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Background Akebia trifoliata (Thunb.) Koidz may have applications as a new potential source of biofuels owing to its high seed count, seed oil content, and in-field yields. However, the pericarp of A. trifoliata cracks longitudinally during fruit ripening, which increases the incidence of pests and diseases and can lead to fruit decay and deterioration, resulting in significant losses in yield. Few studies have evaluated the mechanisms underlying A. trifoliata fruit cracking. Results In this study, by observing the cell wall structure of the pericarp, we found that the cell wall became thinner and looser and showed substantial breakdown in the pericarp of cracking fruit compared with that in non-cracking fruit. Moreover, integrative analyses of transcriptome and proteome profiles at different stages of fruit ripening demonstrated changes in the expression of various genes and proteins after cracking. Furthermore, the mRNA levels of 20 differentially expressed genes were analyzed, and parallel reaction monitoring analysis of 20 differentially expressed proteins involved in cell wall metabolism was conducted. Among the molecular targets, pectate lyases and pectinesterase, which are involved in pentose and glucuronate interconversion, and β-galactosidase 2, which is involved in galactose metabolism, were significantly upregulated in cracking fruits than in non-cracking fruits. This suggested that they might play crucial roles in A. trifoliata fruit cracking. Conclusions Our findings provided new insights into potential genes influencing the fruit cracking trait in A. trifoliata and established a basis for further research on the breeding of cracking-resistant varieties to increase seed yields for biorefineries.

Perennial ryegrass ( ) is one of the most widely used forage and turf grasses in the world due to its desirable agronomic qualities. However, as a cool-season perennial grass species, high temperature is a major factor limiting its performance in warmer and transition regions. In this study, a transcriptome was generated using a cDNA library constructed from perennial ryegrass leaves subjected to short-term heat stress treatment. Then the expression profiling and identification of perennial ryegrass heat response genes by digital gene expression analyses was performed. The goal of this work was to produce expression profiles of high temperature stress responsive genes in perennial ryegrass leaves and further identify the potentially important candidate genes with altered levels of transcript, such as those genes involved in transcriptional regulation, antioxidant responses, plant hormones and signal transduction, and cellular metabolism. The assembly of perennial ryegrass transcriptome in this study obtained more total and annotated unigenes compared to previously published ones. Many DEGs identified were genes that are known to respond to heat stress in plants, including HSFs, HSPs, and antioxidant related genes. In the meanwhile, we also identified four gene candidates mainly involved in C carbon fixation, and one TOR gene. Their exact roles in plant heat stress response need to dissect further. This study would be important by providing the gene resources for improving heat stress tolerance in both perennial ryegrass and other cool-season perennial grass plants.

Starch is the primary component of the endosperm and plays a crucial role in rice quality. Although the enzymes involved in starch synthesis have been extensively studied, the transcription factors that regulate these enzymes remain largely unknown. Here, we identified a MYB family transcription factor, OsMYBR1, that regulates starch biosynthesis in rice. OsMYBR1 is highly expressed during endosperm development. Mutations of OsMYBR1 result in reduced grain thickness and a decrease in 1000-grain weight. The endosperm of osmybr1 mutants exhibit rounded and loosely packed starch granules, decreased amylose content, altered fine structure of amylopectin, and modified physicochemical properties. The analysis of RT-qPCR showed that the expression of several starch-synthesis enzyme-coding genes (SSEGs), including OsGBSSⅠ, OsAGPL1, OsAGPL2, OsBEⅡb, OsISA1, PHOL, and OsSSⅢa, is altered in osmybr1 mutants. Further experiments indicated that OsMYBR1 directly binds to the promoters of OsGBSSⅠ, OsAGPL1, OsAGPL2, OsISA1, OsBEⅡb, and PHOL, resulting in an increase in the expression of OsGBSSⅠ but a decrease in the expression of OsAGPL2, OsISA1, and OsSSⅢa. In contrast, OsMYBR1-overexpressing endosperm appears normal, with starch granule morphology, increased amylopectin content, and improved alkali spreading value, indicating enhanced rice eating and cooking quality (ECQ). These findings suggest that the overexpression of OsMYBR1 could be a promising strategy for improving rice ECQ.

