Molecular basis of plant architecture

Rice domestication-associated transcription factor PROSTRATE GROWTH 1 controls plant and panicle architecture by regulating the expression of LAZY 1 and OsGIGANTEA, respectively

Plant architecture and panicle architecture are two critical agronomic traits that greatly affect the yield of rice (Oryza sativa). PROSTRATE GROWTH 1 (PROG1) encodes a key C2H2-type zinc-finger transcription factor and has pleiotropic effects on the regulation of both plant and panicle architecture, thereby influencing the grain yield. However, the molecular mechanisms through which PROG1 controls plant and panicle architecture remain unclear. In this study, we showed that PROG1 directly binds the LAZY 1 (LA1) promoter and acts as a repressor to inhibit LA1 expression. Conversely, LA1 acts as a repressor of PROG1 by directly binding to the PROG1 promoter. These two genes play antagonistic roles in shaping plant architecture by regulating both tiller angle and tiller number. Interestingly, our data showed that PROG1 controls panicle architecture through direct binding to the intragenic regulatory regions of OsGIGANTEA (OsGI) and subsequent activation of its expression. Collectively, we have identified two crucial targets of PROG1, LA1 and OsGI, shedding light on the molecular mechanisms underlying plant and panicle architecture control by PROG1. Our study provides valuable insights into the regulation of key domestication-related traits in rice and identifies potential targets for future high-yield rice breeding.

GmGAMYB-BINDING PROTEIN 1 promotes small auxin-up RNA gene transcription to modulate soybean maturity and height

Flowering time, maturity, and plant height are crucial agronomic traits controlled by photoperiod that affect soybean (Glycine max [L.] Merr.) yield and regional adaptability. It is important to cultivate soybean cultivars of earlier maturity that adapt to high latitudes. GAMYB-binding protein 1 (GmGBP1), a member of the SNW/SKIP family of transcriptional coregulators in soybean, is induced by short days and interacts with transcription factor GAMYB (GmGAMYB) during photoperiod control of flowering time and maturity. In the present study, GmGBP1:GmGBP1 soybean showed the phenotypes of earlier maturity and higher plant height. Chromatin immunoprecipitation sequencing (ChIP-seq) assays of GmGBP1-binding sites and RNA sequencing (RNA-seq) of differentially expressed transcripts in GmGBP1:GmGBP1 further identified potential targets of GmGBP1, including small auxin-up RNA (GmSAUR). GmSAUR:GmSAUR soybean also showed earlier maturity and higher plant height. GmGBP1 interacted with GmGAMYB, bound to the promoter of GmSAUR and promoted the expression of FLOWER LOCUS T homologs 2a (GmFT2a) and FLOWERING LOCUS D LIKE 19 (GmFDL19). Flowering repressors such as GmFT4 were negatively regulated, resulting in earlier flowering and maturity. Furthermore, the interaction of GmGBP1 with GmGAMYB increased the gibberellin (GA) signal to promote height and hypocotyl elongation by activating GmSAUR and GmSAUR bound to the promoter of the GA-positive activating regulator gibberellic acid-stimulated Arabidopsis 32 (GmGASA32). These results suggested a photoperiod regulatory pathway in which the interaction of GmGBP1 with GmGAMYB directly activated GmSAUR to promote earlier maturity and plant height in soybean.

Selection and Molecular Characterization of Promising Plum Rootstocks (Prunus cerasifera L.) among Seedling-Origin Trees

The plum (Prunus cerasifera Ehrh) has been used worldwide both as a genetic source for breeding new rootstocks and as clonal rootstock for many Prunus species. Considering situations where wild relatives of plums are endangered, in-depth characterization of rootstock traits of genetic diversity of plum germplasm of Turkey with many ecogeographical locations is crucial. In the present study, therefore, three steps were followed for the selection of rootstock candidates among the plum germplasm grown in the Middle Euphrates. This region is characterized by an extremely hot climate with extremely warm summers and very low precipitation in summers. Initially, 79 rootstock candidates were selected based on rootstocks traits, and Myrobalan 29C was also used for the control rootstock in all steps. Hardwood cuttings were taken from each rootstock candidate, and after the rooting process in rootstock candidates, 39 rootstock candidates outperforming other candidates were selected according to root characteristics. Based on rooting ability, forty rootstock candidates with the longest root length below 33.50 mm, root number below 3.00, and rooting cutting number below 30.00% were eliminated. The second step of the study focused on the dwarfing characteristics of 39 rootstock candidates, and 13 and Myrobalan 29C out of 39 rootstock candidates' dwarfing traits showed value higher compared to the other 26 rootstock candidates. Results indicated that the vigor of rootstock candidates was usually found to be strong (26), intermediate (4), and weak (9). Moreover, 13 out of 39 rootstock candidates' dwarfism trait was better than the other 26 rootstock candidates. In Step 3, some morphological, physiological, and molecular evaluations were conducted in 13 rootstock candidates and the Myrobalan 29C clone, and there were significant differences between both rootstock candidates and the parameters evaluated. PCA has also been indicated that the reference rootstock Myrobalan 29C was grouped with 63B62, 63B69, and 63B14. The highest genetic similarity was found between 63B11 and 63B16, as well as between 63B76 and 63B66, while the lowest genetic similarity was observed between 63B72 and 63B61 candidates. Overall, the findings presented here provide valuable information about the level of rootstock candidates that could potentially be superior among previously uncharacterized plum cultivars in this plum-growing region of Turkey.

Photoperiod and gravistimulation-associated Tiller Angle Control 1 modulates dynamic changes in rice plant architecture

KEY MESSAGE

TAC1 is involved in photoperiodic and gravitropic responses to modulate rice dynamic plant architecture likely by affecting endogenous auxin distribution, which could explain TAC1 widespread distribution in indica rice. Plants experience a changing environment throughout their growth, which requires dynamic adjustments of plant architecture in response to these environmental cues. Our previous study demonstrated that Tiller Angle Control 1 (TAC1) modulates dynamic changes in plant architecture in rice; however, the underlying regulatory mechanisms remain largely unknown. In this study, we show that TAC1 regulates plant architecture in an expression dose-dependent manner, is highly expressed in stems, and exhibits dynamic expression in tiller bases during the growth period. Photoperiodic treatments revealed that TAC1 expression shows circadian rhythm and is more abundant during the dark period than during the light period and under short-day conditions than under long-day conditions. Therefore, it contributes to dynamic plant architecture under long-day conditions and loose plant architecture under short-day conditions. Gravity treatments showed that TAC1 is induced by gravistimulation and negatively regulates shoot gravitropism, likely by affecting auxin distribution. Notably, the tested indica rice containing TAC1 displayed dynamic plant architecture under natural long-day conditions, likely explaining the widespread distribution of TAC1 in indica rice. Our results provide new insights into TAC1-mediated regulatory mechanisms for dynamic changes in rice plant architecture.

Fine mapping of BnDM1-the gene regulating indeterminate inflorescence in Brassica napus

KEY MESSAGE

A candidate gene Bndm1 related to determinate inflorescence was mapped to a 128-kb interval on C02 in Brassica napus. Brassica napus plants with determinate inflorescence exhibit improved traits in field production, such as lower plant height, improved lodging resistance, and consistent maturity. Compared to plants with indeterminate inflorescence, such features are favorable for mechanized harvesting techniques. Here, using a natural mutant 6138 with determinate inflorescence, it is demonstrated that determinate inflorescence reduces plant height significantly without affecting thousand-grain weight and yield per plant. Determinacy was regulated by a single recessive gene, Bndm1. Using a combination of SNP arrays and map-based cloning, we mapped the locus of determinacy to a 128-kb region on C02. Based on sequence comparisons and the reported functions of candidate genes in this region, we predicted BnaC02.knu (a homolog of KNU in Arabidopsis) as a possible candidate gene of Bndm1 for controlling determinate inflorescence. We found a 623-bp deletion in a region upstream of the KNU promoter in the mutant. This deletion led to the significant overexpression of BnaC02.knu in the mutant compared to that in the ZS11 line. The correlation between this deletion and determinate inflorescence was examined in natural populations. The results indicated that the deletion affected the normal transcription of BnaC02.knu in the plants with determinate inflorescence and played an important role in maintaining flower development. This study presents as a new material for optimizing plant architecture and breeding novel canola varieties suitable for mechanized production. Moreover, our findings provide a theoretical basis for analyzing the molecular mechanisms underlying the formation of determinate inflorescence in B. napus.

LAZY3 interacts with LAZY2 to regulate tiller angle by modulating shoot gravity perception in rice

Starch biosynthesis in gravity-sensing tissues of rice shoot determines the magnitude of rice shoot gravitropism and thus tiller angle. However, the molecular mechanism underlying starch biosynthesis in rice gravity-sensing tissues is still unclear. We characterized a novel tiller angle gene LAZY3 (LA3) in rice through map-based cloning. Biochemical, molecular and genetic studies further demonstrated the essential roles of LA3 in gravity perception of rice shoot and tiller angle control. The shoot gravitropism and lateral auxin transport were defective in la3 mutant upon gravistimulation. We showed that LA3 encodes a chloroplast-localized tryptophan-rich protein associated with starch granules via Tryptophan-rich region (TRR) domain. Moreover, LA3 could interact with the starch biosynthesis regulator LA2, determining starch granule formation in shoot gravity-sensing tissues. LA3 and LA2 negatively regulate tiller angle in the same pathway acting upstream of LA1 to mediate asymmetric distribution of auxin. Our study defined LA3 as an indispensable factor of starch biosynthesis in rice gravity-sensing tissues that greatly broadens current understanding in the molecular mechanisms underlying the starch granule formation in gravity-sensing tissues, and provides new insights into the regulatory mechanism of shoot gravitropism and rice tiller angle.

