Theoretical and Applied Genetics最新文献

Key message: The AP2/ERF transcription factor CaERF2 in pepper enhanced salt tolerance by scavenging reactive oxygen species. The effects of salt stress on plant development and progression are substantial. Ethylene response factor transcription factors (TFs) play a crucial role in responses to salt stress. Their functions in the salt response, particularly in pepper, are still mostly unknown. This study revealed the function of CaERF2 in salt tolerance of pepper plants. CaERF2 expression was dramatically increased in pepper plants following salt stress treatment. Under salinity treatment, CaERF2-silenced pepper showed decreased activities of superoxide dismutase (SOD), catalase (CAT), and peroxidase (POD), as well as reduced transcription levels of reactive oxygen species (ROS) scavenging-related genes, resulting in increased O^2- and H₂O₂ accumulation and enhanced salt sensitivity. In contrast, overexpression of CaERF2 (OE) in Nicotiana benthamiana resulted in improved salt tolerance. Under salt stress, the OE lines outperformed the wild type in terms of seed germination rates, root lengths, the activity of SOD, POD, and CAT, and ROS-scavenging-related gene transcription. This study demonstrates that CaERF2 effectively enhances the salt tolerance in pepper by adjusting ROS homeostasis. This finding offers fresh perspectives on the significance of plant ERF2 and key candidate genes in the molecular breeding of salt-tolerant crops.

Key message: A major QTL for sucrose content was mapped on chromosome 8 in PI 506593. The novel genetic variants and candidate genes were further identified within the major QTL. Sucrose in soybean [Glycine max (L.) Merr.] contribute to animal feed efficiency and natural sweetness of soy products. Thus, identifying novel genetic resources, such as quantitative trait loci (QTL), associated with sucrose content in soybean is essential for enhancing seed values. In this study, two recombinant inbred line populations derived from the same high sucrose donor parent, PI 506593, were used to identify significant QTLs. A total of 11 sucrose-related regions on chromosomes (Chrs.) 4, 5, 6, 8, 10, and 13 were identified using QTL analysis. Among them, four QTLs (qSUC_08.1, qSUC_08.2, qSUC_08.3, and qSUC_08.4) were clustered in the interval of 40,597,410-42,861,364 bp on Chr. 8, which was considered major QTL region. A desirable marker at 41,834,095 bp was tested in two populations, showing that two phenotypically extreme groups were efficiently differentiated. We further identified 44 and 54 candidate genes with non-synonymous mutations in the major QTL region based on the annotations of Wm82.a2.v1 and Wm82.a5.v1 assemblies, respectively. Among 54 candidate genes from Wm82.a5.v1, Protein Variation Effect Analyzer (PROVEAN) revealed that 18 genes contained 34 variants that had deleterious impacts on biological functions. RNA-seq analysis highlighted five candidate genes that were highly expressed in pod and seed tissues during reproductive stages and other plant parts. A gene, Gm_Wm82_23219 (Glyma.08G293800, Wm82.a2.v1) encoding proline-rich protein 4-like, was highlighted in both PROVEAN and RNA-seq analyses. Novel findings in this study will be valuable genetic resources in soybean breeding programs that aim to improve efficiency in animal feed and human food.

Key message: Improving a hybrid by transferring partially dominant alleles from one parent to the other is feasible if the median level of dominance is moderate and prediction accuracy is high. Convergent improvement within a P₁ × P₂ single-cross hybrid attempts to transfer partially dominant favorable alleles from P₁ to P₂ and from P₂ to P₁. My objective in this simulation study was to determine if convergent improvement is a feasible procedure to develop a better single cross. Heterozygote effects (d) and homozygote effects (a) at quantitative trait loci (QTL) were resampled from an empirical distribution of genomewide marker estimates of d and a for maize (Zea mays L.) grain yield. The d values were scaled (d scale = 30%, 45%, and 60%) to account for the known upward bias when d/a ratios at markers are used to estimate d/a ratios at QTL. Convergent improvement led to positive responses to selection when only 30 QTL controlled the trait. When 250 QTL controlled the trait, convergent improvement led to a positive response when the d scale was 30% but not when the d scale was 60%. For the intermediate d scale of 45%, responses were positive in later backcross generations and when prediction accuracy was 0.60 or 0.80. The largest response was achieved with only one cycle of genomewide recurrent selection; additional cycles compromised the gains achieved from the final step of phenotypic selection among single crosses. Overall, the results suggested that success in convergent improvement is a possibility but not a certainty in maize, and that more consistent results would be expected in species such as rice (Oryza sativa L.) that show weaker heterosis than maize.

