Transcriptomic comparison reveals genetic variation potentially underlying seed developmental evolution of soybeans

Soybean (Glycine max) was domesticated from its wild relative Glycine soja. However, the genetic variations underlying soybean domestication are not well known. Comparative transcriptomics revealed that a small portion of the orthologous genes might have been fast evolving. In contrast, three gene expression clusters were identified as divergent by their expression patterns, which occupied 37.44% of the total genes, hinting at an essential role for gene expression alteration in soybean domestication. Moreover, the most divergent stage in gene expression between wild and cultivated soybeans occurred during seed development around the cotyledon stage (15 d after fertilization, G15). A module in which the co-expressed genes were significantly down-regulated at G15 of wild soybeans was identified. The divergent clusters and modules included substantial differentially expressed genes (DEGs) between wild and cultivated soybeans related to cell division, storage compound accumulation, hormone response, and seed maturation processes. Chromosomal-linked DEGs, quantitative trait loci controlling seed weight and oil content, and selection sweeps revealed candidate DEGs at G15 in the fruit-related divergence of G. max and G. soja. Our work establishes a transcriptomic selection mechanism for altering gene expression during soybean domestication, thus shedding light on the molecular networks underlying soybean seed development and breeding strategy

Genome Survey and Chromosome-Level Draft Genome Assembly of <i>Glycine max</i> var. Dongfudou 3: Insights into Genome Characteristics and Protein Deficiencies

Dongfudou 3 is a highly sought-after soybean variety due to its lack of beany flavor. To support molecular breeding efforts, we conducted a genomic survey using next-generation sequencing. We determined the genome size, complexity, and characteristics of Dongfudou 3. Furthermore, we constructed a chromosome-level draft genome and speculated on the molecular basis of protein deficiency in GmLOX1, GmLOX2, and GmLOX3. These findings set the stage for high-quality genome analysis using third-generation sequencing. The estimated genome size is approximately 1.07 Gb, with repetitive sequences accounting for 72.50%. The genome is homozygous and devoid of microbial contamination. The draft genome consists of 916.00 Mb anchored onto 20 chromosomes, with annotations of 46,446 genes and 77,391 transcripts, achieving Benchmarking Single-Copy Orthologue (BUSCO) completeness of 99.5% for genome completeness and 99.1% for annotation. Deletions and substitutions were identified in the three GmLox genes, and they also lack corresponding active proteins. Our proposed approach, involving k-mer analysis after filtering out organellar DNA sequences, is applicable to genome surveys of all plant species, allowing for accurate assessments of size and complexity. Moreover, the process of constructing chromosome-level draft genomes using closely related reference genomes offers cost-effective access to valuable information, maximizing data utilization

The Evaluation of Agronomic Traits of Wild Soybean Accessions (Glycine soja Sieb. and Zucc.) in Heilongjiang Province, China

Wild soybean germplasm is distributed widely in China, particularly in Heilongjiang Province. In this study, 242 wild soybean accessions from four agricultural divisions in Heilongjiang Province were evaluated based on six qualitative and eight quantitative traits. Results showed that a large amount of variation occurred in these evaluated traits. Abundant qualitative traits included the wild type (78.51%), purple flowers (90.50%), needle leaf (39.26%), black seed (83.88%), brown hilum (52.07%), and mud film (87.60). Results of multivariate analysis based on quantitative traits showed that 100-seed weight, seeds weight per plant, number of seeds per plant, number of effective pods, and number of invalid pods were significantly different among samples (p &lt; 0.05). A total of 27 germplasms were screened. Cluster analysis identified the 242 accessions into two groups, not following the geographical distribution pattern, with rich wild soybean resources revealed in the northern site. The present study indicated that wild soybean in Heilongjiang Province should be conserved in situ. The rich genetic diversity revealed in soybeans of different sites in Heilongjiang Province suggested its significant potential utilization in genetic improvement and breakthrough for soybean breeding. This information will help to exploit and conserve wild soybean accessions in Heilongjiang Province

Heterosis and combining ability estimates in isoflavone content using different parental soybean accessions: wild soybean, a valuable germplasm for soybean breeding.

Isoflavone, a group of secondary metabolites in soybean, is beneficial to human health. Improving isoflavone content in soybean seeds has become one of the most important breeding objectives. However, the narrow genetic base of soybean cultivars hampered crop improvement. Wild soybean is an extraordinarily important gene pool for soybean breeding. In order to select an optimal germplasm for breeding programs to increase isoflavone concentration, 36 F1 soybean progenies from different parental accessions (cultivars, wild, Semi-wild and Interspecific) with various total isoflavone (TIF) concentration (High, Middle, Low) were analyzed for their isoflavone content. Results showed that male parents, except for Cultivars, showed positive GCA effects. In particular, wild soybean had higher positive GCA effects for TIF concentration. Both MP and BP heterosis value declined in the hybrid in which male parents were wild soybean, semi-wild soybean, interspecific offspring and cultivar in turn. In general, combining ability and heterosis in hybrids which had relative higher TIF concentration level parents showed better performance than those which had lower TIF concentration level parents. These results indicated characteristics of isoflavone content were mainly governed by additive type of gene action, and wild relatives could be utilized for breeding of soybean cultivars with this trait. A promising combination was found as the best potential hybrid for isoflavone content improvement