Comparative Microscopic, Transcriptome and IAA Content Analyses Reveal the Stem Growth Variations in Two Cultivars Ilex verticillata

Ilex verticillata is not only an excellent ornamental tree species for courtyards, but it is also a popular bonsai tree. 'Oosterwijk' and 'Red sprite' are two varieties of Ilex verticillata. The former has a long stem with few branches, while the latter has a short stem. In order to explain the stem growth differences between the two cultivars 'Oosterwijk' and 'Red sprite', determination of the microstructure, transcriptome sequence and IAA content was carried out. The results showed that the xylem thickness, vessel area and vessel number of 'Oosterwijk' were larger than in 'Red sprite'. In addition, our analysis revealed that the differentially expressed genes which were enriched in phenylpropanoid biosynthesis; phenylalanine metabolism and phenylalanine, tyrosine and tryptophan biosynthesis in the black and tan modules of the two varieties. We found that AST, HCT and bHLH 94 may be key genes in the formation of shoot difference. Moreover, we found that the IAA content and auxin-related DEGs GH3.6, GH3, ATRP5, IAA27, SAUR36-like, GH3.6-like and AIP 10A5-like may play important roles in the formation of shoot differences. In summary, these results indicated that stem growth variations of 'Oosterwijk' and 'Red sprite' were associated with DEGs related to phenylpropanoid biosynthesis, phenylalanine metabolism and phenylalanine, tyrosine and tryptophan biosynthesis, as well as auxin content and DEGs related to the auxin signaling pathway.

Genome‑wide identification and characterization of miR396 family members and their target genes GRF in sorghum (Sorghum bicolor (L.) moench)

MicroRNAs (miRNAs) widely participate in plant growth and development. The miR396 family, one of the most conserved miRNA families, remains poorly understood in sorghum. To reveal the evolution and expression pattern of Sbi-miR396 gene family in sorghum, bioinformatics analysis and target gene prediction were performed on the sequences of the Sbi-miR396 gene family members. The results showed that five Sbi-miR396 members, located on chromosomes 4, 6, and 10, were identified at the whole-genome level. The secondary structure analysis showed that the precursor sequences of all five Sbi-miR396 potentially form a stable secondary stem-loop structure, and the mature miRNA sequences were generated on the 5' arm of the precursors. Sequence analysis identified the mature sequences of the five sbi-miR396 genes were high identity, with differences only at the 1st, 9th and 21st bases at the 5' end. Phylogenetic analysis revealed that Sbi-miR396a, Sbi-miR396b, and Sbi-miR396c were clustered into Group I, and Sbi-miR396d and Sbi-miR396e were clustered into Group II, and all five sbi-miR396 genes were closely related to those of maize and foxtail millet. Expression analysis of different tissue found that Sbi-miR396d/e and Sbi-miR396a/b/c were preferentially and barely expressed, respectively, in leaves, flowers, and panicles. Target gene prediction indicates that the growth-regulating factor family members (SbiGRF1/2/3/4/5/6/7/8/10) were target genes of Sbi-miR396d/e. Thus, Sbi-miR396d/e may affect the growth and development of sorghum by targeting SbiGRFs. In addition, expression analysis of different tissues and developmental stages found that all Sbi-miR396 target genes, SbiGRFs, were barely expressed in leaves, root and shoot, but were predominantly expressed in inflorescence and seed development stage, especially SbiGRF1/5/8. Therefore, inhibition the expression of sbi-miR396d/e may increase the expression of SbiGRF1/5/8, thereby affecting floral organ and seed development in sorghum. These findings provide the basis for studying the expression of the Sbi-mir396 family members and the function of their target genes.

Cold-upregulated glycosyltransferase gene 1 (OsCUGT1) plays important roles in rice height and spikelet fertility

Glycosyltransferases (GTs) regulate many physiological processes and stress responses in plants. However, little is known about the function of GT in rice development. In this study, molecular analyses revealed that the expression of a rice GT gene (Cold-Upregulated Glycosyltransferase Gene 1, CUGT1) is developmentally controlled and stress-induced. OsCUGT1 was knocked out by using the clustered regularly interspaced short palindromic repeats (CRISPR) system to obtain the mutant oscugt1, which showed a severe dwarf and sterility phenotype. Further cytological analyses indicated that the dwarfism seen in the oscugt1 mutant might be caused by fewer and smaller cells. Histological pollen analysis suggests that the spikelet sterility in oscugt1 mutants may be caused by abnormal microsporogenesis. Moreover, multiple transgenic plants with knockdown of OsCUGT1 expression through RNA interference were obtained, which also showed obvious defects in plant height and fertility. RNA sequencing revealed that multiple biological processes associated with phenylpropanoid biosynthesis, cytokinin metabolism and pollen development are affected in the oscugt1 mutant. Overall, these results suggest that rice OsCUGT1 plays an essential role in rice development.

BnaC01.BIN2, a GSK3-like kinase, modulates plant height and yield potential in Brassica napus

Using map-based cloning and transgenic transformation, we revealed that glycogen kinase synthase 3-like kinase, BnaC01.BIN2, modulates plant height and yield in rapeseed. The modification of plant height is one of the most important goals in rapeseed breeding. Although several genes that regulate rapeseed plant height have been identified, the genetics mechanisms underlying rapeseed plant height regulation remain poorly understood, and desirable genetic resources for rapeseed ideotype breeding are scarce. Here, we map-based cloned and functionally verified that the rapeseed semi-dominant gene, BnDF4, greatly affects rapeseed plant height. Specifically, BnDF4 encodes brassinosteroid (BR)-insensitive 2, a glycogen synthase kinase 3 primarily expressed in the lower internodes to modulate rapeseed plant height by blocking basal internode-cell elongation. Transcriptome data showed that several cell expansion-related genes involving auxin and BRs pathways were significantly downregulated in the semi-dwarf mutant. Heterozygosity in the BnDF4 allele results in small stature with no marked differences in other agronomic traits. Using BnDF4 in the heterozygous condition, the hybrid displayed strong yield heterosis through optimum intermediate plant height. Our results provide a desirable genetic resource for breeding semi-dwarf rapeseed phenotypes and support an effective strategy for breeding rapeseed hybrid varieties with strong yield heterosis.

The DnaJ domain-containing heat-shock protein NAL11 determines plant architecture by mediating gibberellin homeostasis in rice (Oryza sativa)

Ideal Plant Architecture 1 (IPA1) is a key regulator of plant architecture. However, knowledge of downstream genes applicable for improving rice plant architecture is very limited. We identified the plant architecture regulatory gene NARROW LEAF 11 (NAL11), which encodes a heat-shock protein (HSP) containing a DnaJ domain. A promising rare allele of NAL11 (NAL11^-923del-1552 ) positively selected in Aus cultivars was identified; this allele exhibited increased expression and generated relatively few tillers, thick stems, and large panicles, components of the ideal plant architecture (IPA). NAL11 is involved in regulating the cell cycle and cell proliferation. NAL11 loss-of-function mutants present impaired chloroplast development and gibberellin (GA) defects. Biochemical analyses show that IPA1 directly binds to elements in the missing fragment of the NAL11^-923del-1552 promoter and negatively regulates NAL11 expression. Genetic analyses support the hypothesis that NAL11 acts downstream of IPA1 to regulate IPA by modulating GA homeostasis, and NAL11 may be an essential complement for IPA1. Our work revealed that avoidance of the inhibition of NAL11^-923del-1552 caused by IPA1 represents a positive strategy for rescuing GA defects accompanied by the upregulation of IPA1 in breeding high-yield rice.

Conserved and plant-specific histone acetyltransferase complexes cooperate to regulate gene transcription and plant development

Although a conserved SAGA complex containing the histone acetyltransferase GCN5 is known to mediate histone acetylation and transcriptional activation in eukaryotes, how to maintain different levels of histone acetylation and transcription at the whole-genome level remains to be determined. Here we identify and characterize a plant-specific GCN5-containing complex, which we term PAGA, in Arabidopsis thaliana and Oryza sativa. In Arabidopsis, the PAGA complex consists of two conserved subunits (GCN5 and ADA2A) and four plant-specific subunits (SPC, ING1, SDRL and EAF6). We find that PAGA and SAGA can independently mediate moderate and high levels of histone acetylation, respectively, thereby promoting transcriptional activation. Moreover, PAGA and SAGA can also repress gene transcription via the antagonistic effect between PAGA and SAGA. Unlike SAGA, which regulates multiple biological processes, PAGA is specifically involved in plant height and branch growth by regulating the transcription of hormone biosynthesis and response related genes. These results reveal how PAGA and SAGA cooperate to regulate histone acetylation, transcription and development. Given that the PAGA mutants show semi-dwarf and increased branching phenotypes without reduction in seed yield, the PAGA mutations could potentially be used for crop improvement.