Key message: The location of alien chromatin in Xiaoyan 6 was identified using mc-GISH analysis, genetic mapping and whole genome re-sequencing, and its possible origin was discussed. As a founder parent, Xiaoyan 6 has played an important role in distant hybridization breeding in China. Although it came from the cross between common wheat and Thinopyrum ponticum (Podp.) Barkworth and D.R. Dewey, the location of its alien chromatin has not been determined using traditional genomic in situ hybridization (GISH). In the present study, chromosome variation in Xiaoyan 6 was discovered by multicolor GISH analysis. Four alien-specific markers were developed by specific-locus amplified fragment sequencing technique. Their amplified sequences were analyzed by basic local alignment search tool with the reference genome sequences of common wheat Chinese Spring (CS) and Th. elongatum, and the whole genome re-sequencing reads of Th. ponticum and CS. Furthermore, the four markers were mapped on three different chromosomes in two RIL populations. By dissecting the mapped reads depth of the whole genome re-sequencing of Xiaoyan 6, we found that the depth of nine chromosome regions was obviously lower than the average. Among these, three regions on 1A, 3A and 7B were demonstrated as the alien introgressions in Xiaoyan 6 by multiple methods. Finally, the genetic transmission of the alien chromatin was analyzed in a set of wheat-Th. ponticum introgression lines. Some stable QTLs for morphological and physiological traits have been mapped near the alien chromatin.

Anthocyanins not only serve as critical pigments determining floral hues but also play essential roles in attracting insects for pollination, feeding animals and mitigating abiotic stress. However, the molecular mechanisms underlying the regulation of flower color in sesame has not yet been reported. In this study, an F₂ population was constructed by crossing 'Ganzhi 9' (purple-flowered) with 'BS377' (white-flowered). Genetic analysis revealed that purple flower is controlled by a single locus named as SiFC (Sesamum indicum flower color). Using the BSA-seq approach, SiFC was preliminarily identified on chromosome 6, which was further mapped to a 473 kb interval using Kompetitive Allele Specific PCR (KASP) marker analysis. Moreover, functional annotation, expression profiling, and sequence analyses confirmed that the SibHLHA (Sesame10992) was the most likely candidate gene for SiFC. In addition, SibHLHA, highly homologous to AtTT8 (a key regulator in the anthocyanin synthesis pathway), was found to interact with WER-like or TTG1 proteins, enhancing anthocyanin accumulation in tobacco leaves. Furthermore, an SNP in the second exon of Sibhlha (BS377 variant) was found to alter the encoding amino acids, which affected Sibhlha binding to MYB protein and showed low anthocyanin in tobacco leaves compared with SibHLHA binding with WER-like or TTG1 proteins. These findings not only deepen our understanding of the molecular mechanisms controlling sesame corolla color, but also provide valuable insights for developing ornamental and consumable sesame varieties.

The tiller angle, one of the critical factors that determine the rice plant type, is closely related to rice yield. An appropriate rice tiller angle can improve rice photosynthetic efficiency and increase yields. In this study, we identified a transcription factor, TILLRE ANGLE CONTROL 8 (TAC8), that is highly expressed in the rice tiller base and positively regulates the tiller angle by regulating cell length and endogenous auxin content; TAC8 encodes a TEOSINTE BRANCHED1/CYCLOIDEA/PCF transcriptional activator that is highly expressed in the nucleus. RNA-seq revealed that TAC8 is involved mainly in the photoperiod and abiotic stress response in rice. Yeast two-hybrid assays verified that TAC8 interacts with CHLOROPHYLL A/B-BINDING PROTEIN 1, which responds to photoperiod, and haplotype analysis revealed that a 34-bp deletion at position 1516 in the promoter region and a 9-bp deletion at position 153 in the coding region can result in impaired function or loss of function of TAC8. This study provides a new genetic resource for designing ideal plant types with appropriate rice tiller angle.

Key message: Loss-of-function mutations induced by CRISPR-Cas9 in the TaGS3 gene homoeologs show non-additive dosage-dependent effects on grain size and weight and have potential utility for increasing grain yield in wheat. The grain size in cereals is one of the component traits contributing to yield. Previous studies showed that loss-of-function (LOF) mutations in GS3, encoding Gγ subunit of the multimeric G protein complex, increase grain size and weight in rice. While an association between allelic variation in the GS3 homologs of wheat and grain weight/size has been detected previously, the effects of LOF alleles at TaGS3 on these traits remain unknown. We used genome editing to create TaGS3 mutant lines with varying LOF homeo-allele dosages. Contrary to the results obtained in rice, editing all three TaGS3 homoeologous copies resulted in a significant decrease in grain length (4.4%), width (3.4%), grain area (7.3%) and weight (7.5%), without affecting the number of grains per spike. Compared to the wild type, the highest increase in grain weight (up to 9.6%) and area (up to 5.0%) was observed in homozygous mutants with one or two genomes carrying LOF homeo-alleles, suggesting non-additive suppressive effects of TaGS3 on grain size and weight in wheat. Our results suggest that the regulatory effects of GS3 homologs in wheat and rice have diverged. The newly developed LOF homeo-alleles of TaGS3 expand the set of CRISPR-Cas9-induced variants of yield component genes that have potential to increase grain weight in wheat.

