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The basic helix-loop-helix transcription factors play important roles in diverse cellular and molecular processes. Comparative functional genomics can provide powerful approaches to draw inferences about gene function and evolution among species. The comprehensive comparison of bHLH gene family in different gramineous plants has not yet been reported. In this study, a total of 183, 231 and 571 bHLHs were identified in rice, maize and wheat genomes respectively, and 1154 bHLH genes from the three species and Arabidopsis were classified into 36 subfamilies. Of the identified genes, 110 OsbHLHs, 188 ZmbHLHs and 209 TabHLHs with relatively high mRNA abundances were detected in one or more tissues during development, and some of them exhibited tissue-specific expression such as TabHLH454–459, ZmbHLH099–101 and OsbHLH037 in root, TabHLH559–562, − 046, − 047 and ZmbHLH010, − 072, − 226 in leaf, TabHLH216–221, − 333, − 335, − 340 and OsbHLH005, − 141 in inflorescence, TabHLH081, ZmbHLH139 and OsbHLH144 in seed. Forty five, twenty nine and thirty one differentially expressed bHLHs were respectively detected in wheat, maize and rice under drought stresses using RNA-seq technology. Among them, the expressions of TabHLH046, − 047, ZmbHLH097, − 098, OsbHLH006 and − 185 were strongly induced, whereas TabHLH303, − 562, ZmbHLH155, − 154, OsbHLH152 and − 113 showed significant down-regulation. Twenty two TabHLHs were induced after stripe rust infection at 24 h and nine of them were suppressed at 72 hpi, whereas 28 and 6 TabHLHs exhibited obviously down- and up-regulation after powdery mildew attack respectively. Forty one ZmbHLHs were differentially expressed in response to F. verticillioides infection. Twenty two co-expression modules were identified by the WGCNA, some of which were associated with particular tissue types. And GO enrichment analysis for the modules showed that some TabHLHs were involved in the control of several biological processes, such as tapetal PCD, lipid metabolism, iron absorption, stress responses and signal regulation. The present study identifies the bHLH family in rice, maize and wheat genomes, and detailedly discusses the evolutionary relationships, expression and function of bHLHs. This study provides some novel and detail information about bHLHs, and may facilitate understanding the molecular basis of the plant growth, development and stress physiology.

Anthocyanin, các sắc tố có màu sắc, đã được sử dụng từ lâu như nguyên liệu trong thực phẩm và dược phẩm nhờ vào những lợi ích sức khỏe tiềm năng của chúng, nhưng các tín hiệu trung gian mà qua đó các yếu tố môi trường hoặc phát triển điều chỉnh quá trình sinh tổng hợp anthocyanin vẫn chưa được hiểu rõ. Các loại quả thịt đã trở thành hệ thống tốt để nghiên cứu về việc điều chỉnh sinh tổng hợp anthocyanin, và việc khám phá cơ chế của sự chuyển hóa sắc tố rất có giá trị trong việc kiểm soát độ chín của trái cây. Nghiên cứu hiện tại cho thấy rằng ABA tích tụ trong quá trình chín quả Lycium, và sự tích tụ này có mối tương quan tích cực với hàm lượng anthocyanin và mức độ bản sao LbNCED1. Việc áp dụng ABA ngoại sinh và chất ức chế sinh tổng hợp ABA fluridon đã làm tăng và giảm hàm lượng anthocyanin trong quả Lycium, tương ứng. Đây là báo cáo đầu tiên cho thấy rằng ABA thúc đẩy sự tích tụ của anthocyanin trong quả Lycium. Sự biến đổi trong hàm lượng anthocyanin nhất quán với sự biến đổi trong biểu hiện của các gen mã hóa phức hợp yếu tố phiên mã MYB-bHLH-WD40 hoặc các enzyme liên quan đến sinh tổng hợp anthocyanin. Việc làm tĩnh lặng gen LbNCED1 do virus gây ra đã làm chậm đáng kể quá trình thay đổi màu sắc của trái cây và giảm cả sự tích tụ anthocyanin và ABA trong quá trình chín của quả Lycium. Phân tích qRT-PCR cho thấy rằng việc làm tĩnh lặng gen LbNCED1 đã rõ ràng làm giảm mức độ bản sao của cả các gen cấu trúc và điều hòa trong con đường sinh tổng hợp flavonoid. Dựa trên các kết quả, một mô hình sinh tổng hợp anthocyanin phụ thuộc vào phát triển trung gian bởi ABA và màu sắc của trái cây trong quá trình chín của quả Lycium đã được đề xuất. Trong mô hình này, các tín hiệu phát triển kích hoạt phiên mã LbNCED1 và do đó làm tăng sự tích tụ của phytohormone ABA, và ABA tích tụ kích thích phiên mã của phức hợp yếu tố phiên mã MYB-bHLH-WD40 nhằm tăng cường biểu hiện của các gen cấu trúc trong con đường sinh tổng hợp flavonoid và từ đó thúc đẩy sản xuất anthocyanin và màu sắc của trái cây. Kết quả của chúng tôi cung cấp một chiến lược quý giá có thể được sử dụng trong thực tiễn để điều chỉnh sự chín và chất lượng của trái cây tươi trong các loại cây thuốc và thực phẩm bằng cách điều chỉnh phytohormone ABA.