CRISPR/Cas9 editing of wheat Ppd-1 gene homoeologs alters spike architecture and grain morphometric traits

Mutations in Photoperiod-1 (Ppd-1) gene are known to modify flowering time and yield in wheat. We cloned TaPpd-1 from wheat and found high similarity among the three homoeologs of TaPpd-1. To clarify the characteristics of TaPpd-1 homoeologs in different photoperiod conditions for inflorescence architecture and yield, we used CRISPR/Cas9 system to generate Tappd-1 mutant plants by simultaneous modification of the three homoeologs of wheat Ppd-1. Tappd-1 mutant plants showed no off-target mutations. Four T₀-edited lines under short-day length and three lines under long-day length conditions with the mutation frequency of 25% and 21%, respectively. These putative transgenic plants of all the lines were self-fertilized and generated T₁ and T₂ progenies and were evaluated by phenotypic and expression analysis. Results demonstrated that simultaneously edited TaPpd-1- A1, B1, and D1 homoeologs gene copies in T2_SDL-8-4, T2_SDL-4-5, T2_SDL-3-9, and T2_{_}LDL-10-9 showed similar spike inflorescence, flowering time, and significantly increase in 1000-grain weight, grain area, grain width, grain length, plant height, and spikelets per spike due to mutation in both alleles of Ppd-B1 and Ppd-D1 homoeologs but only spike length was decreased in T2_SDL-8-4, T2_SDL-4-5, and T2_{_}LDL-13-3 mutant lines due to mutation in both alleles of Ppd-A1 homoeolog under both conditions. Our results indicate that all TaPpd1 gene homoeologs influence wheat spike development by affecting both late flowering and earlier flowering but single mutant TaPpd-A1 homoeolog affect lowest as compared to the combination with double mutants of TaPpd-B1 and TaPpd-D1, TaPpd-A1 and TaPpd-B1, and TaPpd-A1 and TaPpd-D1 homoeologs for yield enhancement. Our findings further raised the idea that the relative expression of the various genomic copies of TaPpd-1 homoeologs may have an impact on the spike inflorescence architecture and grain morphometric features in wheat cultivars.

Integration of high-throughput phenotyping, GWAS, and predictive models reveals the genetic architecture of plant height in maize

Plant height (PH) is an essential trait in maize (Zea mays) that is tightly associated with planting density, biomass, lodging resistance, and grain yield in the field. Dissecting the dynamics of maize plant architecture will be beneficial for ideotype-based maize breeding and prediction, as the genetic basis controlling PH in maize remains largely unknown. In this study, we developed an automated high-throughput phenotyping platform (HTP) to systematically and noninvasively quantify 77 image-based traits (i-traits) and 20 field traits (f-traits) for 228 maize inbred lines across all developmental stages. Time-resolved i-traits with novel digital phenotypes and complex correlations with agronomic traits were characterized to reveal the dynamics of maize growth. An i-trait-based genome-wide association study identified 4945 trait-associated SNPs, 2603 genetic loci, and 1974 corresponding candidate genes. We found that rapid growth of maize plants occurs mainly at two developmental stages, stage 2 (S2) to S3 and S5 to S6, accounting for the final PH indicators. By integrating the PH-association network with the transcriptome profiles of specific internodes, we revealed 13 hub genes that may play vital roles during rapid growth. The candidate genes and novel i-traits identified at multiple growth stages may be used as potential indicators for final PH in maize. One candidate gene, ZmVATE, was functionally validated and shown to regulate PH-related traits in maize using genetic mutation. Furthermore, machine learning was used to build predictive models for final PH based on i-traits, and their performance was assessed across developmental stages. Moderate, strong, and very strong correlations between predictions and experimental datasets were achieved from the early S4 (tenth-leaf) stage. Colletively, our study provides a valuable tool for dissecting the spatiotemporal formation of specific internodes and the genetic architecture of PH, as well as resources and predictive models that are useful for molecular design breeding and predicting maize varieties with ideal plant architectures.

Insights on the stem elongation of spur-type bud sport mutant of 'Red Delicious' apple

The decreased capacity of auxin-, CTK-, and BR-mediated cell division and cell enlargement pathways, combined with the enhanced capacity of GA and ETH-, JA-, ABA-, SA-mediated stress-resistant pathways were presumed to be the crucial reasons for the formation of spur-type 'Red Delicious' mutants. Vallee Spur', which exhibit short internodes and compact tree shape, is the fourth generation of the spur-type bud sport mutant of 'Red Delicious'. However, the underlying molecular mechanism of these properties remains unclear. Here, comparative phenotypic, full-length transcriptome and phytohormone analyses were performed between 'Red Delicious' (NSP) and 'Vallee Spur' (SP). The new shoot internode length of NSP was ˃ 1.53-fold higher than that of the SP mutant. Cytological analysis showed that the stem cells of the SP mutant were smaller and more tightly arranged relative to the NSP. By Iso-Seq, a total of 1426 differentially expressed genes (DEGs) were detected, including 808 upregulated and 618 downregulated genes in new shoot apex with 2 leaves of the SP mutant. Gene expressions involved in auxin, cytokinin (CTK), and brassinosteroid (BR) signal transduction were mostly downregulated in the SP mutant, whereas those involved in gibberellin (GA), ethylene (ETH), jasmonate (JA), ABA, and salicylic acid (SA) signal transduction were mostly upregulated. The overall thermogram analysis of hormone levels in the shoot apex carrying two leaves detected by LC-MS/MS absolute quantification showed that the levels of IAA-Asp, IAA, iP7G, OPDA, and 6-deoxyCS were significantly upregulated in the SP mutant, while the remaining 28 hormones were significantly downregulated. It is speculated that the decreased capacity of auxin, CTK, and BR-mediated cell division and cell enlargement pathways is crucial for the formation of the SP mutant. GA and stress-resistant pathways of ETH, JA, ABA, and SA also play vital roles in stem elongation. These results highlight the involvement of phytohormones in the formation of stem elongation occurring in 'Red Delicious' spur-type bud sport mutants and provide information for exploring its biological mechanism.

Recent progression and future perspectives in cotton genomic breeding

Upland cotton is an important global cash crop for its long seed fibers and high edible oil and protein content. Progress in cotton genomics promotes the advancement of cotton genetics, evolutionary studies, functional genetics, and breeding, and has ushered cotton research and breeding into a new era. Here, we summarize high-impact genomics studies for cotton from the last 10 years. The diploid Gossypium arboreum and allotetraploid Gossypium hirsutum are the main focus of most genetic and genomic studies. We next review recent progress in cotton molecular biology and genetics, which builds on cotton genome sequencing efforts, population studies, and functional genomics, to provide insights into the mechanisms shaping abiotic and biotic stress tolerance, plant architecture, seed oil content, and fiber development. We also suggest the application of novel technologies and strategies to facilitate genome-based crop breeding. Explosive growth in the amount of novel genomic data, identified genes, gene modules, and pathways is now enabling researchers to utilize multidisciplinary genomics-enabled breeding strategies to cultivate "super cotton", synergistically improving multiple traits. These strategies must rise to meet urgent demands for a sustainable cotton industry.

IPA1 improves drought tolerance by activating SNAC1 in rice

Drought is a major abiotic stress to rice (Oryza sativa) during growth. Ideal Plant Architecture (IPA1), the first cloned gene controlling the ideal plant type in rice, has been reported to function in both ideal rice plant architecture and biotic resistance. Here, we report that the IPA1/OsSPL14, encoding a transcriptional factor, positively regulates drought tolerance in rice. The IPA1 is constitutively expressed and regulated by H₂O₂, abscisic acid, NaCl and polyethylene glycol 6000 treatments in rice. Furthermore, the IPA1-knockout plants showed much greater accumulation of H₂O₂ as measured by 3,3'-diaminobenzidine staining in leaves compared with WT plants. Yeast one-hybrid, dual-luciferase and electrophoretic mobility shift assays indicated that the IPA1 directly activates the promoter of SNAC1. Expression of SNAC1 is significantly down-regulated in IPA1 knockout plants. Further investigation indicated that the IPA1 plays a positive role in drought-stress tolerance by inducing reactive oxygen species scavenging in rice. Together, these findings indicated that the IPA1 played important roles in drought tolerance by regulating SNAC1, thus activating the antioxidant system in rice.

Formin protein DRT1 affects gross morphology and chloroplast relocation in rice

Plant height and tiller number are two major factors determining plant architecture and yield. However, in rice (Oryza sativa), the regulatory mechanism of plant architecture remains to be elucidated. Here, we reported a recessive rice mutant presenting dwarf and reduced tillering phenotypes (drt1). Map-based cloning revealed that the phenotypes are caused by a single point mutation in DRT1, which encodes the Class I formin protein O. sativa formin homolog 13 (OsFH13), binds with F-actin, and promotes actin polymerization for microfilament organization. DRT1 protein localized on the plasma membrane (PM) and chloroplast (CP) outer envelope. DRT1 interacted with rice phototropin 2 (OsPHOT2), and the interaction was interrupted in drt1. Upon blue light stimulus, PM localized DRT1 and OsPHOT2 were translocated onto the CP membrane. Moreover, deficiency of DRT1 reduced OsPHOT2 internalization and OsPHOT2-mediated CP relocation. Our study suggests that rice formin protein DRT1/OsFH13 is necessary for plant morphology and CP relocation by modulating the actin-associated cytoskeleton network.

