Chinese cabbage is an economically important Brassica vegetable worldwide, and clubroot, which is caused by the soil-borne protist plant pathogen Plasmodiophora brassicae is regarded as a destructive disease to Brassica crops.  Previous studies on the gene transcripts related to Chinese cabbage resistance to clubroot mainly employed RNA-seq technology, although it cannot provide accurate transcript assembly and structural information.  In this study, PacBio RS II SMRT sequencing was used to generate full-length transcriptomes of mixed roots at 0, 2, 5, 8, 13, and 22 days after P. brassicae infection in the clubroot-resistant line DH40R.  Overall, 39 376 high-quality isoforms and 26 270 open reading frames (ORFs) were identified from the SMRT sequencing data.  Additionally, 426 annotated long noncoding RNAs (lncRNAs), 56 transcription factor (TF) families, 1 883 genes with poly(A) sites and 1 691 alternative splicing (AS) events were identified.  Furthermore, 1 201 of the genes had at least one AS event in DH40R.  A comparison with RNA-seq data revealed six differentially expressed AS genes (one for disease resistance and five for defensive response) that are potentially involved in P. brassicae resistance.  The results of this study provide valuable resources for basic research on clubroot resistance in Chinese cabbage.

Somatic embryogenesis (SE) is an effective approach of in vitro regeneration that depends on plant cell totipotency. However, largely unknown of molecular mechanisms of SE in woody plants such as Chinese chestnut (Castanea mollissima Blume), limits the development of the woody plant industry. Here, we report the MADS-box transcription factor CmAGL11 in Chinese chestnut. CmAGL11 transcripts specifically accumulated in the globular embryo. Overexpression of CmAGL11 in chestnut callus enhanced its SE capacity, and the development of somatic embryos occurred significantly faster than in the control. RNA-seq results showed that CmAGL11 affects the expression of several genes related to the gibberellin, auxin, and ethylene pathways. Moreover, the analysis of DNA methylation status indicated that the promoter methylation plays a role in regulation of CmAGL11 expression during SE. Our results demonstrated that CmAGL11 plays an important role in the SE process in Chinese chestnut, possibly by regulating gibberellin, auxin, and ethylene pathways. It will help establish an efficient platform to accelerate genetic improvement and germplasm innovation in Chinese chestnut.

    Kernel color is an important trait for assessing the commercial and nutritional quality of foxtail millet.  Yellow pigment content (YPC) and carotenoid components (lutein and zeaxanthin) of 270 foxtail millet accessions, including 50 landraces and 220 improved cultivars, from four different eco-regions in China were surveyed using spectrophotometry and high performance liquid chromatography methods.  Results indicated that YPC had rich variance, ranging from 1.91 to 28.54 mg kg^–1, with an average value of 17.80 mg kg^–1.  The average YPC of improved cultivars (18.31 mg kg^–1) was significantly higher than that of landraces (15.51 mg kg^–1).  The YPC in cultivars from the Loess Plateau spring sowing region (LPSSR) was the highest (20.59 mg kg^–1), followed by the North China summer sowing region (NCSSR, 18.25 mg kg^–1), the northeast spring sowing region (NSSR, 17.25 mg kg^–1), and the Inner Mongolia Plateau spring sowing region (IMPSSR, 13.92 mg kg^–1).  The variation coefficients of YPC in cultivars from NSSR, LPSSR, and IMPSSR were higher than that from NCSSR.  A similar carotenoid profile was also obtained for 270 foxtail millet cultivars.  Lutein and zeaxanthin accounted for approximately 55–65% of YPC in accessions.  The lutein content was higher than zeaxanthin content in all cultivars.  The ratio of lutein to zeaxanthin ranged from 1.51 to 6.06 with an average of 3.34.  YPC was positively correlated with lutein (r=0.935, P<0.01), zeaxanthin (r=0.808, P<0.01), and growth duration (r=0.488, P<0.01), whereas it was negatively correlated with grain protein (r=−0.332, P<0.01) and 1 000-kernel weight (r=−0.153, P<0.05).  Our study is useful for screening and selecting cultivars with high levels of yellow pigment and for enhancing phytochemical concentrations in breeding programs.

    Interspecific hybridization is an important approach to improve cultivated peanut varieties. Cytological markers such as tandem repeats will facilitate alien gene introgression in peanut. Telomeric repeats have also been frequently used in chromosome research. Most plant telomeric repeats are (TTTAGGG)_n that are mainly distributed at the chromosome ends, although interstitial telomeric repeats (ITRs) are also commonly identified. In this study, the telomeric repeat was chromosomally localized in 10 Arachis species through sequential GISH (genomic in situ hybridization) and FISH (fluorescence in situ hybridization) combined with 4’,6-diamidino-2-phenylindole (DAPI) staining. Six ITRs were identified such as in the centromeric region of chromosome Bⁱ5 in Arachis ipaënsis, pericentromeric regions of chromosomes A^s5 in A. stenosperma, B^ho7 in A. hoehnei and A^v5 in A. villosa, nucleolar organizer regions of chromosomes A^s3 in A. stenosperma and A^di3 in A. diogoi, subtelomeric regions of chromosomes B^ho9 in A. hoehnei and A^du7 in A. duranensis, and telomeric region of chromosome E^s7 in A. stenophylla. The distributions of the telomeric repeat, 5S rDNA, 45S rDNA and DAPI staining pattern provided not only ways of distinguishing different chromosomes, but also karyotypes with a higher resolution that could be used in evolutionary genome research. The distribution of telomeric repeats, 5S rDNA and 45S rDNA sites in this study, along with inversions detected on the long arms of chromosomes K^b10 and B^ho10, indicated frequent chromosomal rearrangements during evolution of Arachis species.