Cotton fibers (produced by Gossypium species) are the premier natural fibers for textile production. The two tetraploid species, G. barbadense (Gb) and G. hirsutum (Gh), differ significantly in their fiber properties, the former having much longer, finer and stronger fibers that are highly prized. A better understanding of the genetics and underlying biological causes of these differences will aid further improvement of cotton quality through breeding and biotechnology. We evaluated an inter-specific Gh × Gb recombinant inbred line (RIL) population for fiber characteristics in 11 independent experiments under field and glasshouse conditions. Sites were located on 4 continents and 5 countries and some locations were analyzed over multiple years. The RIL population displayed a large variability for all major fiber traits. QTL analyses were performed on a per-site basis by composite interval mapping. Among the 651 putative QTLs (LOD > 2), 167 had a LOD exceeding permutation based thresholds. Coincidence in QTL location across data sets was assessed for the fiber trait categories strength, elongation, length, length uniformity, fineness/maturity, and color. A meta-analysis of more than a thousand putative QTLs was conducted with MetaQTL software to integrate QTL data from the RIL and 3 backcross populations (from the same parents) and to compare them with the literature. Although the global level of congruence across experiments and populations was generally moderate, the QTL clustering was possible for 30 trait x chromosome combinations (5 traits in 19 different chromosomes) where an effective co-localization of unidirectional (similar sign of additivity) QTLs from at least 5 different data sets was observed. Most consistent meta-clusters were identified for fiber color on chromosomes c6, c8 and c25, fineness on c15, and fiber length on c3. Meta-analysis provided a reliable means of integrating phenotypic and genetic mapping data across multiple populations and environments for complex fiber traits. The consistent chromosomal regions contributing to fiber quality traits constitute good candidates for the further dissection of the genetic and genomic factors underlying important fiber characteristics, and for marker-assisted selection.

Nitro (N) là một nguyên tố dinh dưỡng chính cho sự phát triển của cây trồng. Trong cây, các thành viên của gia đình gen vận chuyển peptide (PTR) có thể liên quan đến việc hấp thụ và vận chuyển nitrat. Ở đây, chúng tôi đã xác định bộ gen PTR trong lúa và phân tích biểu hiện của chúng ở các dòng gần đồng sinh. Chúng tôi đã xác định được 96, 85 và 78 gen PTR trong Nipponbare, R498 và Oryza glaberrima, và cây phát sinh loài (phylogenetic trees) tương tự nhau ở lúa trồng châu Á và lúa trồng châu Phi. Số lượng gen PTR cao hơn ở cây lạc (125) và đậu nành (127). Có 521 gen PTR trong lúa, ngô, sorgum, lạc, đậu nành và Arabidopsis có thể được phân loại thành 4 nhóm, và sự phân bố của chúng khác nhau giữa thực vật một lá mầm và hai lá mầm. Trong bộ gen Nipponbare, 25 gen PTR được phân bố ở 5 vùng sao chép phân đoạn lớn trên nhiễm sắc thể 1, 2, 3, 4, 5, 7, 8, 9 và 10. Các gen PTR trong lúa có từ 0–11 intron và 1–12 exon, và 16 trong số đó có miền NPF (gia đình NRT1/PTR). Kết quả RNA-seq cho thấy số lượng gen biểu hiện khác biệt (DEGs) giữa NIL15 và NIL19 ở ba giai đoạn lần lượt là 928, 1467 và 1586. Trong điều kiện N thấp, số lượng gen PTR biểu hiện khác biệt tăng lên đáng kể. Dữ liệu RNA-seq được phân tích bằng WGCNA để dự đoán khả năng tương tác giữa các gen. Chúng tôi đã phân loại các gen có mô hình biểu hiện tương tự thành một mô-đun, và thu được 25 mô-đun mục tiêu. Trong số các mô-đun này, ba mô-đun có thể tham gia vào việc hấp thụ và sử dụng N ở lúa, đặc biệt là mô-đun nâu, trong đó các gen trung tâm được chú thích là protein kinase có thể điều chỉnh quá trình chuyển hóa N ở lúa. Trong nghiên cứu này, chúng tôi đã phân tích toàn diện bộ gen PTR trong lúa. 96 gen PTR đã được xác định trong bộ gen Nipponbare và 25 trong số đó được định vị trên năm vùng sao chép phân đoạn lớn. Tỉ lệ Ka/Ks cho thấy nhiều gen PTR đã trải qua sự chọn lọc tích cực. Kết quả RNA-seq cho thấy nhiều gen PTR tham gia vào hiệu quả sử dụng nitrogen (NUE) của lúa, và các protein kinase có thể đóng vai trò quan trọng trong quá trình này. Những kết quả này cung cấp cơ sở nền tảng để cải thiện hiệu quả sử dụng N của lúa thông qua giống cây trồng phân tử.

