园艺-分子生物合辑Horticulture — Genetics · Breeding
Rose is one of the most important ornamental and economic plants in the world. Modern rose cultivars are primarily tetraploid, and during meiosis, they may exhibit double reduction or preferential chromosome pairing. Therefore, the construction of a high density genetic map of tetraploid rose is both challenging and instructive. In this study, a tetraploid rose population was used to conduct a genetic analysis using genome sequencing. A total of 17 382 single nucleotide polymorphism (SNP) markers were selected from 2 308 042 detected SNPs. Combined with 440 previously developed simple sequence repeats (SSR) and amplified fragment length polymorphism (AFLP) markers, a marker dosage of 6 885 high quality markers was successfully assigned by GATK software in the tetraploid model. These markers were used in the construction of a high density genetic map, containing the expected seven linkage groups with 6 842 markers, a total map length of 1 158.9 cM, and an average inter-marker distance of 0.18 cM. Quantitative trait locus (QTL) analysis was subsequently performed to characterize the genetic architecture of petal number and flower diameter. One major QTL (qpnum-3-1) was detected for petal number in three consecutive years, which explained 20.18–22.11% of the variation in petal number. Four QTLs were detected for flower diameter; the main locus, qfdia-2-2, was identified in two consecutive years. Our results will benefit the molecular marker-assisted breeding of modern rose cultivars. In addition, this study provides a guide for the genetic and QTL analysis of autotetraploid plants using sequencing-based genotyping methods.
Embryo rescue technology plays an important role in seedless grape breeding. However, the efficiency of embryo rescue, including the embryo formation, germination, and seedling rates, is closely related to the parental genotypes, degree of abortion, growth medium, and plant growth regulators. In this study, we investigated the effects of different concentrations of paclobutrazol (PAC), a plant growth regulator, and embryo collection times on the embryo formation, germination, and seedling rates for different hybrid combinations of grape breeding varieties used for their aroma and cold-resistance traits. The results showed that the different PAC concentrations had varying impacts on the development of ovules and embryos from the different grape varieties. The embryo formation rates of the ‘Sultanina Rose’×‘Beibinghong’ and ‘Kunxiang Seedless’×‘Taishan-2’ crosses were the highest under the 5.1 μmol L–1 PAC treatment. The 1.0 μmol L–1 PAC treatment was optimal for the germination and seedling development of the ‘Sultanina Rose’×‘Beibinghong’ embryos, whereas the 0.2 μmol L–1 PAC treatment induced the highest germination rate for the ‘Sultanina Rose’×‘Kunxiang Seedless’ cross. The optimal sampling times for each cross varied as 39 d after pollination (DAP) for the ‘Flame Seedless’×‘Muscat Hamburg’ cross, 46 DAP for the ‘Kunxiang Seedless’×‘Beibinghong’ cross, and 41 DAP for the ‘Ruby Seedless’×‘Beibinghong’ and ‘Fantasy Seedless’×‘Shuangyou’ crosses. Moreover, the medium modified with 0.5 g L–1 of indole-3-butyric acid allowed the malformed seedlings to develop into plantlets and achieve larger progenies. This study provides a useful basis for further studies into grape embryo rescue and could improve breeding efforts for new seedless grape varieties.
Organic acids are one of the most important factors influencing fruit flavors. The predominant organic acid in most pear cultivars is malic acid, but the mechanism controlling its accumulation remains unclear. In this study, by comparing gene expression levels and organic acid content, we revealed that the expression of PbPH5, which encodes a P3A-ATPase, is highly correlated with malic acid accumulation in different pear species, with correlation coefficients of 0.932**, 0.656*, 0.900**, and 0.518* (*, P<0.05 or **, P<0.01) in Pyrus bretschneideri Rehd., P. communis Linn., P. pyrifolia Nakai., and P. ussuriensis Maxim., respectively. Moreover, the overexpression of PbPH5 in pear significantly increased the malic acid content. In contrast, silencing PbPH5 via RNA interference significantly decreased its transcript level and the pear fruit malic acid content. A subcellular localization analysis indicated that PbPH5 is located in the tonoplast. Additionally, a phylogenetic analysis proved that PbPH5 is a PH5 homolog gene that is clustered with Petunia hybrida, Malus domestica, and Citrus reticulata genes. Considered together, these findings suggest PbPH5 is a functionally conserved gene. Furthermore, the accumulation of malic acid in pear fruits is at least partly related to the changes in PbPH5 transcription levels.