Ramie (Boehmeria nivea L. Gaudich) is a major natural fiber crop cultivated in East Asia. The improvement of its fiber yield and fineness are important breeding goals. Fiber yield is a complex quantitative trait comprising ramet number, stem diameter, plant height, skin thickness, and fiber percentage. The fiber fineness is a crucial trait for ramie fiber quality. However, there are few association studies for fiber yield traits and fiber fineness on ramie, and lack high-density SNP maps in natural ramie population. Here, a panel of 112 core ramie germplasms were genotyped by 215,376 consistent single-nucleotide polymorphisms (SNPs) from specific-locus amplified-fragment sequencing (SLAF-seq), and used for genome-wide association study of fiber fineness and yield. Subsequently, the genetic diversity, linkage disequilibrium (LD), and population structure was conducted based on 215,376 SNPs. Population cluster analysis disclosed five subpopulations. Neighbor-joining (NJ) analysis revealed three major clusters. No obvious relationships were identified between them and their geographic origins. The genome-wide LD decayed to r2 = 0.1 was ~ 11.75 kbp in physical distance. One, seven, one, seven, and twenty-seven significant SNP marker associations were detected for fiber fineness (third season), stem diameter (third season), stem skin thickness (third season), fiber percentage (second season), and fiber percentage (third season), respectively. Two promising candidate genes, whole_GLEAN_10029622 and whole_GLEAN_10029638 resided in the significant trait-SNP association for fiber fineness (third season), which annotated as a cotton fiber-expressed protein and an Arabidopsis thaliana homebox protein ATH1, respectively and validated by qPCR. The identified loci or genes for fiber fineness and yield may provide the basis for future research on fiber fineness and yield and marker-assisted selection breeding for ramie.

Background Ramie ( Boehmeria nivea L.) is one of the most important natural fiber crops and an important forage grass in south China. Ramet number, which is a quantitative trait controlled by multigenes, is one of the most important agronomic traits in plants because the ramet number per plant is a key component of grain yield and biomass. However, the genetic variation and genetic architecture of ramie ramet number are rarely known. Results A genome-wide association study was performed using a panel of 112 core germplasms and 108,888 single nucleotide polymorphisms (SNPs) detected using specific-locus amplified fragment sequencing technology. Trait-SNP association analysis detected 44 significant SNPs that were associated with ramet number at P  < 0.01. The favorable SNP Marker20170–64 emerged at least twice in the three detected stages and was validated to be associated with the ramie ramet number using genomic DNA polymerase chain reaction with an F 1 hybrid progeny population. Comparative genome analysis predicted nine candidate genes for ramet number based on Marker20170–64. Real-time quantitative polymerase chain reaction analysis indicated that six of the genes were specific to upregulation in the ramie variety with high ramet number. These results suggest that these genes could be considered as ramet number-associated candidates in ramie. Conclusions The identified loci or genes may be promising targets for genetic engineering and selection for modulating the ramet number in ramie. Our work improves understanding of the genetics of ramet number in ramie core germplasms and provides tools for marker-assisted selection for improvement of agricultural traits.

Seed plumules comprise multiple developing tissues and are key sites for above-ground plant organ morphogenesis. Here, the spatial expression of genes in developing rice seed plumules was characterized by single-cell transcriptome sequencing in Zhongjiazao 17, a popular Chinese indica rice cultivar. Of 15 cell clusters, 13 were assigned to cell types using marker genes and cluster-specific genes. Marker genes of multiple cell types were expressed in several clusters, suggesting a complex developmental system. Some genes for signaling by phytohormones such as abscisic acid were highly expressed in specific clusters. Various cis-elements in the promoters of genes specifically expressed in cell clusters were calculated, and some key hormone-related motifs were frequent in certain clusters. Spatial expression patterns of genes involved in rapid seed germination, seedling growth, and development were identified. These findings enhanced our understanding of cellular diversity and specialization within plumules of rice, a monocotyledonous model crop.

Summary Rice (Oryza sativa L.) is one of the most important food crops. Starch is the main substance of rice endosperm and largely determines the grain quality and yield. Starch biosynthesis in endosperm is very complex, requiring a series of enzymes which are also regulated by many transcription factors (TFs). But until now, the large‐scale regulatory network for rice endosperm starch biosynthesis has not been established. Here, we constructed a rice endosperm starch biosynthesis regulatory network comprised of 277 TFs and 15 starch synthesis enzyme‐encoding genes (SSEGs) using DNA affinity chromatography/pull‐down combined with liquid chromatography‐mass spectrometry (DNA pull‐down and LC–MS). In this regulatory network, each SSEG is directly regulated by 7–46 TFs. Based on this network, we found a new pathway ‘ABA‐OsABI5‐OsERF44‐SSEGs’ that regulates rice endosperm starch biosynthesis. We also knocked out five TFs targeting the key amylose synthesis enzyme gene OsGBSSI in japonica rice ‘Nipponbare’ background and found that all mutants had moderately decreased amylose content (AC) in endosperm and improved eating and cooking quality (ECQ). Notably, the knockout of OsSPL7 and OsB3 improves the ECQ without compromising the rice appearance quality, which was further validated in the indica rice ‘Zhongjiazao17’ background. In summary, this gene regulatory network for rice endosperm starch biosynthesis established here will provide important theoretical and practical guidance for the genetic improvement of rice quality.