Peanut kernels rich in oil, particularly those with oleic acid as their primary fatty acid, are sought after by consumers, the food industry, and farmers due to their superior nutritional content, extended shelf life, and health benefits.  The oil content and fatty acid composition are governed by multiple genetic factors.  Identifying the quantitative trait loci (QTL) related to these attributes would facilitate marker-assisted selection or genomic selection, thus enhancing the quality-focused peanut breeding program.  For this purpose, we developed a population of 521 recombinant inbred lines (RIL) and tested their kernel quality traits across five different environments. We identified two major and stable QTLs for oil content (qOCAh12.1 and qOCAh16.1).  The markers linked to these QTLs were designed by competitive allele-specific PCR (KASP) and were subsequently validated.  Moreover, we found that the superior haplotype of oil content in the qOCAh16.1 region was conserved within the PI germplasm cluster, as evidenced by a diverse peanut accession panel.  In addition, we determined that qAh09 and qAh19.1, which harbor the key gene encoding fatty acid desaturase 2 (FAD2), influence all seven fatty acids, including palmitic, stearic, oleic, linoleic, arachidic, gadoleic, and behenic acids.  As for protein content and the long-chain saturated fatty acid behenic acid, qAh07 emerged as the major and stable QTLs, accounting for over 10% of the phenotypic variation explained (PVE).  These findings would enhance marker-assisted selection in peanut breeding, aiming to improve oil content, and deepen our understanding of the genetic mechanisms that shape fatty acid composition. 

Genetic improvement of meat production traits has always been the primary goal of pig breeding. Geographical isolation, natural and artificial selection led to significant differences in the phenotypes of meat production traits between Chinese local pigs and Western commercial pigs. Comparative genomics and transcriptomics analysis provided powerful tools to identify genetic variants and genes associated with skeletal muscle growth. However, the number of available genetic variants and genes are still limited. In this study, a comprehensive comparison of transcriptomes showed that ribosomal protein S27-like (RPS27L) gene was highly expressed in skeletal muscle and up-regulated in Chinese local pigs when compared with Western commercial pigs. Functional analysis revealed that overexpression of RPS27L promoted myoblast proliferation and repressed differentiation in pig skeletal muscle cells. Conversely, the knockdown of RPS27L led to the inhibition of myoblast proliferation and the promotion of differentiation. Notably, a 13-bp insertion-deletion (InDel) mutation was identified within the RPS27L promoter, inserted in Chinese local breeds and predominantly deleted in Western commercial breeds. Luciferase reporter assay suggested this InDel modulated RPS27L expression by influencing transcription factor 3 (TCF3) and myogenic differentiation antigen (MYOD) binding to promoter. Furthermore, a positive correlation was observed between the expression of RPS27L expression and backfat thickness. Association studies demonstrated this InDel was significantly associated with the body weight of pigs at the age of 240 days. Together, our results suggested that RPS27L was a regulator of skeletal muscle development and growth, and was a candidate marker for improving meat production traits in pigs. This study not only provided a biomarker for animal breeding, but also was helpful for understanding skeletal muscle development and muscle-related disease in humans.

Understanding the genetic changes behind the phenotypic variation of Chinese donkeys is helpful to the genetic improvement and breeding of donkeys. However, the population structure and novel genes associated with morphological (coat color and body size) and adaptive (high-altitude adaptation) traits of Chinese donkeys remain largely unknown. Here, we analyzed 391 whole-genome sequencing (WGS) data of Chinese donkeys. Population genomic analyses showed that Chinese native donkey breeds mainly consist of three distinct populations (Southwest plateau, North plain, and Guanzhong plain), and a newly discovered population (Guanzhong plain) was identified. Moreover, we characterized a high-confidence list of 127, 117, and 169 selective signal genes for coat color, body size, and high-altitude adaptation, respectively. We discovered ARID3B gene with strong signals of selection, which may account for coat color in Chinese donkeys. Our study identified EPAS1 as a high-altitude adaptive gene. However, the FAM184B gene shows a stronger signal in response to high-altitude environments in Chinese donkeys. The selective sweep and GWAS analysis showed that LCORL and TMEM154 genes are potentially associated with body size in Chinese donkeys. Utilizing PacBio HiFi sequencing data, this study presents 15,954 highly reliable structural variations (SVs) between large-sized and small-sized donkeys. Utilizing SV data and a graph-based method, we identified an 880-bp deletion in the TMEM154 gene in Sichuan donkeys (small-sized) compared to Guanzhong donkeys (large-sized), which was verified by PCR and is a candidate SV related to body size. Transcriptome sequencing data showed that the TMEM154 gene is highly expressed in the muscle of Guanzhong donkeys (large-sized) compared to Sichuan donkeys (small-sized). Multi-species alignment analysis revealed that the region surrounding the 880-bp deletion in the TMEM154 gene region is conserved in horse, zebra, kiang, as well as two large-sized donkey breeds (Dezhou and Guanzhong), except in in the small-sized Sichuan donkey. Furthermore, after the 880 bp deletion was transfected into 3T3-L1 and HEK293T cells, it was demonstrated that the relative luciferase activity of the mutation was markedly decreased in comparison with that of the wild type. These results suggest that this 880-bp deletion in the TMEM154 gene may play an important role in body size trait of donkey. This study provides valuable genome resources for donkey breeding and sheds light on the domestication history of Chinese donkeys.