Greater yam (Dioscorea alata L.) is a major tropical and subtropical staple crop cultivated for its starchy tubers. Breeding of this dioecious species is hampered by its erratic flowering, yet little is currently known on the genetic determinism of its sexual reproduction. Here we used a genome-wide association approach and identified a major genetic barrier to reproduction in yam on chromosome 1, as represented by two candidate genes. A deleterious effect on male fitness could be hypothesized considering the involvement of these two genes in male reproduction and the low frequency of this non-flowering dominant allele within the male genepool. We also extended the hypothesis of a XX/XY sex-determination system located on chromosome 6 in D. alata to encompass most of the species diversity. Moreover, a kompetitive allele-specific PCR (KASPar) marker was designed and validated that enables accurate cultivar sex estimation. The reconstruction of chromosome 6 associated with the detection of highly putative structural variations confirmed the possible involvement of a major part of the chromosome. The findings of this study, combined with proper estimation of accession ploidy levels to avoid endosperm incompatibility issues, could facilitate the design of future promising parental combinations in D. alata breeding programs. Moreover, the discovery of this genetic barrier to reproduction opens new avenues for gaining insight into yam reproductive biology and diversification.

Members of plant WRKY transcription factor families are widely implicated in defense responses and various other physiological processes. For canola (Brassica napus L.), no WRKY genes have been described in detail. Because of the economic importance of this crop, and its evolutionary relationship to Arabidopsis thaliana, we sought to characterize a subset of canola WRKY genes in the context of pathogen and hormone responses.

In this study, we identified 46 WRKY genes from canola by mining the expressed sequence tag (EST) database and cloned cDNA sequences of 38 BnWRKYs. A phylogenetic tree was constructed using the conserved WRKY domain amino acid sequences, which demonstrated that BnWRKYs can be divided into three major groups. We further compared BnWRKYs to the 72 WRKY genes from Arabidopsis and 91 WRKY from rice, and we identified 46 presumptive orthologs of AtWRKY genes. We examined the subcellular localization of four BnWRKY proteins using green fluorescent protein (GFP) and we observed the fluorescent green signals in the nucleus only.

The responses of 16 selected BnWRKY genes to two fungal pathogens, Sclerotinia sclerotiorum and Alternaria brassicae, were analyzed by quantitative real time-PCR (qRT-PCR). Transcript abundance of 13 BnWRKY genes changed significantly following pathogen challenge: transcripts of 10 WRKYs increased in abundance, two WRKY transcripts decreased after infection, and one decreased at 12 h post-infection but increased later on (72 h). We also observed that transcript abundance of 13/16 BnWRKY genes was responsive to one or more hormones, including abscisic acid (ABA), and cytokinin (6-benzylaminopurine, BAP) and the defense signaling molecules jasmonic acid (JA), salicylic acid (SA), and ethylene (ET). We compared these transcript expression patterns to those previously described for presumptive orthologs of these genes in Arabidopsis and rice, and observed both similarities and differences in expression patterns.

We identified a set of 13 BnWRKY genes from among 16 BnWRKY genes assayed, that are responsive to both fungal pathogens and hormone treatments, suggesting shared signaling mechanisms for these responses. This study suggests that a large number of BnWRKY proteins are involved in the transcriptional regulation of defense-related genes in response to fungal pathogens and hormone stimuli.