Ramie is one of the most ancient cellulose fiber crops, having been used for at least 6000 years. It is also one of the strongest and longest natural fine textile fibers in the world and is principally used for fabric production. Although ramie is very important and has a high economic value, the genetic basis of its yield-related and fiber quality traits remains poorly understood and is insufficient owing to the lack of assessment in multiple environments. Here, we evaluated the population structure and genomic variation in ramie based on resequencing of 319 core accessions and detected several candidate genes associated with fiber yield and quality traits by combining them with linkage mapping. We obtained approximately 3.49 million high-quality single nucleotide polymorphisms (SNPs), 2,089,798 insertions and deletions (Indels), and 88,087 structure variations (SVs). The investigation of phenotypes for plant height (PL), stem diameter (SD), bark thickness (BT), fiber diameter (FD), fiber fineness (FF), and ramet number (RN) found these traits showed abundant variation and correlation. Several genetic loci and candidate genes were identified associated with three yield-related traits and fiber fineness. A gene within pleiotropic loci encoding NAC domain containing protein (BnNAC29) was found to be significantly correlated with stem diameter and bark thickness. Another variation of large fragment insertions and deletions in two candidate genes, BnVIT1 and BnAEP, may also be responsible for the increase of stem diameter and bark thickness, respectively. Favorable gene haplotypes were identified as having the same tendency in stem diameter and bark thickness. Moreover, we presumed that plant height-related genes had undergone selection from landraces to breeding cultivars, even though there was minor differentiation during domestication. Our study provides new insights into the genetic architecture of yield and fiber quality traits in ramie. Moreover, the identification of fiber yield-related genetic loci and large-scale genomic variation represent valuable resources for genomics-assisted breeding of this fiber crop.

Ramie (Boehmeria nivea L.) is one of the most important natural fiber crops and an important forage grass in south China. Ramet number, which is a quantitative trait controlled by multigenes, is one of the most important agronomic traits in plants because the ramet number per plant is a key component of grain yield and biomass. However, the genetic variation and genetic architecture of ramie ramet number are rarely known. A genome-wide association study was performed using a panel of 112 core germplasms and 108,888 single nucleotide polymorphisms (SNPs) detected using specific-locus amplified fragment sequencing technology. Trait-SNP association analysis detected 44 significant SNPs that were associated with ramet number at P < 0.01. The favorable SNP Marker20170-64 emerged at least twice in the three detected stages and was validated to be associated with the ramie ramet number using genomic DNA polymerase chain reaction with an F.sub.1 hybrid progeny population. Comparative genome analysis predicted nine candidate genes for ramet number based on Marker20170-64. Real-time quantitative polymerase chain reaction analysis indicated that six of the genes were specific to upregulation in the ramie variety with high ramet number. These results suggest that these genes could be considered as ramet number-associated candidates in ramie. The identified loci or genes may be promising targets for genetic engineering and selection for modulating the ramet number in ramie. Our work improves understanding of the genetics of ramet number in ramie core germplasms and provides tools for marker-assisted selection for improvement of agricultural traits.

Ramie (Boehmeria nivea L.) is one of the most important natural fiber crops and an important forage grass in south China. Ramet number, which is a quantitative trait controlled by multigenes, is one of the most important agronomic traits in plants because the ramet number per plant is a key component of grain yield and biomass. However, the genetic variation and genetic architecture of ramie ramet number are rarely known. A genome-wide association study was performed using a panel of 112 core germplasms and 108,888 single nucleotide polymorphisms (SNPs) detected using specific-locus amplified fragment sequencing technology. Trait-SNP association analysis detected 44 significant SNPs that were associated with ramet number at P < 0.01. The favorable SNP Marker20170-64 emerged at least twice in the three detected stages and was validated to be associated with the ramie ramet number using genomic DNA polymerase chain reaction with an F.sub.1 hybrid progeny population. Comparative genome analysis predicted nine candidate genes for ramet number based on Marker20170-64. Real-time quantitative polymerase chain reaction analysis indicated that six of the genes were specific to upregulation in the ramie variety with high ramet number. These results suggest that these genes could be considered as ramet number-associated candidates in ramie. The identified loci or genes may be promising targets for genetic engineering and selection for modulating the ramet number in ramie. Our work improves understanding of the genetics of ramet number in ramie core germplasms and provides tools for marker-assisted selection for improvement of agricultural traits.