‘Corollas and spines’ is an important trait for fresh market cucumber. In a unique cucumber line, ‘6457’, the super ovary is much larger and corolla opening is delayed by 4–5 days, thus the resulting fruit has a flower that remains on the tip, which has a high commodity value. In this study, to better understand the molecular basis of corolla opening, mRNA and miRNA transcriptome analyses were performed during corolla development of the super and normal ovaries. A total of 234 differentially expressed miRNAs (DEMs) and 291 differentially expressed target genes (DE-target genes) were identified from four developmental stages, and the greatest number of DEMs was found at the yellow bud stage. Thirty of the DE-target genes were regulated by more than five DEMs, among which, CsHD-Zip was regulated by 28 DEMs, followed by DD2X (18). In addition, the expression patterns of miRNA_104, miRNA_157, miRNA_349, miRNA_242, and miRNA_98 were similar during corolla development, and they shared the same target gene, CsCuRX. Moreover, several critical candidate DEMs and DE-target genes were characterized and profiled by a qRT-PCR experiment. Three of the miRNAs, miRNA_157-CsCuRX, miRNA_411-CsGH3.6, and miRNA_161/297/257-CsHD-Zip, might be responsible for corolla opening in the cucumber super ovary. This integrated study on the transcriptional and post-transcriptional profiles can provide insights into the molecular regulatory mechanism underlying corolla opening in the cucumber.
Seedlessness in grape (Vitis vinifera) is an important commercial trait for both the fresh and drying markets. However, despite numerous studies, the mechanisms and key genes regulating grape seedlessness are mostly unknown. In this study, we sequenced the genomes of the V. vinifera seeded cultivar ‘Red Globe’, the seedless cultivar ‘Centennial Seedless’, and the derived hybrids. Nonsynonymous single nucleotide polymorphisms (SNPs) were identified by genome sequencing and analyzed using published transcriptome data. Nonsynonymous SNPs occurred in genes related to seed development, which were identified as protein kinases, transcription factors, and cytochrome P450s and showed differential expression during ovule development in both seeded and seedless grapes. These nonsynonymous SNP-associated genes were mainly involved in biological processes such as hormone balance, seed coat and endosperm development, reproductive organ development, oxidation and reduction, senescence and cell death. A potential quantitative trait locus (QTL) region associated with seed size was characterized based on the SNP-index, and expression analysis of candidate genes in the QTL region during ovule development in multiple seeded and seedless grape cultivars were conducted. Three SNPs were further subjected to SNaPshot analysis and one SNP in G8 showed 67.5% efficiency in the grape progeny validation. Overall, the data obtained in this study shed light on the differences in seed development between seeded and seedless progeny at the genomic level, which provides valuable resources for future functional studies and grape breeding.
Soft rot caused by Pectobacterium carotovorum (Pc) is a devastating disease of Brassica rapa, causing substantial reductions in crop yield and quality. Identifying genes related to soft rot resistance is the key to solving this problem. To characterize soft rot resistance, we screened a soft rot-susceptible Chinese cabbage (A03), a resistant pakchoi (‘Huaguan’), and a resistant mutant (sr). An F2 population was generated by crossing susceptible Chinese cabbage A03 and resistant pakchoi ‘Huaguan’ to identify quantitative trait loci (QTLs) that confer soft rot resistance. A high-density genetic map was constructed and the three QTLs identified contain 166 genes. Based on available transcriptome data, we analyzed the expression of the 166 genes during an important defense regulatory period in Pc infection in both A03 and the resistant mutant sr. Among the 166 genes, six candidate genes were related to the soft rot defense response in B. rapa. TIFY10B (JAZ2, BraA07g038660.3C) was located in the major soft rot resistance QTL, DRQTL-3 on A07, and we speculate that this gene may play an important role in the defense mechanism against soft rot in B. rapa. This study lays the foundation for further investigations on the mechanism of soft rot resistance in B. rapa crops.
