Crop Journal最新文献

Automatic collecting of phenotypic information from plants has become a trend in breeding and smart agriculture. Targeting mature soybean plants at the harvesting stage, which are dense and overlapping, we have proposed the SPP-extractor (soybean plant phenotype extractor) algorithm to acquire phenotypic traits. First, to address the mutual occultation of pods, we augmented the standard YOLOv5s model for target detection with an additional attention mechanism. The resulting model could accurately identify pods and stems and could count the entire pod set of a plant in a single scan. Second, considering that mature branches are usually bent and covered with pods, we designed a branch recognition and measurement module combining image processing, target detection, semantic segmentation, and heuristic search. Experimental results on real plants showed that SPP-extractor achieved respective $R^2$ scores of 0.93–0.99 for four phenotypic traits, based on regression on manual measurements.

Stripe rust, caused by Puccinia striiformis f. sp. tritici (Pst), threatens wheat production worldwide, and resistant varieties tend to become susceptible after a period of cultivation owing to the variation of pathogen races. In this study, a new resistance gene against Pst race CYR34 was identified and predicted using the descendants of a cross between AS1676, a highly resistant Chinese landrace, and Avocet S, a susceptible cultivar. From a heterozygous plant from a F₇ recombinant inbred line (RIL) population lacking the Yr18 gene, a near-isogenic line (NIL) population was developed to map the resistance gene. An all-stage resistance gene, YrAS1676, was identified on chromosome arm 1AL via bulked-segregant exome-capture sequencing. By analyzing a large NIL population consisting of 6537 plants, the gene was further mapped to the marker interval between KA1A_485.36 and KA1A_490.13, spanning 485.36–490.13 Mb on 1AL. A total of 66 annotated genes have been reported in this region. To characterize and predict the candidate gene(s), an RNA-seq was performed using NIL-R and NIL-S seedlings 3 days after CYR34 inoculation. Compared to NIL-S plants, NIL-R plants showed stronger immune reaction and higher expression levels of genes encoding pathogenesis-associated proteins. These differences may help to explain why NIL-R plants were more resistant to Pst race CYR34 than NIL-S plants. By combining fine-mapping and transcriptome sequencing, a calcium-dependent protein kinase gene was finally predicted as the potential candidate gene of YrAS1676. This gene contained a single-nucleotide polymorphism. The candidate gene was more highly expressed in NIL-R than in NIL-S plants. In field experiments with Pst challenge, the YrAS1676 genotype showed mitigation of disease damage and yield loss without adverse effects on tested agronomic traits. These results suggest that YrAS1676 has potential use in wheat stripe rust resistance breeding.

Puccinia triticina (Pt), as the causal agent of wheat leaf rust, employs a plethora of effector proteins to modulate wheat immunity for successful colonization. Understanding the molecular mechanisms underlying Pt effector-mediated wheat susceptibility remains largely unexplored. In this study, an effector Pt_21 was identified to interact with the apoplast-localized wheat thaumatin-like protein TaTLP1 using a yeast two-hybrid assay and the Pt_21-TaTLP1 interaction was characterized. The interaction between Pt_21 and TaTLP1 was validated by in vivo co-immunoprecipitation assay. A TaTLP1 variant, TaTLP1^C71A, that was identified by the site-directed mutagenesis failed to interact with Pt_21. Pt_21 was able to suppress Bax-mediated cell death in leaves of Nicotiana benthamiana and inhibit TaTLP1-mediated antifungal activity. Furthermore, infiltration of recombinant protein Pt_21 into leaves of transgenic wheat line overexpressing TaTLP1 enhanced the disease development of leaf rust compared to that in wild-type leaves. These findings demonstrate that Pt_21 suppresses host defense response by directly targeting wheat TaTLP1 and inhibiting its antifungal activity, which broadens our understanding of the molecular mechanisms underlying Pt effector-mediated susceptibility in wheat.