Biotic and abiotic stresses are the major cause of reduced growth, persistence, and yield in agriculture. Over the past decade, RNA-Sequencing and the use of transgenics with altered expression of stress related genes have been utilized to gain a better understanding of the molecular mechanisms leading to salt tolerance in a variety of species. Identification of transcription factors that, when overexpressed in plants, improve multiple stress tolerance may be valuable for crop improvement, but sometimes overexpression leads to deleterious effects during normal plant growth. Brachypodium constitutively expressing the BdbZIP26:GFP gene showed reduced stature compared to wild type plants (WT). RNA-Seq analysis comparing WT and bZIP26 transgenic plants revealed 7772 differentially expressed genes (DEGs). Of these DEGs, 987 of the DEGs were differentially expressed in all three transgenic lines. Many of these DEGs are similar to those often observed in response to abiotic and biotic stress, including signaling proteins such as kinases/phosphatases, calcium/calmodulin related proteins, oxidases/reductases, hormone production and signaling, transcription factors, as well as disease responsive proteins. Interestingly, there were many DEGs associated with protein turnover including ubiquitin-related proteins, F-Box and U-box related proteins, membrane proteins, and ribosomal synthesis proteins. Transgenic and control plants were exposed to salinity stress. Many of the DEGs between the WT and transgenic lines under control conditions were also found to be differentially expressed in WT in response to salinity stress. This suggests that the over-expression of the transcription factor is placing the plant in a state of stress, which may contribute to the plants diminished stature. The constitutive expression of BdbZIP26:GFP had an overall negative effect on plant growth and resulted in stunted plants compared to WT plants under control conditions, and a similar response to WT plants under salt stress conditions. The results of gene expression analysis suggest that the transgenic plants are in a constant state of stress, and that they are trying to allocate resources to survive.

Proanthocyanidins (PAs), or condensed tannins, are flavonoid polymers, widespread throughout the plant kingdom, which provide protection against herbivores while conferring organoleptic and nutritive values to plant-derived foods, such as wine. However, the genetic basis of qualitative and quantitative PA composition variation is still poorly understood. To elucidate the genetic architecture of the complex grape PA composition, we first carried out quantitative trait locus (QTL) analysis on a 191-individual pseudo-F1 progeny. Three categories of PA variables were assessed: total content, percentages of constitutive subunits and composite ratio variables. For nine functional candidate genes, among which eight co-located with QTLs, we performed association analyses using a diversity panel of 141 grapevine cultivars in order to identify causal SNPs. Multiple QTL analysis revealed a total of 103 and 43 QTLs, respectively for seed and skin PA variables. Loci were mainly of additive effect while some loci were primarily of dominant effect. Results also showed a large involvement of pairwise epistatic interactions in shaping PA composition. QTLs for PA variables in skin and seeds differed in number, position, involvement of epistatic interaction and allelic effect, thus revealing different genetic determinisms for grape PA composition in seeds and skin. Association results were consistent with QTL analyses in most cases: four out of nine tested candidate genes (VvLAR1, VvMYBPA2, VvCHI1, VvMYBPA1) showed at least one significant association with PA variables, especially VvLAR1 revealed as of great interest for further functional investigation. Some SNP-phenotype associations were observed only in the diversity panel. This study presents the first QTL analysis on grape berry PA composition with a comparison between skin and seeds, together with an association study. Our results suggest a complex genetic control for PA traits and different genetic architectures for grape PA composition between berry skin and seeds. This work also uncovers novel genomic regions for further investigation in order to increase our knowledge of the genetic basis of PA composition.

Heading and aftermath heading are important traits in perennial ryegrass because they impact forage quality. So far, genome-wide association analyses in this major forage species have only identified a small number of genetic variants associated with heading date that overall explained little of the variation. Some possible reasons include rare alleles with large phenotypic affects, allelic heterogeneity, or insufficient marker density. We established a genome-wide association panel with multiple genotypes from multiple full-sib families. This ensured alleles were present at the frequency needed to have sufficient statistical power to identify associations. We genotyped the panel via partial genome sequencing and performed genome-wide association analyses with multi-year phenotype data collected for heading date, and aftermath heading. Genome wide association using a mixed linear model failed to identify any variants significantly associated with heading date or aftermath heading. Our failure to identify associations for these traits is likely due to the extremely low linkage disequilibrium we observed in this population. However, using single marker analysis within each full-sib family we could identify markers and genomic regions associated with heading and aftermath heading. Using the ryegrass genome we identified putative orthologs of key heading genes, some of which were located in regions of marker-trait associations. Given the very low levels of LD, genome wide association studies in perennial ryegrass populations are going to require very high SNP densities. Single marker analysis within full-sibs enabled us to identify significant marker-trait associations. One of these markers anchored proximal to a putative ortholog of TFL1, homologues of which have been shown to play a key role in continuous heading of some members of the rose family, Rosaceae.