TaSPL14-7A is a conserved regulator controlling plant architecture and yield traits in common wheat (Triticum aestivum L.)

Plant architecture is a crucial influencing factor of wheat yield and adaptation. In this study, we cloned and characterized TaSPL14, a homologous gene of the rice ideal plant architecture gene OsSPL14 in wheat. TaSPL14 homoeologs (TaSPL14-7A, TaSPL14-7B and TaSPL14-7D) exhibited similar expression patterns, and they were all preferentially expressed in stems at the elongation stage and in young spikes. Moreover, the expression level of TaSPL14-7A was higher than that of TaSPL14-7B and TaSPL14-7D. Overexpression of TaSPL14-7A in wheat resulted in significant changes in plant architecture and yield traits, including decreased tiller number and increased kernel size and weight. Three TaSPL14-7A haplotypes were identified in Chinese wheat core collection, and haplotype-based association analysis showed that TaSPL14-7A-Hap1/2 were significantly correlated with fewer tillers, larger kernels and higher kernel weights in modern cultivars. The haplotype effect resulted from a difference in TaSPL14-7A expression levels among genotypes, with TaSPL14-7A-Hap1/2 leading to higher expression levels than TaSPL14-7A-Hap3. As favorable haplotypes, TaSPL14-7A-Hap1/2 underwent positive selection during global wheat breeding over the last century. Together, the findings of our study provide insight into the function and genetic effects of TaSPL14 and provide a useful molecular marker for wheat breeding.

BRASSINOSTEROID-SIGNALING KINASE1-1, a positive regulator of brassinosteroid signalling, modulates plant architecture and grain size in rice

Brassinosteroids (BRs) are a crucial class of plant hormones that regulate plant growth and development, thus affecting many important agronomic traits in crops. However, there are still significant gaps in our understanding of the BR signalling pathway in rice. In this study, we provide multiple lines of evidence to indicate that BR-SIGNALING KINASE1-1 (OsBSK1-1) likely represents a missing component in the BR signalling pathway in rice. We showed that knockout mutants of OsBSK1-1 are less sensitive to BR and exhibit a pleiotropic phenotype, including lower plant height, less tiller number and shortened grain length, whereas transgenic plants overexpressing a gain-of-function dominant mutant form of OsBSK1-1 (OsBSK1-1A295V) are hypersensitive to BR, and exhibit some enhanced BR-responsive phenotypes. We found that OsBSK1-1 physically interacts with the BR receptor BRASSINOSTEROID INSENSITIVE1 (OsBRI1), and GLYCOGEN SYNTHASE KINASE2 (OsGSK2), a downstream component crucial for BR signalling. Moreover, we showed that OsBSK1-1 can be phosphorylated by OsBRI1 and can inhibit OsGSK2-mediated phosphorylation of BRASSINOSTEROID RESISTANT1 (OsBZR1). We further demonstrated that OsBSK1-1 genetically acts downstream of OsBRI1, but upstream of OsGSK2. Together, our results suggest that OsBSK1-1 may serve as a scaffold protein directly bridging OsBRI1 and OsGSK2 to positively regulate BR signalling, thus affecting plant architecture and grain size in rice.

Integrating GWAS, linkage mapping and gene expression analyses reveal the genetic control of first branch height in Brassica napus L

Rapeseed (Brassica napus L.) is a crucial oil crop cultivated worldwide. First branch height, an essential component of rapeseed plant architecture, has an important effect on yield and mechanized harvesting; however, the underlying genetic mechanism remains unclear. In this study, based on the 60K single nucleotide polymorphism array and a recombinant inbred lines population derived from M083 and 888-5, a total of 19 QTLs were detected in five environments, distributed on linkage groups A02, A09, A10, C06, and C07, which explained phenotypic variation ranging from 4.87 to 29.87%. Furthermore, 26 significant SNPs were discovered on Chr.A02 by genome-wide association study in a diversity panel of 324 re-sequencing accessions. The major QTL of the first branch height trait was co-located on Chr.A02 by integrating linkage mapping and association mapping. Eleven candidate genes were screened via allelic variation analysis, inter-subgenomic synteny analysis, and differential expression of genes in parental shoot apical meristem tissues. Among these genes, BnaA02g13010D, which encodes a TCP transcription factor, was confirmed as the target gene according to gene function annotation, haplotype analysis, and full-length gene sequencing, which revealed that TATA insertion/deletion in the promoter region was closely linked to significantly phenotypic differences BnaA02.TCP1 ^M083 overexpression resulted in decreased branch height and increased branch number in Arabidopsis. These results provide a genetic basis for first branch height and the ideal architecture of B. napus.

OsSRK1, a lectin receptor-like kinase, controls plant height by mediating internode elongation in Oryza sativa L

LecRLKs (lectin receptor-like kinases) is a subfamily of RLKs (receptor like kinase) and takes part in mounds of biological processes in plant-environment interaction. However, the roles of LecRLKs in plant development are still elusive. Here, we showed that OsSRK1, belonging to LecRLK family in rice, had a relative higher expression in internode and stem in comparison with that in root and leaf. Importantly, srk1-1 and srk1-2, two genome-edited mutants of OsSRK1 using CRISPR/Cas9 system, exhibited obviously a decreased plant height and shorter length of the first internode and second internode compared with those in WT. Subsequently, histochemical sectioning showed that the stem diameter and the cell length in stem are significantly reduced in srk1-1 and srk1-2 compared with WT. Moreover, analyzing the expression of four gibberellin biosynthesis related genes showed that CPS, KAO, KS1, and GA3ox2 expression had similar levels between WT and mutants. Importantly, we further verified that OsSRK1 can directly interact with gibberellin receptor GID1. Together, our results revealed that LecRLKs family member OsSRK1 positively regulated plant height by controlling internode elongation which maybe depended on OsSRK1-GID1 interaction mediated gibberellin signaling transduction.

Supplementary Information

The online version contains supplementary material available at 10.1007/s11032-022-01340-6.

Two alternative splicing variants of a wheat gene TaNAK1, TaNAK1.1 and TaNAK1.2, differentially regulate flowering time and plant architecture leading to differences in seed yield of transgenic Arabidopsis

In wheat production, appropriate flowering time and ideal plant architecture are the prerequisites for high grain yield. Alternative splicing (AS) is a vital process that regulates gene expression at the post-transcriptional level, and AS events in wheat have been found to be closely related to grain-related traits and abiotic stress tolerance. However, AS events and their biological roles in regulating flowering time and plant architecture in wheat remain unclear. In this study, we report that TaNAK1 undergoes AS, producing three splicing variants. Molecular characterization of TaNAK1 and its splicing variants demonstrated that all three protein isoforms have a conserved NB-ARC domain and a protein kinase domain, but the positions of these two domains and the length of the protein kinase domains are different among them, implying that they may have different three-dimensional structures and therefore have different functions. Further investigations showed that the two splicing variants of TaNAK1, TaNAK1.1 and TaNAK1.2, exhibited different expression patterns during wheat growth and development, while the other one, TaNAK1.3, was not detected. Subcellular localization demonstrated that TaNAK1.1 was mainly localized in the cytoplasm, while TaNAK1.2 was localized in the nucleus and cytoplasm. Both TaNAK1.1 and TaNAK1.2 exhibit protein kinase activity in vitro. Ectopic expression of TaNAK1.1 and TaNAK1.2 in Arabidopsis demonstrated that these two splicing variants play opposite roles in regulating flowering time and plant architecture, resulting in different seed yields. TaNAK1.2 positive regulates the transition from vegetative to reproductive growth, plant height, branching number, seed size, and seed yield of Arabidopsis, while TaNAK1.1 negatively regulates these traits. Our findings provide new gene resource for regulating flowering time and plant architecture in crop breeding for high grain yield.

Biomolecular Strategies for Vascular Bundle Development to Improve Crop Yield

The need to produce crops with higher yields is critical due to a growing global population, depletion of agricultural land, and severe climate change. Compared with the "source" and "sink" transport systems that have been studied a lot, the development and utilization of vascular bundles (conducting vessels in plants) are increasingly important. Due to the complexity of the vascular system, its structure, and its delicate and deep position in the plant body, the current research on model plants remains basic knowledge and has not been repeated for crops and applied to field production. In this review, we aim to summarize the current knowledge regarding biomolecular strategies of vascular bundles in transport systems (source-flow-sink), allocation, helping crop architecture establishment, and influence of the external environment. It is expected to help understand how to use sophisticated and advancing genetic engineering technology to improve the vascular system of crops to increase yield.