Physical dormancy (PY) commonly present in the seeds of higher plants is believed to be responsible for the germination failure by impermeable seed coat in hard seeds of legume species, instead of physiological dormancy (PD). In this study, a non-destructive approach involving multispectral imaging was used to successfully identify hard seeds from non-hard seeds in Medicago sativa, with accuracy as high as 96.8%–99.0%. We further adopted multiple-omics strategies to investigate the differences of physiology, metabolomics, methylomics, and transcriptomics in alfalfa hard seeds, with non-hard seeds as control. The hard seeds showed dramatically increased antioxidants and 125 metabolites of significant differences in non-targeted metabolomics analysis, which are enriched in the biosynthesis pathways of flavonoids, lipids and hormones, especially with significantly higher ABA, a hormone known to induce dormancy. In our transcriptomics results, the enrichment pathway of “response to abscisic acid” of differential expressed genes (DEG) supported the key role of ABA in metabolomics results. The methylome analysis identified 54,899, 46,216 and 54,452 differential methylation regions for contexts of CpG, CHG and CHH, and 344 DEGs might be regulated by hypermethylation and hypomethylation of promoter and exon regions, including four ABA- and JA-responsive genes. Among 8% hard seeds in seed lots, 24.5% still did not germinate after scarifying seed coat, and were named as non-PY hard seeds. Compared to hard seeds, significantly higher contents of ABA/IAA and ABA/JA were identified in non-PY hard seeds, which indicated the potential presence of PD. In summary, the significantly changed metabolites, gene expressions, and methylations all suggested involvement of ABA responses in hard seeds, and germination failure of alfalfa hard seeds was caused by combinational dormancy (PY + PD), rather than PY alone.

Although a few cases of genetic epistasis in plants have been reported, the combined analysis of genetically phenotypic segregation and the related molecular mechanism remains rarely studied. Here, we have identified a gene (named GaPC) controlling petal coloration in Gossypium arboreum and following a heritable recessive epistatic genetic model. Petal coloration is controlled by a single dominant gene, GaPC. A loss-of-function mutation of GaPC leads to a recessive gene Gapc that masks the phenotype of other color genes and shows recessive epistatic interactions. Map-based cloning showed that GaPC encodes an R2R3-MYB transcription factor. A 4814-bp long terminal repeat retrotransposon insertion at the second exon led to GaPC loss of function and disabled petal coloration. GaPC controlled petal coloration by regulating the anthocyanin and flavone biosynthesis pathways. Expression of core genes in the phenylpropanoid and anthocyanin pathways was higher in colored than in white petals. Petal color was conferred by flavonoids and anthocyanins, with red and yellow petals rich in anthocyanin and flavonol glycosides, respectively. This study provides new insight on molecular mechanism of recessive epistasis, also has potential breeding value by engineering GaPC to develop colored petals or fibers for multi-functional utilization of cotton.

As a natural genetic reservoir, wild rice contains many favorable alleles and mutations conferring high yield and resistance to biotic and abiotic stresses. However, there are few reports describing favorable genes or QTL from the AA genome wild rice O. longistaminata, which is characterized by tall and robust habit and long tassels and anthers and shows high potential for use in cultivated rice improvement. We constructed a stable BC₂F₂₀ backcross inbred line (BIL) population of 152 lines from the cross of 9311 × O. longistaminat. Some BILs showed large panicles, large seeds, and strong resistance to rice false smut, bacterial leaf blight, rice blast spot, and brown planthopper. Genomic resequencing showed that the 152 BILs covered about 99.6% of the O. longistaminata genome. QTL mapping with 2432 bin markers revealed 13 QTL associated with seven yield traits and eight with resistance to brown planthopper and to four diseases. Of these QTL, 12 for grain yield and 11 for pest and disease resistance are novel in Oryza species. A large-panicle NIL1880 line containing QTL qPB8.1 showed a nearly 50% increase in spikelet number and 27.5% in grain yield compared to the recurrent parent 9311. These findings support the potential value of O. longistaminata for cultivated rice improvement.

