diverse core collection showed high allelic diversity; moreover, this allelic diversity was higher than that previously reported. Cluster analysis revealed the presence of four distinct clusters of accessions in this collection. [ABSTRACT FROM AUTHOR]

China, one of the primary centers of genetic diversity for the genus Malus, is very rich in wild apple germplasm. In this study, genetic diversity in 29 Malus accessions, including 12 accessions from 7 Chinese Malus species, 4 Chinese landraces, and 13 introduced apple cultivars, was assessed using a set of 19 single-locus simple sequence repeat (SSR) markers distributed across all 17 linkage groups of the apple genome. The number of alleles detected at each locus ranged from 2 to 11, with an average of 5.3 per SSR marker. In some accessions, 16 unique alleles were identified. Ten out of these 16 unique alleles (62.5%) were detected exclusively in wild species, indicating that these Chinese wild apple species have considerable genetic diversity and can be used in breeding programs to increase the genetic diversity of apple cultivars. Using 19 SSRs, an unweighted pair-group method with arithmetic average cluster analysis was conducted, and the resulting dendrogram revealed that all cultivars, except for EфpeMeBckoe, were clustered together in the same group. The Russian cultivar EфpeMeBckoe was closely related to the Chinese crabapple Baihaitang ( M. prunifolia), with a high similarity coefficient value of 0.94. Of the two M. sieversii accessions used, one accession showed a close relationship to apple cultivars, while the other accession was closely related to wild apple species, suggesting the presence of a wider genetic diversity in Chinese M. sieversii species. The influence of SSR marker selection on genetic diversity analysis in this Malus collection was also discussed. [ABSTRACT FROM AUTHOR]

Apparent amylose content (AAC), gel consistency (GC), and gelatinization temperature (GT) are recognized as the most important determinants of rice eating and cooking qualities. The contributions of major starch-synthesis genes to these three traits have been investigated in the three consecutive experiments. In an initial QTL mapping with 130 doubled haploid (DH) lines, derived from an inter-subspecific cross of ‘Nanjing11’/‘Balilla’, the major QTLs responsible for AAC, GC, and GT coincided with the Wx (granule-bound starch synthase gene), Wx, and Sss IIa (soluble starch synthase gene) loci, respectively. In the second experiment, contributions of the major starch-synthesis genes to AAC, GC, and GT variations were estimated by using a multiple linear regression analysis. As shown, the Wx locus was a principal determinant for both AAC and GC, and could account for 58.5% and 38.9% of the phenotypic variations, respectively; while the Sss IIa locus was associated with GT, and could explain 25.5% of the observed variation. Eventually, a F2 population consisting of 501 individuals, derived from an inter-subspecific cross of the two sticky rice varieties ‘Suyunuo’ and ‘Yangfunuo 4’, was examined with gene-tagged markers. In the absence of the Wx gene, none of the starch-synthesis genes investigated could dominate the GC variation, however, the Sss IIa locus could also explain 25.1% of the GT variation. In summary, the Wx locus dominates the AAC variation, and meanwhile plays a major role in the GC variation. The Sss IIa locus is a major factor in explaining the GT variation. Apart from the major genes, other genetic factors may also contribute to the GC/GT variations. [ABSTRACT FROM AUTHOR]

Reports research on transgenic wheat and gene silencing. Use of particle bombardment to insert the plasmid containing the promoter Act1, the coat protein (cp) gene of wheat yellow mosaic virus (WYMV) and the selectable bar gene, into immature embryos of a wheat cultivars; PCR and PCR-RFLP used to screen for the cp gene in TO and T1 generations; How seeds from the positive T1 plants were sowed in WYMV-contaminated soil to determine their resistance; Finding that one of the transgenic wheat lines, PS-T2, showed high disease-resistance; Western blot and RT-PCR analysis indicating the expression level of cp gene in the resistant transgenic line was reduced significantly; Conclusion that the mechanism of the virus induced gene silencing stimulated resistance.