DWARF AND ROBUST PLANT regulates plant height via modulating gibberellin biosynthesis in chrysanthemum

YABBY (YAB) genes are specifically expressed in abaxial cells of lateral organs and determine abaxial cell fate. However, most studies have focused on few model plants, and the molecular mechanisms of YAB genes are not well understood. Here, we identified a YAB transcription factor in chrysanthemum (Chrysanthemum morifolium), Dwarf and Robust Plant (CmDRP), that belongs to a distinct FILAMENTOUS FLOWER (FlL)/YAB3 sub-clade lost in Brassicaceae. CmDRP was expressed in various tissues but did not show any polar distribution in chrysanthemum. Overexpression of CmDRP resulted in a semi-dwarf phenotype with a significantly decreased active GA3 content, while reduced expression generated the opposite phenotype. Furthermore, plant height of transgenic plants was partially rescued through the exogenous application of GA3 and Paclobutrazol, and expression of the GA biosynthesis gene CmGA3ox1 was significantly altered in transgenic plants. Yeast one-hybrid, luciferase, and chromatin immunoprecipitation-qPCR analyses showed that CmDRP could directly bind to the CmGA3ox1 promoter and suppress its expression. Our research reveals a nonpolar expression pattern of a YAB family gene in dicots and demonstrates it regulates plant height through the GA pathway, which will deepen the understanding of the genetic and molecular mechanisms of YAB genes.

MINI BODY1, encoding a MATE/DTX family transporter, affects plant architecture in mungbean (Vigna radiata L.)

It has been shown that multidrug and toxic compound extrusion/detoxification (MATE/DTX) family transporters are involved in the regulation of plant development and stress response. Here, we characterized the mini body1 (mib1) mutants in mungbean, which gave rise to increased branches, pentafoliate compound leaves, and shortened pods. Map-based cloning revealed that MIB1 encoded a MATE/DTX family protein in mungbean. qRT-PCR analysis showed that MIB1 was expressed in all tissues of mungbean, with the highest expression level in the young inflorescence. Complementation assays in Escherichia coli revealed that MIB1 potentially acted as a MATE/DTX transporter in mungbean. It was found that overexpression of the MIB1 gene partially rescued the shortened pod phenotype of the Arabidopsis dtx54 mutant. Transcriptomic analysis of the shoot buds and young pods revealed that the expression levels of several genes involved in the phytohormone pathway and developmental regulators were altered in the mib1 mutants. Our results suggested that MIB1 plays a key role in the control of plant architecture establishment in mungbean.

Rice OsUBR7 modulates plant height by regulating histone H2B monoubiquitination and cell proliferation

Plant height is an important agronomic trait for lodging resistance and yield. Here, we report a new plant-height-related gene, OsUBR7 in rice (Oryza sativa L.); knockout of OsUBR7 caused fewer cells in internodes, resulting in a semi-dwarf phenotype. OsUBR7 encodes a putative E3 ligase containing a plant homeodomain finger and a ubiquitin protein ligase E3 component N-recognin 7 (UBR7) domain. OsUBR7 interacts with histones and monoubiquitinates H2B (H2Bub1) at lysine148 in coordination with the E2 conjugase OsUBC18. OsUBR7 mediates H2Bub1 at a number of chromatin loci for the normal expression of target genes, including cell-cycle-related and pleiotropic genes, consistent with the observation that cell-cycle progression was suppressed in the osubr7 mutant owing to reductions in H2Bub1 and expression levels at these loci. The genetic divergence of OsUBR7 alleles among japonica and indica cultivars affects their transcriptional activity, and these alleles may have undergone selection during rice domestication. Overall, our results reveal a novel mechanism that mediates H2Bub1 in plants, and UBR7 orthologs could be utilized as an untapped epigenetic resource for crop improvement.

Genome-wide association study reveals a GLYCOGEN SYNTHASE KINASE 3 gene regulating plant height in Brassica napus

Rapeseed (Brassica napus) is an allotetraploid crop that is the main source of edible oils and feed proteins in the world. The ideal plant architecture breeding is a major objective of rapeseed breeding and determining the appropriate plant height is a key element of the ideal plant architecture. Therefore, this study aims to improve the understanding of the genetic controls underlying plant height. The plant heights of 230 rapeseed accessions collected worldwide were investigated in field experiments over two consecutive years in Wuhan, China. Whole-genome resequencing of these accessions yielded a total of 1,707,194 informative single nucleotide polymorphisms (SNPs) that were used for genome-wide association analysis (GWAS). GWAS and haplotype analysis showed that BnaA01g09530D, which encodes BRASSINOSTEROID-INSENSITIVE 2 and belongs to the GLYCOGEN SYNTHASE KINASE 3 (GSK3) family, was significantly associated with plant height in B. napus. Moreover, a total of 31 BnGSK3s with complete domains were identified from B. napus genome and clustered into four groups according to phylogenetic analysis, gene structure, and motif distribution. The expression patterns showed that BnGSK3s exhibited significant differences in 13 developmental tissues in B. napus, suggesting that BnGSK3s may be involved in tissue-specific development. Sixteen BnGSK3 genes were highly expressed the in shoot apical meristem, which may be related to plant height or architecture development. These results are important for providing new haplotypes of plant height in B. napus and for extending valuable genetic information for rapeseed genetic improvement of plant architecture.

Regional association and transcriptome analysis revealed candidate genes controlling plant height in Brassica napus

Plant height is a key morphological trait in rapeseed, which not only plays an important role in determining plant architecture, but is also an important characteristic related to yield. Presently, the improvement of plant architecture is a major challenge in rapeseed breeding. This work was carried out to identify genetic loci related to plant height in rapeseed. In this study, a genome-wide association study (GWAS) of plant height was performed using a Brassica 60 K Illumina Infinium SNP array and 203 Brassica napus accessions. Eleven haplotypes containing important candidate genes were detected and significantly associated with plant height on chromosomes A02, A03, A05, A07, A08, C03, C06, and C09. Moreover, regional association analysis of 50 resequenced rapeseed inbred lines was used to further analyze these eleven haplotypes and revealed nucleotide variation in the BnFBR12-A08 and BnCCR1-C03 gene regions related to the phenotypic variation in plant height. Furthermore, coexpression network analysis showed that BnFBR12-A08 and BnCCR1-C03 were directly connected with hormone genes and transcription factors and formed a potential network regulating the plant height of rapeseed. Our results will aid in the development of haplotype functional markers to further improve plant height in rapeseed.

Supplementary Information

The online version contains supplementary material available at 10.1007/s11032-022-01337-1.

Genetic dissection of branch architecture in oilseed rape (Brassica napus L.) germplasm

Branch architecture is an important factor influencing rapeseed planting density, mechanized harvest, and yield. However, its related genes and regulatory mechanisms remain largely unknown. In this study, branch angle (BA) and branch dispersion degree (BD) were used to evaluate branch architecture. Branch angle exhibited a dynamic change from an increase in the early stage to a gradual decrease until reaching a stable state. Cytological analysis showed that BA variation was mainly due to xylem size differences in the vascular bundle of the branch junction. The phenotypic analysis of 327 natural accessions revealed that BA in six environments ranged from 24.3° to 67.9°, and that BD in three environments varied from 4.20 cm to 21.4 cm, respectively. A total of 115 significant loci were detected through association mapping in three models (MLM, mrMLM, and FarmCPU), which explained 0.53%-19.4% of the phenotypic variations. Of them, 10 loci were repeatedly detected in different environments and models, one of which qBAD.A03-2 was verified as a stable QTL using a secondary segregation population. Totally, 1066 differentially expressed genes (DEGs) were identified between branch adaxial- and abaxial- sides from four extremely large or small BA/BD accessions through RNA sequencing. These DEGs were significantly enriched in the pathways related to auxin biosynthesis and transport as well as cell extension such as indole alkaloid biosynthesis, other glycan degradation, and fatty acid elongation. Four known candidate genes BnaA02g16500D (PIN1), BnaA03g10430D (PIN2), BnaC03g06250D (LAZY1), and BnaC06g20640D (ARF17) were identified by both GWAS and RNA-seq, all of which were involved in regulating the asymmetric distribution of auxins. Our identified association loci and candidate genes provide a theoretical basis for further study of gene cloning and genetic improvement of branch architecture.

The Global Assessment of Oilseed Brassica Crop Species Yield, Yield Stability and the Underlying Genetics

The global demand for oilseeds is increasing along with the human population. The family of Brassicaceae crops are no exception, typically harvested as a valuable source of oil, rich in beneficial molecules important for human health. The global capacity for improving Brassica yield has steadily risen over the last 50 years, with the major crop Brassica napus (rapeseed, canola) production increasing to ~72 Gt in 2020. In contrast, the production of Brassica mustard crops has fluctuated, rarely improving in farming efficiency. The drastic increase in global yield of B. napus is largely due to the demand for a stable source of cooking oil. Furthermore, with the adoption of highly efficient farming techniques, yield enhancement programs, breeding programs, the integration of high-throughput phenotyping technology and establishing the underlying genetics, B. napus yields have increased by >450 fold since 1978. Yield stability has been improved with new management strategies targeting diseases and pests, as well as by understanding the complex interaction of environment, phenotype and genotype. This review assesses the global yield and yield stability of agriculturally important oilseed Brassica species and discusses how contemporary farming and genetic techniques have driven improvements.