Sorghum (Sorghum bicolor (L.) Moench) is a major world crop that is a reliable source of fodder and food grain in arid regions. However, unlike other cereals, sorghum grain has low nutritional value, owing mainly to the resistance of its storage proteins (kafirins) to protease digestion. Changing the composition of kafirins or their primary structure may address this problem. To induce mutations in kafirin-encoding genes that were expected to disturb their accumulation in endosperm cells, we used a genome-editing approach. By Agrobacterium-mediated genetic transformation of immature embryos of cv. Avans, we obtained 14 transgenic plants with genetic constructs for site-directed mutagenesis of the k1C5 and gKAF1 genes encoding 22 kDa α- and 28 kDa γ-kafirins, respectively. Sequencing of 5 regenerants obtained by using k1C5-addressing vector revealed two plants with mutations. T₁ progeny of these mutants had higher in vitro digestibility of endosperm proteins (86%–92%), in comparison with the donor Avans (63%–67%). The kernels of these plants had a thick vitreous endosperm. A mutant with increased in vitro protein digestibility and vitreous endosperm, carrying a mutation in the target sequence, was also obtained by use of the gKAF1-addressing vector. Thus, using genome editing technology, we have obtained mutants with improved kafirin digestibility that can be used in sorghum breeding.

Lesion mimic mutants (LMMs) are advantageous materials for studying programmed cell death (PCD). Although some rice LMM genes have been cloned, the diversity of functions of these genes indicates that the mechanism of cell death regulation in LMMs needs further study. In this study, we identified a rice light-dependent leaf lesion mimic mutant 4 (llm4) that showed abnormal chloroplast structure, photoinhibition, reduced photosynthetic protein levels, massive accumulation of reactive oxygen species (ROS), and PCD. Map-based cloning and complementation testing revealed that LLM4 encodes zeaxanthin epoxidase (ZEP), an enzyme involved in the xanthophyll cycle, which functions in plant photoprotection, ROS scavenging, and carotenoid and abscisic acid (ABA) biosynthesis. The ABA content was decreased, and the contents of 24 carotenoids differed between the llm4 mutant and the wild type (WT). The llm4 mutant showed reduced dormancy and greater sensitive to ABA than the WT. We concluded that the mutation of LLM4 resulted in the failure of xanthophyll cycle, in turn causing ROS accumulation. The excessive ROS accumulation damaged chloroplast structure and induced PCD, leading eventually to the formation of lesion mimics.

Drought stress impairs plant growth and other physiological functions. MeHDZ14, a homeodomain-leucine zipper I transcription factor, is strongly induced by drought stress in various cassava cultivars. However, the role of MeHDZ14 in cassava growth regulation has remained unclear. Here we report that MeHDZ14 affected plant height, such that a dwarf phenotype and altered internode elongation were observed in transgenic cassava lines. MeHDZ14 was found to negatively regulate the biosynthesis of lignin. Its overexpression resulted in abaxially rolled leaves. The morphogenesis of leaf epidermal cells was inhibited by overexpression of MeHDZ14, with decreased auxin and gibberellin and increased cytokinin contents. MeHDZ14 was found to regulate many drought-responsive genes, including genes involved in cell wall synthesis and expansion. MeHDZ14 bound to the promoter of caffeic acid 3-O-methyltransferase 1 (MeCOMT1), acting as a transcriptional repressor of genes involved in cell wall development. MeHDZ14 appears to act as a negative regulator of internode elongation and epidermal cell morphogenesis during cassava leaf development.

Lignin is one of the main components of cell walls and is essential for resistance to insect pests in plants. Cotton plants are damaged by aphid (Aphis gossypii) worldwide but resistant breeding is undeveloped due to scarce knowledge on resistance genes and the mechanism. This study reported a lignin biosynthesis-related gene identified in the F₂ population derived from the cross between cotton cultivars Xinluzao 61 (resistant to aphid) and Xinluzao 50 (susceptible to aphid). A quantitative trait locus was mapped on chromosome D04 with a logarithm of odds (LOD) score of 5.99 and phenotypic effect of 27%. RNA-seq analysis of candidate intervals showed that the expression level of GH_D04G1418 was higher in the resistant cultivar than in the susceptible cultivar. This locus is close to AtLAC4 in the phylogenetic tree and contains a conserved laccase domain. Hence, it was designated GhLAC4-3. Silencing of GhLAC4-3 in Xinluzao 61 via virus-induced gene silencing (VIGS) resulted in decreased lignin content and increased susceptibility to aphids. These results suggest that GhLAC4-3 might enhance aphid resistance by regulating lignin biosynthesis in cotton.