Auxin response factors (ARFs) play key roles throughout the whole process of plant growth and development, and mediate auxin response gene transcription by directly binding with auxin response elements (AuxREs). However, their functions in abiotic stresses are largely limited, especially in apples. Here, the auxin response factor gene MdARF2 (HF41569) was cloned from apple cultivar ‘Royal Gala’ (Malus×domestica Borkh.). Phylogenetic analysis showed that ARF2 proteins are highly conserved among different species and MdARF2 is the closest relative to PpARF2 of Prunus persica, but they differ at the DNA level. MdARF2 contains three typical conserved domains including the B3 DNA-binding domain, Auxin_resp domain and AUX_IAA domain. The subcellular localization demonstrated that MdARF2 is localized in the nucleus. The three-dimensional structure prediction of the proteins showed that MdARF2 is highly similar with AtARF2, and they contain helices, folds, and random coils. The promoter of MdARF2 contains cis-acting elements which respond to various stresses, as well as environmental and hormonal signals. Expression analysis showed that MdARF2 is widely expressed in all tissues of apple, with the highest expression of MdARF2 in root. Functional analysis with a series of MdARF2 transgenic apple calli indicated that MdARF2 can reduce the sensitivity to ABA signaling and enhance salt tolerance in apple. In summary, the results of this research provide a new basis for studying the regulation of abiotic stresses by ARFs.
Germplasm resources are an important basis for genetic breeding and analysis of complex traits, and research on genetic diversity is conducive to the exploration and creation of new types of germplasm. In this study, the distribution frequency, coefficient of variation, Shannon–Wiener index, and variance and cluster analyses were used to analyze the diversity and trait differences of 39 fruit phenotypic traits from 570 pear accessions, which included 456 pear accessions from 11 species and 114 interspecific hybrid cultivars that had been stored in the National Germplasm Repository of Apple and Pear (Xingcheng, China). The comprehensive evaluation indices were screened by correlation, principal component and regression analyses. A total of 132 variant types were detected in 28 categorical traits of pear germplasm fruit, which indicate a rich diversity. The diversity indices in decreasing order were: fruit shape (1.949), attitude of calyx (1.908), flesh texture type (1.700), persistency of calyx (1.681), russet location (1.658), relief of area around eye basin (1.644), flavor (1.610) and ground color (1.592). The coefficient of variation of titratable acidity in the 11 numerical traits of pear germplasm fruit was as high as 128.43%, which could more effectively reflect the differences between pear accessions. The phenotypic differentiation coefficient Vst (66.4%) among the five cultivated pear species, including Pyrus bretschneideri (White Pear), P. pyrifolia (Sand Pear), P. ussuriensis (Ussurian Pear), P. sinkiangensis (Xinjiang Pear), and P. communis (European Pear), was higher than the within population phenotypic differentiation coefficient Vst (33.6%). The variation among populations was the main source of variation in pear fruit traits. A hierarchical cluster analysis divided the 389 accessions of six cultivated pear species, including P. pashia (Himalayan Pear), into six categories. There were certain characteristics within the populations, and the differences between populations were not completely clustered by region. For example, Sand Pear cultivars from Japan and the Korean Peninsula clustered together with those from China. Most of the White Pear cultivars clustered with the Sand Pear, and a few clustered with the Ussurian Pear cultivars. The Ussurian Pear and European Pear cultivars clustered separately. The Xinjiang Pear and Himalayan Pear did not cluster together, and neither did the cultivars. Seventeen traits, three describing fruit weight and edible rate (fruit diameter, fruit length and fruit core size), five describing outer quality and morphological characteristics (over color, amount of russeting, dot obviousness, fruit shape, and stalk length), and nine describing inner quality (flesh color, juiciness of flesh, aroma, flavor, flesh texture, flesh texture type, soluble solid contents, titratable acidity, and eating quality) were selected from the 39 traits by principal component and stepwise regression analyses. These 17 traits could reflect 99.3% of the total variation and can be used as a comprehensive evaluation index for pear germplasm resources.