Map-based cloning and transcriptome analysis of the more-tiller and small-grain mutant in rice

A G to T nucleotide substitution of OsTSG2 led to more tillers and smaller grains in rice by participating in phytohormone signal transduction and starch and sucrose metabolism. Rice is one of the most important food crops worldwide. Grain size and tiller number are the most important factors determining rice yield. The more-tiller and small-grain 2 (tsg2) mutant in rice, developed by ethyl methanesulfonate (EMS) mutagenesis, has smaller grains, more tillers, and a higher yield per plant relative to the wild-type (WT). Based on the genetic analysis, the tsg2 traits were conferred by a single recessive nuclear gene located on the long arm of chromosome 2. After fine-mapping the OsTSG2 locus, a G to T nucleotide substitution was identified, which resulted in an A to S mutation in a highly conserved domain of the growth-regulation factor protein. The single-strand conformation polymorphism (SSCP) marker was developed based on the SNP associated with the phenotypic segregation of traits. The functional complementation of OsTSG2 from the tsg2 mutant to the WT led to an increase in grain size and weight. The differentially expressed genes (DEGs) identified by RNA sequencing were involved in phytohormone signal transduction and starch and sucrose metabolism. Enzyme-linked immunosorbent assay (ELISA) analysis detected variation in the indole acetic acid (IAA) and jasmonic acid (JA) content in the tsg2 inflorescence, while the cellular organization, degree of chalkiness, gel consistency, amylose content, and alkaline spreading value were affected in the tsg2 grains. The findings elucidated the regulatory mechanisms of the tsg2 traits. This mutant could be used in marker-assisted breeding for high-yield and good-quality rice.

Leaf Count Aided Novel Framework for Rice (Oryza sativa L.) Genotypes Discrimination in Phenomics: Leveraging Computer Vision and Deep Learning Applications

Drought is a detrimental factor to gaining higher yields in rice (Oryza sativa L.), especially amid the rising occurrence of drought across the globe. To combat this situation, it is essential to develop novel drought-resilient varieties. Therefore, screening of drought-adaptive genotypes is required with high precision and high throughput. In contemporary emerging science, high throughput plant phenotyping (HTPP) is a crucial technology that attempts to break the bottleneck of traditional phenotyping. In traditional phenotyping, screening significant genotypes is a tedious task and prone to human error while measuring various plant traits. In contrast, owing to the potential advantage of HTPP over traditional phenotyping, image-based traits, also known as i-traits, were used in our study to discriminate 110 genotypes grown for genome-wide association study experiments under controlled (well-watered), and drought-stress (limited water) conditions, under a phenomics experiment in a controlled environment with RGB images. Our proposed framework non-destructively estimated drought-adaptive plant traits from the images, such as the number of leaves, convex hull, plant-aspect ratio (plant spread), and similarly associated geometrical and morphological traits for analyzing and discriminating genotypes. The results showed that a single trait, the number of leaves, can also be used for discriminating genotypes. This critical drought-adaptive trait was associated with plant size, architecture, and biomass. In this work, the number of leaves and other characteristics were estimated non-destructively from top view images of the rice plant for each genotype. The estimation of the number of leaves for each rice plant was conducted with the deep learning model, YOLO (You Only Look Once). The leaves were counted by detecting corresponding visible leaf tips in the rice plant. The detection accuracy was 86-92% for dense to moderate spread large plants, and 98% for sparse spread small plants. With this framework, the susceptible genotypes (MTU1010, PUSA-1121 and similar genotypes) and drought-resistant genotypes (Heera, Anjali, Dular and similar genotypes) were grouped in the core set with a respective group of drought-susceptible and drought-tolerant genotypes based on the number of leaves, and the leaves' emergence during the peak drought-stress period. Moreover, it was found that the number of leaves was significantly associated with other pertinent morphological, physiological and geometrical traits. Other geometrical traits were measured from the RGB images with the help of computer vision.

A SNP mutation in the CsCLAVATA1 leads to pleiotropic variation in plant architecture and fruit morphogenesis in cucumber (Cucumis sativus L.)

Plant architectures is predominantly determined by branching pattern, internode elongation, phyllotaxis, shoot determinacy and reproductive organs. Domestication or improvement of this critical agronomic trait played an important role in the breakthrough of crop yield. Here, we identified a mutant with fasciated plant architecture, named fas, from an ethyl methanesulfonate (EMS) induced mutant population in cucumber. The mutant exhibited abnormal phyllotaxy, flattened main stem, increased number of floral organs, and significantly shorter and thicker fruits. However, the molecular mechanism conferring this pleiotropic effect remains unknown. Using a map-based cloning strategy, we isolated the gene CsaV3_3G045960, encoding a leucine-rich repeat receptor-like kinase, a putative direct homolog of the Arabidopsis CLAVATA1 protein referred to as CsCLV1. Endogenous hormone assays showed that IAA and GA₃ levels in fas stems and ovaries were significantly reduced. Conformably, RNA-seq analysis showed that CsCLV1 regulates cucumber stem and ovary development by coordinating hormones and transcription factors. Our results contribute to the understanding of the function of CsCLV1 throughout the growth cycle, provide new evidence that the CLV signaling system is functionally conserved in Cucurbitaceae.

Rice cellulose synthase-like protein OsCSLD4 coordinates the trade-off between plant growth and defense

Plant cell wall is a complex and changeable structure, which is very important for plant growth and development. It is clear that cell wall polysaccharide synthases have critical functions in rice growth and abiotic stress, yet their role in plant response to pathogen invasion is poorly understood. Here, we describe a dwarf and narrowed leaf in Hejiang 19 (dnl19) mutant in rice, which shows multiple growth defects such as reduced plant height, enlarged lamina joint angle, curled leaf morphology, and a decrease in panicle length and seed setting. MutMap analysis, genetic complementation and gene knockout mutant show that cellulose synthase-like D4 (OsCSLD4) is the causal gene for DNL19. Loss function of OsCSLD4 leads to a constitutive activation of defense response in rice. After inoculation with rice blast and bacterial blight, dnl19 displays an enhanced disease resistance. Widely targeted metabolomics analysis reveals that disruption of OsCSLD4 in dnl19 resulted in significant increase of L-valine, L-asparagine, L-histidine, L-alanine, gentisic acid, but significant decrease of L-aspartic acid, malic acid, 6-phosphogluconic acid, glucose 6-phosphate, galactose 1-phosphate, gluconic acid, D-aspartic acid. Collectively, our data reveals the importance of OsCSLD4 in balancing the trade-off between rice growth and defense.

Genome-wide association study and transcriptome analysis reveal key genes controlling fruit branch angle in cotton

Fruit branch angle (FBA), a pivotal component of cotton plant architecture, is vital for field and mechanical harvesting. However, the molecular mechanism of FBA formation is poorly understood in cotton. To uncover the genetic basis for FBA formation in cotton, we performed a genome-wide association study (GWAS) of 163 cotton accessions with re-sequencing data. A total of 55 SNPs and 18 candidate genes were significantly associated with FBA trait. By combining GWAS and transcriptome analysis, four genes underlying FBA were identified. An FBA-associated candidate gene Ghi_A09G08736, which is homologous to SAUR46 in Arabidopsis thaliana, was detected in our study. In addition, transcriptomic evidence was provided to show that gravity and light were implicated in the FBA formation. This study provides new insights into the genetic architecture of FBA that informs architecture breeding in cotton.

Genome-wide characterization of ovate family protein gene family associated with number of seeds per silique in Brassica napus

Ovate family proteins (OFPs) were firstly identified in tomato as proteins controlling the pear shape of the fruit. Subsequent studies have successively proved that OFPs are a class of negative regulators of plant development, and are involved in the regulation of complex traits in different plants. However, there has been no report about the functions of OFPs in rapeseed growth to date. Here, we identified the OFPs in rapeseed at the genomic level. As a result, a total of 67 members were obtained. We then analyzed the evolution from Arabidopsis thaliana to Brassica napus, illustrated their phylogenetic and syntenic relationships, and compared the gene structure and conserved domains between different copies. We also analyzed their expression patterns in rapeseed, and found significant differences in the expression of different members and in different tissues. Additionally, we performed a GWAS for the number of seeds per silique (NSPS) in a rapeseed population consisting of 204 natural accessions, and identified a new gene BnOFP13_2 significantly associated with NSPS, which was identified as a novel function of OFPs. Haplotype analysis revealed that the accessions with haplotype 3 had a higher NSPS than other accessions, suggesting that BnOFP13_2 is associated with NSPS. Transcript profiling during the five stages of silique development demonstrated that BnOFP13_2 negatively regulates NSPS. These findings provide evidence for functional diversity of OFP gene family and important implications for oilseed rape breeding.

Dwarf and High Tillering1 represses rice tillering through mediating the splicing of D14 pre-mRNA

Strigolactones (SLs) constitute a class of plant hormones that regulate many aspects of plant development, including repressing tillering in rice (Oryza sativa). However, how SL pathways are regulated is still poorly understood. Here, we describe a rice mutant dwarf and high tillering1 (dht1), which exhibits pleiotropic phenotypes (such as dwarfism and increased tiller numbers) similar to those of mutants defective in SL signaling. We show that DHT1 encodes a monocotyledon-specific hnRNP-like protein that acts as a previously unrecognized intron splicing factor for many precursor mRNAs (pre-mRNAs), including for the SL receptor gene D14. We find that the dht1 (DHT1I232F) mutant protein is impaired in its stability and RNA binding activity, causing defective splicing of D14 pre-mRNA and reduced D14 expression, and consequently leading to the SL signaling-defective phenotypes. Overall, our findings deepen our understanding of the functional diversification of hnRNP-like proteins and establish a connection between posttranscriptional splicing and SL signaling in the regulation of plant development.