Transcriptome analysis of strawberry (Fragaria × ananasa) responsive to Colletotrichum gloeosporioides inoculation and mining of resistance genes

AbstractStrawberry has high nutritional and economic value and is an important horticultural crop widely cultivated worldwide. Strawberry anthracnose is the most harmful disease in strawberry production, which causes huge production losses every year. Mining disease resistance genes and breeding high-quality strawberry varieties are the fundamental way to solve the problem of strawberry anthracnose. In this study, transcriptome analysis and disease resistance-related genes mining were targeted on strawberry anthracnose. The main results are as follows: (1) A total of 100.45 Gb clean reads were obtained, with no less than 6.26 Gb for each sample; (2) The clean reads for each sample were aligned to the reference genome efficiently at 91.30% − 92.27%; (3) 93,042 genes were annotated; (4) 16 anti-anthracnose-related genes were identified, including FaAUX1, FaARF18, FaSAUR50, FaGH3.6, FaAHP1, FaARR (3, 5 and 11), FaPYR1, FaPYL11, FaPP2C (6, 16, 24, 37 and 51) and FaPR1. The above results can provide theoretical guidance for the molecular breeding of disease resistance of strawberry

Average total isoflavone (TIF) concentration (μg/g) of hybrids gained by fifteen parents.

<p>Male parents were divided into four groups which are cultivars, wild, Semi-wild and Interspecific offspring based on plant taxonomy. Female parents comprised 3 lines each based on TIF concentration which is H (high), M (middle) and L (low). </p

Estimates of mid parents (MP) and better parent (BP) heterosis (%) for total isoflavone (TIF) concentration in 36 hybrids.

<p>Combinations were classified based on plant taxonomy of parents. C cultivars, W wild, S semi-wild, I interspecific offspring. </p

Transcriptome analysis of strawberry (<i>Fragaria</i> × <i>ananasa</i>) responsive to <i>Colletotrichum gloeosporioides</i> inoculation and mining of resistance genes

Strawberry has high nutritional and economic value and is an important horticultural crop widely cultivated worldwide. Strawberry anthracnose is the most harmful disease in strawberry production, which causes huge production losses every year. Mining disease resistance genes and breeding high-quality strawberry varieties are the fundamental way to solve the problem of strawberry anthracnose. In this study, transcriptome analysis and disease resistance-related genes mining were targeted on strawberry anthracnose. The main results are as follows: (1) A total of 100.45 Gb clean reads were obtained, with no less than 6.26 Gb for each sample; (2) The clean reads for each sample were aligned to the reference genome efficiently at 91.30% − 92.27%; (3) 93,042 genes were annotated; (4) 16 anti-anthracnose-related genes were identified, including FaAUX1, FaARF18, FaSAUR50, FaGH3.6, FaAHP1, FaARR (3, 5 and 11), FaPYR1, FaPYL11, FaPP2C (6, 16, 24, 37 and 51) and FaPR1. The above results can provide theoretical guidance for the molecular breeding of disease resistance of strawberry.</p

Long-Term Corn&ndash;Soybean Rotation and Soil Fertilization: Impacts on Yield and Agronomic Traits

Although crop rotations have been widely shown as an effective approach for improving yield or soil quality in the long term, the relationship between crop rotations and quality traits of crop or biochar-based fertilization is still unclear. To address this, we conducted a long-term field experiment in the Heilongjiang province of China to investigate the effects of crop rotation and biochar-based fertilizer application on the crop yield, soil parameters, crop quality, and agronomic traits in 2014&ndash;2020. The effects of rotations on crop production and soil properties were evaluated with the average yield variability during the 7 years of this study. Our results showed that the diversified corn and soybean rotations had a significant positive effect on average crop yield compared with their monocultures. The corn yield was enhanced by 0.6 Mg ha&minus;1 (5.4%) in the corn&ndash;soybean&ndash;corn (CSC) crop sequence compared with monoculture corn. Similarly, soybean yield was enhanced by 0.21 Mg ha&minus;1 (9.7%) in the soybean&ndash;corn&ndash;corn (SCC) crop sequence compared with monoculture soybean. However, a negative effect of crop rotations was detected on the protein content of soybean compared with the monoculture soybean, while a positive effect was detected on oil content. Additionally, no differences were detected in crop yield between biochar-based fertilization and mineral fertilization treatments, but a significant positive effect of biochar-based fertilization was observed for any crop on both protein and oil content. A significant effect of crop rotation was found on the percentage of total soil N (TN), available soil N (AN), and available soil K (AK) content. The SSS crop sequence treatment illustrated the highest TN values at 0.18%. The CCC crop sequence treatment increased AN and AK content by 9.1% and 7.8%, respectively, compared with SSS (p &lt; 0.05). We conclude that crop rotations increase crop yield and biochar-based fertilizer application, improving crop quality traits in the long term. Thus, the addition of biochar-based fertilizer could efficiently enhance the yield and quality of crop in the rotation cropping system. The findings of this study may provide useful information for designing sustainable cropping systems based on rotations