Key message: BrCYP71 encoding multifunctional oxidase was mapped using BSA-Seq and linkage analysis, and its function in stay-green of pak choi was verified through Arabidopsis heterologous transgenic experiment. Stay-green refers to the phenomenon that plant leaves remain green during senescence and even after death, which is of great significance for improving the commerciality of leafy vegetables during storage or transportation and extending their shelf life. In this study, we identified a stay-green mutant of pak choi and named it nye2. Genetic analysis showed that the stay-green trait was controlled by a recessive nuclear gene. We obtained a 550 kb candidate region on chromosome A03 using BSA-Seq and linkage analysis. In this interval, BraA03g049920.3.5C, named BrCYP71, was identified as a candidate gene using sequence variation analysis. BrCYP71 is an ortholog of Arabidopsis AT4G13290, which encodes a multifunctional oxidase. A 4 bp insertion from T to TGATC in the first exon of BrCPY71 in the mutant led to the formation of a stop codon, TAA. Ectopic overexpression of BrCYP71 in Arabidopsis cyp71 could restored the wild-type phenotype. These results indicate that BrCYP71 contributes to the stay-green of nye2. The expression levels of chlorophyll catabolism-related genes in nye2 were significantly reduced compared to those in the wild-type, suggesting that BrCPY71 affected chlorophyll catabolism. Our achievement provides a novel genetic resource for breeding the stay-green varieties of Brassica rapa.

Cotton is an important crop for fiber production, but the genetic basis underlying key agronomic traits, such as fiber quality and flowering days, remains complex. While machine learning (ML) has shown great potential in uncovering the genetic architecture of complex traits in other crops, its application in cotton has been limited. Here, we applied five machine learning models-AdaBoost, Gradient Boosting Regressor, LightGBM, Random Forest, and XGBoost-to identify loci associated with fiber quality and flowering days in cotton. We compared two SNP dataset down-sampling methods for model training and found that selecting SNPs with an Fscale value greater than 0 outperformed randomly selected SNPs in terms of model accuracy. We further performed machine learning quantitative trait loci (mlQTLs) analysis for 13 traits related to fiber quality and flowering days. These mlQTLs were then compared to those identified through genome-wide association studies (GWAS), revealing that the machine learning approach not only confirmed known loci but also identified novel QTLs. Additionally, we evaluated the effect of population size on model accuracy and found that larger population sizes resulted in better predictive performance. Finally, we proposed candidate genes for the identified mlQTLs, including two argonaute 5 proteins, Gh_A09G104100 and Gh_A09G104400, for the FL3/FS2 locus, as well as GhFLA17 and Syntaxin-121 (Gh_D09G143700) for the FSD09_2/FED09_2 locus. Our findings demonstrate the efficacy of machine learning in enhancing the identification of genetic loci in cotton, providing valuable insights for improving cotton breeding strategies.

Complex traits influenced by multiple genes pose challenges for marker-assisted selection (MAS) in breeding. Genomic selection (GS) is a promising strategy for achieving higher genetic gains in quantitative traits by stacking favorable alleles into elite cultivars. Resistance to Fusarium oxysporum f. sp. niveum (Fon) race 2 in watermelon is a polygenic trait with moderate heritability. This study evaluated GS as an additional approach to quantitative trait loci (QTL) analysis/marker-assisted selection (MAS) for enhancing Fon race 2 resistance in elite watermelon cultivars. Objectives were to: (1) assess the accuracy of genomic prediction (GP) models for predicting Fon race 2 resistance in a F_2:3 versus a recombinant inbred line (RIL) population, (2) rank and select families in each population based on genomic estimated breeding values (GEBVs) for developing testing populations, and (3) determined how many of the most superior families based on GEBV also have all QTL associated with Fon race 2 resistance. GBS-SNP data from genotyping-by-sequencing (GBS) for two populations were used, and parental line genome sequences were used as references. The GBLUP and random forest outperformed the other three parametric (GBLUP, Bayes B, Bayes LASSO) and three nonparametric AI (random forest, SVM linear, and SVM radial) models, with correlations of 0.48 and 0.68 in the F_2:3 and RIL population, respectively. Selection intensities (SI) of 10%, 20%, and 30% showed that superior families with highest GEBV can also comprise all QTL associated with Fon race 2 resistance, highlighting GP efficacy in improving elite watermelon cultivars with polygenic traits of disease resistance.