Blocking Rice Shoot Gravitropism by Altering One Amino Acid in LAZY1

Tiller angle is an important trait that determines plant architecture and yield in cereal crops. Tiller angle is partially controlled during gravistimulation by the dynamic re-allocation of LAZY1 (LA1) protein between the nucleus and plasma membrane, but the underlying mechanism remains unclear. In this study, we identified and characterized a new allele of LA1 based on analysis of a rice (Oryza sativa L.) spreading-tiller mutant la1^G74V, which harbors a non-synonymous mutation in the predicted transmembrane (TM) domain-encoding region of this gene. The mutation causes complete loss of shoot gravitropism, leading to prostrate growth of plants. Our results showed that LA1 localizes not only to the nucleus and plasma membrane but also to the endoplasmic reticulum. Removal of the TM domain in LA1 showed spreading-tiller phenotype of plants similar to la1^G74V but did not affect the plasma membrane localization; thus, making it distinct from its ortholog ZmLA1 in Zea mays. Therefore, we propose that the TM domain is indispensable for the biological function of LA1, but this domain does not determine the localization of the protein to the plasma membrane. Our study provides new insights into the LA1-mediated regulation of shoot gravitropism.

Genetic basis underlying tiller angle in rice (Oryza sativa L.) by genome-wide association study

Novel alleles of two reported tiller angle genes and eleven candidate genes for rice tiller angle were identified by combining GWAS with transcriptomic, qRT-PCR and haplotype analysis. Rice tiller angle is a key agronomic trait determining rice grain yield. Several quantitative trait loci (QTLs) affecting rice tiller angle have been mapped in the past decades. Little is known about the genetic base of tiller angle in rice, because rice tiller angle is a complex polygenic trait. In this study, we performed genome-wide association study (GWAS) on tiller angle in rice using a population of 164 japonica varieties derived from the 3 K Rice Genomes Project (3 K RGP). We detected a total of 18 QTLs using 1135519 single-nucleotide polymorphisms (SNP) based on three GWAS models (GLM, FastLMM and FarmCPU). Among them, two identified QTLs, qTA8.3 and qTA8.4, overlapped with PAY1 and TIG1, respectively, and additional 16 QTLs were identified for the first time. Combined with haplotype and expression analyses, we further revealed that PAY1 harbors one non-synonymous variation at its coding region, likely leading to variable tiller angle in the population, and that nature variations in the promoter of TIG1 significantly affect its expression, closely correlating with tiller angle phenotypes observed. Similarly, using qRT-PCR and haplotype analysis, we identified 1 and 7 candidate genes in qTA6.1 and qTA8.1 that were commonly detected by two GWAS models, respectively. In addition, we identified 3 more candidate genes in the remaining 14 novel QTLs after filtering by transcriptome analysis and qRT-PCR. In summary, this study provides new insights into the genetic architecture of rice tiller angle and candidate genes for rice breeding.

OsCPL3 is involved in brassinosteroid signaling by regulating OsGSK2 stability

Glycogen synthase kinase 3 (GSK3) proteins play key roles in brassinosteroid (BR) signaling during plant growth and development by phosphorylating various substrates. However, how GSK3 protein stability and activity are themselves modulated is not well understood. Here, we demonstrate in vitro and in vivo that C-TERMINAL DOMAIN PHOSPHATASE-LIKE 3 (OsCPL3), a member of the RNA Pol II CTD phosphatase-like family, physically interacts with OsGSK2 in rice (Oryza sativa). OsCPL3 expression was widely detected in various tissues and organs including roots, leaves and lamina joints, and was induced by exogenous BR treatment. OsCPL3 localized to the nucleus, where it dephosphorylated OsGSK2 at the Ser-222 and Thr-284 residues to modulate its protein turnover and kinase activity, in turn affecting the degradation of BRASSINAZOLE-RESISTANT 1 (BZR1) and BR signaling. Loss of OsCPL3 function resulted in higher OsGSK2 abundance and lower OsBZR1 levels, leading to decreased BR responsiveness and alterations in plant morphology including semi-dwarfism, leaf erectness and grain size, which are of fundamental importance to crop productivity. These results reveal a previously unrecognized role for OsCPL3 and add another layer of complexity to the tightly controlled BR signaling pathway in plants.

Melon shoot organization 1, encoding an AGRONAUTE7 protein, plays a crucial role in plant development

A melon gene MSO1 located on chromosome 10 by map-based cloning strategy, which encodes an ARGONAUTE 7 protein, is responsible for the development of shoot organization. Plant endogenous small RNAs (sRNAs) are involved in various plant developmental processes. In Arabidopsis, sRNAs combined with ARGONAUTE (AGO) proteins are incorporated into the RNA-induced silencing complex (RISC), which functions in RNA silencing or biogenesis of trans-acting siRNAs (ta-siRNAs). However, their roles in melon (Cucumis melo L.) are still unclear. Here, the melon shoot organization 1 (mso1) mutant was identified and shown to exhibit pleiotropic phenotypes in leaf morphology and plant architecture. Positional cloning of MSO1 revealed that it encodes a homologue of Arabidopsis AGO7/ZIPPY, which is required for the production of ta-siRNAs. The AG-to-C mutation in the second exon of MSO1 caused a frameshift mutation and significantly reduced its expression. Ectopic expression of MSO1 rescued the Arabidopsis ago7 phenotype. RNA-seq analysis showed that several genes involved in transcriptional regulation and plant hormones were significantly altered in mso1 compared to WT. A total of 304 and 231 miRNAs were identified in mso1 and WT by sRNA sequencing, respectively, and among them, 42 known and ten novel miRNAs were differentially expressed. cme-miR390a significantly accumulated, and the expression levels of the two ta-siRNAs were almost completely abolished in mso1. Correspondingly, their targets, the ARF3 and ARF4 genes, showed dramatically upregulated expression, indicating that the miR390-TAS3-ARF pathway has conserved roles in melon. These findings will help us better understand the molecular mechanisms of MSO1 in plant development in melon.

The miR319/TaGAMYB3 module regulates plant architecture and improves grain yield in common wheat (Triticum aestivum)

Plant architecture is a key determinant of crop productivity and adaptation. The highly conserved microRNA319 (miR319) family functions in various biological processes, but little is known about how miR319 regulates plant architecture in wheat (Triticum aestivum). Here, we determined that the miR319/TaGAMYB3 module controls plant architecture and grain yield in common wheat. Repressing tae-miR319 using short tandem target mimics resulted in favorable plant architecture traits, including increased plant height, reduced tiller number, enlarged spikes and flag leaves, and thicker culms, as well as enhanced grain yield in field plot tests. Overexpressing tae-miR319 had the opposite effects on plant architecture and grain yield. Although both TaPCF8 and TaGAMYB3 were identified as miR319 target genes, genetic complementation assays demonstrated that only miR319-resistant TaGAMYB3 (rTaGAMYB3) abolished tae-miR319-mediated growth inhibition of flag leaves and spikes. TaGAMYB3 functions as a transcriptional activator of downstream genes, including TaPSKR1, TaXTH23, TaMADS5 and TaMADS51, by binding to their promoters. Furthermore, TaGAMYB3 physically interacts with TaBA1, an important regulator of spike development, to additively activate the transcription of downstream genes such as TaMADS5. Our findings provide insight into how the miR319/TaGAMYB3 module regulates plant architecture and improves grain yield in common wheat.

In vitro Induction and Phenotypic Variations of Autotetraploid Garlic (Allium sativum L.) With Dwarfism

Garlic (Allium sativum L.) is a compelling horticultural crop with high culinary and therapeutic values. Commercial garlic varieties are male-sterile and propagated asexually from individual cloves or bulbils. Consequently, its main breeding strategy has been confined to the time-consuming and inefficient selection approach from the existing germplasm. Polyploidy, meanwhile, plays a prominent role in conferring plants various changes in morphological, physiological, and ecological properties. Artificial polyploidy induction has gained pivotal attention to generate new genotype for further crop improvement as a mutational breeding method. In our study, efficient and reliable in vitro induction protocols of autotetraploid garlic were established by applying different antimitotic agents based on high-frequency direct shoot organogenesis initiated from inflorescence explant. The explants were cultured on solid medium containing various concentrations of colchicine or oryzalin for different duration days. Afterward, the ploidy levels of regenerated plantlets with stable and distinguished characters were confirmed by flow cytometry and chromosome counting. The colchicine concentration at 0.2% (w/v) combined with culture duration for 20 days was most efficient (the autotetraploid induction rate was 21.8%) compared to the induction rate of 4.3% using oryzalin at 60 μmol L-1 for 20 days. No polymorphic bands were detected by simple sequence repeat analysis between tetraploid and diploid plantlets. The tetraploids exhibited a stable and remarkable dwarfness effect rarely reported in artificial polyploidization among wide range of phenotypic variations. There are both morphological and cytological changes including extremely reduced plant height, thickening and broadening of leaves, disappearance of pseudostem, density reduction, and augmented width of stomatal. Furthermore, the level of phytohormones, including, indole propionic acid, gibberellin, brassinolide, zeatin, dihydrozeatin, and methyl jasmonate, was significantly lower in tetraploids than those in diploid controls, except indole acetic acid and abscisic acid, which could partly explain the dwarfness in hormonal regulation aspect. Moreover, as the typical secondary metabolites of garlic, organosulfur compounds including allicin, diallyl disulfide, and diallyl trisulfide accumulated a higher content significantly in tetraploids. The obtained dwarf genotype of autotetraploid garlic could bring new perspectives for the artificial polyploids breeding and be implemented as a new germplasm to facilitate investigation into whole-genome doubling consequences.

