Construction of a high-density genetic map for yardlong bean and identification of ANT1 as a regulator of anthocyanin biosynthesis.

Because its long, tender pods supply essential proteins, vitamins, and fibers to humans, yardlong bean (Vigna unguiculata ssp. sesquipedalis) is a commonly consumed vegetable, especially in Southeast Asia. To provide insights into the genetic bases of key agricultural traits in yardlong bean, we here created a high-density bin-map with 2084 bin markers using 514 227 SNPs from a recombinant-inbred line (RIL) population. Quantitative trait loci (QTL) mapping was carried out to identify loci associated with anthocyanin content (ANT), vitamin E content (VE), total soluble protein content (TSP), pod length (PL), hundred-seed weight (HSW), seed length and width (SL and SW, respectively), and seed coat color (SCC). In total, 20 related QTLs were isolated, explaining 7.58-56.03% of the phenotypic variation. Of these, five major QTLs (qANT5, qTSP11, qVE7, qPL3, and qSCC9) were detected in 2020, 2021, and the combined environment, explaining 11.96-56.03% of the phenotypic variation. VuANT1 was identified as a causal gene for the QTL qANT5, which regulated anthocyanin content; VuANT1 was highly expressed in immature purple pods but barely detectable in white pods. VuANT1 overexpression in tobacco leaves and yardlong bean hairy roots resulted in purple coloration as a result of anthocyanin accumulation. These findings suggested that VuANT1 was a key regulator of anthocyanin accumulation in yardlong bean. Our results lay a firm foundation for target agricultural trait improvement and clarification of the genetic mechanisms underlying agricultural traits in yardlong bean.

Chromosome-level genomes of three key Allium crops and their trait evolution.

Allium crop breeding remains severely hindered due to the lack of high-quality reference genomes. Here we report high-quality chromosome-level genome assemblies for three key Allium crops (Welsh onion, garlic and onion), which are 11.17 Gb, 15.52 Gb and 15.78 Gb in size with the highest recorded contig N50 of 507.27 Mb, 109.82 Mb and 81.66 Mb, respectively. Beyond revealing the genome evolutionary process of Allium species, our pathogen infection experiments and comparative metabolomic and genomic analyses showed that genes encoding enzymes involved in the metabolic pathway of Allium-specific flavor compounds may have evolved from an ancient uncharacterized plant defense system widely existing in many plant lineages but extensively boosted in alliums. Using in situ hybridization and spatial RNA sequencing, we obtained an overview of cell-type categorization and gene expression changes associated with spongy mesophyll cell expansion during onion bulb formation, thus indicating the functional roles of bulb formation genes.

Erysiphe ruyongzhengiana sp. nov., a new powdery mildew species on Aristolochia debilis, belonging to the Erysiphe aquilegiae clade.

Powdery mildew was found on Aristolochia debilis (Aristolochiaceae) in Jiangsu Province and Shandong Province, China. This fungus is characterized by having long conidiophore foot-cells which are straight or curved at the base, and chasmothecia with numerous appendages. Phylogenetic analysis using internal transcribed spacer sequences showed that five sequences on A. debilis determined in this study and two sequences retrieved from Erysiphe sp. on A. debilis formed an independent cluster within the Erysiphe aquilegiae clade with 58% bootstrap support. This powdery mildew differs from allied species of the E. aquilegiae clade in producing longer conidia and conidiophores with longer foot-cells, which are often curved at the base. Morphological observations and molecular phylogenetic analysis revealed a new powdery mildew species, described as Erysiphe ruyongzhengiana.

Characterization of the complete chloroplast genome of Cucun mismelo L. var. Agrestis Naud.

Cucumis melo L. var. Agrestis Naud chloroplast genome sequence was first reported. The size of the chloroplast genome is 156,016 bp in length, including a large single copy region (LSC) of 86,334 bp, a small single copy region (SSC) of 18,088 bp, and a pair of inverted repeat (IRa and IRb) regions with 25,797 bp. Cucumis melo L. var. Agrestis Naud chloroplast genome encodes 133 genes, including 88 mRNA genes, 37 tRNA genes, and eight rRNA genes. Phylogenetic analysis with the reported chloroplast sequences shows that Cucumis melo L. var. Agrestis Naud was closely related to Cucumis melo subsp. melo.

Characterization of the complete mitochondrial genome of yellow stripe mutant in onion (Allium cepa L.).

The complete onion of yellow stripe mutant tissues mitochondrial genome was determined and analyzed in this study. The complete sequence length is 324,182 bp, including 37 CDS, 13 tRNA, and G + C content percentage of 45. Compared with the normal onions, 556 SNPs, 279 small indel numbers were detected, and the mutations of 14 SNPs and two small indels in the exon region affected the translation of proteins. Phylogenetic tree analysis showed that yellow stripe mutant onion is closely clustered with other Allium cepa L. The mutant of onion plays an important role in developing molecular marker-assisted breeding.

Activity and expression of ADP-glucose pyrophosphorylase during rhizome formation in lotus (Nelumbo nucifera Gaertn.).

BACKGROUND: Lotus root is a traditional and popular aquatic vegetable in China. Starch is an important component of the rhizome and directly affects the quality of processed products. ADP -glucose pyrophosphorylase (AGPase) is a rate-limiting enzyme associated with starch biosynthesis in plants. Therefore, in the present study, AGPase activity and NnAGP expression during rhizome development of lotus were analyzed. RESULTS: Among 15 cultivars analyzed, the contents of amylose and total starch in the rhizome were highest in 'Mei Ren Hong'. 'Su Zhou' and 'Zhen Zhu' showed the lowest amylose, amylopectin and total starch contents. In the rhizome, activity of AGPase was highest at the middle swelling stage of development, and higher activity was observed in the 'Hou ba' leaf and terminational leaf at the same stage. Three AGPase genes, comprising two large subunit genes (NnAGPL1 and NnAGPL2) and one small subunit gene (NnAGPS), were isolated and identified. The deduced amino acid sequences showed 40.5 % similarity among the three genes. Full-length genomic DNA sequences of NnAGPL1, NnAGPL2, and NnAGPS were 4841, 11,346 and 4169 bp, respectively. Analysis of the temporal and spatial expression patterns revealed that the transcription levels of NnAGPL1 and NnAGPS were higher in the rhizome, followed by the 'Hou ba' leaf, whereas NnAGPL2 was significantly detected in the 'Hou ba' leaf and terminational leaf. The initial swelling stage of rhizome development was accompanied by the highest accumulation of mRNAs of NnAGPL1, whereas expression of NnAGPL2 was not detected during rhizome development. The transcript level of NnAGPS was highest at the initial swelling stage compared with the other rhizome developmental stages. Transcription of NnAGPL1, NnAGPL2, and NnAGPS was induced within 24 h after treatment with exogenous sucrose. The mRNA level of NnAGPL1 and NnAGPS was increased by exogenous ABA, whereas transcription of NnAGPL2 was not affected by ABA. CONCLUSIONS: The three AGPase genes display marked differences in spatial and temporal expression patterns. Regulation of AGPase in relation to starch synthesis in lotus is indicated to be complex.