Cassava is an important tropical cash crop. Severe drought stresses affect cassava productivity and quality, and cause great economic losses in agricultural production. Enhancing the drought tolerance of cassava can effectively improve its yield. Long non-coding RNAs (lncRNAs) are present in a wide variety of eukaryotes. Recently, increasing evidence has shown that lncRNAs play a critical role in the responses to abiotic stresses. However, the function of cassava lncRNAs in the drought response remains largely unknown. In this study, we identified a novel lncRNA, DROUGHT-INDUCED INTERGENIC lncRNA (DIR). Gene expression analysis showed that DIR was significantly induced by drought stress treatment, but did not respond to abscisic acid (ABA) or jasmonic acid (JA) treatments. In addition, overexpression of the DIR gene enhanced proline accumulation and drought tolerance in transgenic cassava. RNA-seq analysis revealed that DIR preferentially affected drought-related genes that were linked to transcription and metabolism. Moreover, RNA pull-down mass spectrometry analysis showed that DIR interacted with 325 proteins. A protein–protein interaction (PPI) analysis found a marked enrichment in proteins associated with the mRNA export and protein quality control pathways. Collectively, these results suggest that DIR and its interacting proteins that regulate mRNA or protein metabolism are involved in mediating the drought stress response. Thus, regulating DIR expression has potential for improving cassava yield under drought conditions.
Rosa sterilis S. D. Shi is an important economic tree in China that produces fruits with high nutritional and medicinal value. Many of R. sterilis’ organs are covered with different types of trichomes or prickles that directly affect fruit appearance and plant management. This study used RNA sequencing technology to analyze the transcriptomes of two parts of the inflorescence branch, namely inflorescence stems with flagellated trichomes and pedicels with both flagellated and glandular trichomes. Comparative transcriptomic analysis showed that many transcription factors (TFs) are potentially involved in the formation and development of trichomes. The accumulation of RsETC1, a TF of the R3-MYB family, was significantly higher in inflorescence stems than in pedicels; quantitative reverse transcription PCR (qRT-PCR) verified that its expression was significantly higher in inflorescence stems than in pedicels during the first three development stages, indicating its inhibitory action on the initiation of glandular trichomes in R. sterilis. The mRNA level of RsETC1 accumulated to significantly higher levels in trichomeless tissues than in tissues with trichromes, suggesting that this gene may inhibit the formation of trichomes in R. sterilis. Over-expression of RsETC1 in Arabidopsis resulted in glabrous phenotypes, and the expression of trichome-related endogenous genes, except for TTG1, was markedly reduced. In addition, the contents of the phytohormones jasmonic acid (JA), gibberellin A3 (GA3), and cytokinins (CKs) in pedicels were significantly higher than those in inflorescence stems, and the expression patterns of the genes related to hormone biosynthesis and signal transduction presented consistent responses, suggesting that the transduction of these hormones might be crucial for trichome initiation and development. These data provide a new perspective for revealing the molecular mechanism of trichome formation in R. sterilis.
Copyright © Journal of Integrative Agriculture
Sponsored by Chinese Academy of Agricultural Sciences (CAAS)
Co-sponsored by China Association of Agricultural Science Societies (CAASS)
Publishing Service by Elsevier B.V.
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