Rice STOMATAL CYTOKINESIS DEFECTIVE2 regulates cell expansion by affecting vesicular trafficking in rice

Vesicular trafficking plays critical roles in cell expansion in yeast and mammals, but information linking vesicular trafficking and cell expansion in plants is limited. Here, we isolated and characterized a rice (Oryza sativa) mutant, decreased plant height 1-1 (dph1-1), which exhibited a wide spectrum of developmental phenotypes, including reduced plant height and smaller panicles and grains. Cytological analysis revealed that limited cell expansion was responsible for the dph1-1 mutant phenotype compared to the wild-type. Map-based cloning revealed that DPH1 encodes a plant-specific protein, OsSCD2, which is homologous to Arabidopsis (Arabidopsis thaliana) STOMATAL CYTOKINESIS DEFECTIVE2 (SCD2). Subcellular localization revealed that OsSCD2 is associated with clathrin. Confocal microscopy showed that the dph1-1 mutant has defective endocytosis and post-Golgi trafficking. Biochemical and confocal data indicated that OsSCD2 physically interacts with OsSCD1 and that they are associated with intracellular structures that colocalize with microtubules. Furthermore, we found that cellulose synthesis was affected in the dph1-1 mutant, evidenced by reduced cellulose synthase gene accumulation at the transcript and protein levels, most likely resulting from an impaired localization pattern. Our results suggest that OsSCD2 is involved in clathrin-related vesicular trafficking with an important role in maintaining plant growth in rice.

Introgression of chromosome 1P from Agropyron cristatum reduces leaf size and plant height to improve the plant architecture of common wheat

Introducing Agropyron cristatum chromosome 1P into common wheat can significantly reduce the plant height and leaf size, which can improve the plant architecture of common wheat. A new direction in crop breeding is the improvement of plant architecture for dense plantings to obtain higher yields. Wild relatives carry an abundant genetic variation that can increase the diversity of genes for crop genetic improvement. In this study, the A. cristatum 1P addition line, 1PS and 1PL telosomic addition lines were obtained by backcrossing the addition/substitution line II-3-1 (2n = 20'' W + 1P" + 2P") with the commercial recurrent parent cv. Jimai 22. Four continuous years of agronomic trait investigation in the genetic populations suggested that the introduction of A. cristatum chromosome 1P into wheat can significantly improve wheat plant architecture by reducing the plant height, leaf length and leaf width. A. cristatum chromosome arm 1PS reduced the plant height and leaf length of wheat, whereas introducing A. cristatum chromosome arm 1PL reduced the plant height, leaf length and leaf width. Altogether, our results demonstrated that A. cristatum chromosome 1P carries the dominant genes for small leaves and a dwarf habit for the enhancement of plant architecture in wheat. This study highlights wild relative donors as new gene resources for improving wheat plant architecture for dense planting.

TCP Transcription Factors Involved in Shoot Development of Ma Bamboo (Dendrocalamus latiflorus Munro)

Ma bamboo (Dendrocalamus latiflorus Munro) is the most widely cultivated clumping bamboo in Southern China and is valuable for both consumption and wood production. The development of bamboo shoots involving the occurrence of lateral buds is unique, and it affects both shoot yield and the resulting timber. Plant-specific TCP transcription factors are involved in plant growth and development, particularly in lateral bud outgrowth and morphogenesis. However, the comprehensive information of the TCP genes in Ma bamboo remains poorly understood. In this study, 66 TCP transcription factors were identified in Ma bamboo at the genome-wide level. Members of the same subfamily had conservative gene structures and conserved motifs. The collinear analysis demonstrated that segmental duplication occurred widely in the TCP transcription factors of Ma bamboo, which mainly led to the expansion of a gene family. Cis-acting elements related to growth and development and stress response were found in the promoter regions of DlTCPs. Expression patterns revealed that DlTCPs have tissue expression specificity, which is usually highly expressed in shoots and leaves. Subcellular localization and transcriptional self-activation experiments demonstrated that the five candidate TCP proteins were typical self-activating nuclear-localized transcription factors. Additionally, the transcriptome analysis of the bamboo shoot buds at different developmental stages helped to clarify the underlying functions of the TCP members during the growth of bamboo shoots. DlTCP12-C, significantly downregulated as the bamboo shoots developed, was selected to further verify its molecular function in Arabidopsis. The DlTCP12-C overexpressing lines exhibited a marked reduction in the number of rosettes and branches compared with the wild type in Arabidopsis, suggesting that DlTCP12-C conservatively inhibits lateral bud outgrowth and branching in plants. This study provides useful insights into the evolutionary patterns and molecular functions of the TCP transcription factors in Ma bamboo and provides a valuable reference for further research on the regulatory mechanism of bamboo shoot development and lateral bud growth.

Bulk RNA-Seq Analysis Reveals Differentially Expressed Genes Associated with Lateral Branch Angle in Peanut

Lateral branch angle (LBA), or branch habit, is one of the most important agronomic traits in peanut. To date, the underlying molecular mechanisms of LBA have not been elucidated in peanut. To acquire the differentially expressed genes (DEGs) related to LBA, a TI population was constructed through the hybridization of a bunch-type peanut variety Tifrunner and prostrate-type Ipadur. We report the identification of DEGs related to LBA by sequencing two RNA pools, which were composed of 45 F₃ lines showing an extreme opposite bunch and prostrate phenotype. We propose to name this approach Bulk RNA-sequencing (BR-seq) as applied to several plant species. Through BR-seq analysis, a total of 3083 differentially expressed genes (DEGs) were identified, including 13 gravitropism-related DEGs, 22 plant hormone-related DEGs, and 55 transcription factors-encoding DEGs. Furthermore, we also identified commonly expressed alternatively spliced (AS) transcripts, of which skipped exon (SE) and retained intron (RI) were most abundant in the prostrate and bunch-type peanut. AS isoforms between prostrate and bunch peanut highlighted important clues to further understand the post-transcriptional regulatory mechanisms of branch angle regulation. Our findings provide not only important insights into the landscape of the regulatory pathway involved in branch angle formation but also present practical information for peanut molecular breeding in the future.

The kinesin-13 protein BR HYPERSENSITIVE 1 is a negative brassinosteroid signaling component regulating rice growth and development

Phytohormones performed critical roles in regulating plant architecture and thus determine grain yield in rice. However, the roles of brassinosteroids (BRs) compared to other phytohormones in shaping rice architecture are less studied. In this study, we report that BR hypersensitive1 (BHS1) plays a negative role in BR signaling and regulate rice architecture. BHS1 encodes the kinesin-13a protein and regulates grain length. We found that bhs1 was hypersensitive to BR, while BHS1-overexpression was less sensitive to BR compare to WT. BHS1 was down-regulated at RNA and protein level upon exogenous BR treatment, and proteasome inhibitor MG132 delayed the BHS1 degradation, indicating that both the transcriptional and posttranscriptional regulation machineries are involved in BHS1-mediated regulation of plant growth and development. Furthermore, we found that the BR-induced degradation of BHS1 was attenuated in Osbri1 and Osbak1 mutants, but not in Osbzr1 and Oslic mutants. Together, these results suggest that BHS1 is a novel component which is involved in negative regulation of the BR signaling downstream player of BRI1.

The SINGLE FLOWER (SFL) gene encodes a MYB transcription factor that regulates the number of flowers produced by the inflorescence of chickpea

Legumes usually have compound inflorescences, where flowers/pods develop from secondary inflorescences (I2), formed laterally at the primary inflorescence (I1). Number of flowers per I2, characteristic of each legume species, has important ecological and evolutionary relevance as it determines diversity in inflorescence architecture; moreover, it is also agronomically important for its potential impact on yield. Nevertheless, the genetic network controlling the number of flowers per I2 is virtually unknown. Chickpea (Cicer arietinum) typically produces one flower per I2 but single flower (sfl) mutants produce two (double-pod phenotype). We isolated the SFL gene by mapping the sfl-d mutation and identifying and characterising a second mutant allele. We analysed the effect of sfl on chickpea inflorescence ontogeny with scanning electron microscopy and studied the expression of SFL and meristem identity genes by RNA in situ hybridisation. We show that SFL corresponds to CaRAX1/2a, which codes a MYB transcription factor specifically expressed in the I2 meristem. Our findings reveal SFL as a central factor controlling chickpea inflorescence architecture, acting in the I2 meristem to regulate the length of the period for which it remains active, and therefore determining the number of floral meristems that it can produce.