MutL homolog 1 participates in interference-sensitive meiotic crossover formation in soybean.

MutL homolog 1 (MLH1), a member of the MutL-homolog family, is required for normal recombination in most organisms. However, its role in soybean (Glycine max) remains unclear to date. Here, we characterized the Glycine max female and male sterility 1 (Gmfms1) mutation that reduces pollen grain viability and increases embryo sac abortion in soybean. Map-based cloning revealed that the causal gene of Gmfms1 is Glycine max MutL homolog 1 (GmMLH1), and CRISPR/Cas9 knockout approach further validated that disruption of GmMLH1 confers the female-male sterility phenotype in soybean. Loss of GmMLH1 function disrupted bivalent formation, leading to univalent mis-segregation during meiosis and ultimately to female-male sterility. The Gmmlh1 mutant showed about a 78.16% decrease in meiotic crossover frequency compared to the wild type. The residual chiasmata followed a Poisson distribution, suggesting that interference-sensitive crossover formation was affected in the Gmmlh1 mutant. Furthermore, GmMLH1 could interact with GmMLH3A and GmMLH3B both in vivo and in vitro. Overall, our work demonstrates that GmMLH1 participates in interference-sensitive crossover formation in soybean, and provides additional information about the conserved functions of MLH1 across plant species.

Genetic Mapping of the Gmpgl3 Mutant Reveals the Function of GmTic110a in Soybean Chloroplast Development.

The generation of oxygen and organic matter in plants mainly depends on photosynthesis, which directly affects plant growth and development. The chloroplast is the main organelle in which photosynthesis occurs. In this study, a Glycine max pale green leaf 3-1 (Gmpgl3-1) mutant was isolated from the soybean mutagenized population. The Gmpgl3-1 mutant presented with decreased chlorophyll contents, reduced chloroplast stroma thylakoids, reduced yields, and decreased numbers of pods per plant. Bulked segregant analysis (BSA) together with map-based cloning revealed a single-nucleotide non-synonymous mutation at the 341st nucleotide of the first exon of the chloroplast development-related GmTic110a gene. The phenotype of the knockout plants was the same as that of the mutant. The GmTic110a gene was highly expressed in the leaves at various developmental stages, and its protein was localized to the inner chloroplast membrane. Split luciferase complementation assays and coimmunoprecipitation (co-IP) experiments revealed that GmTic110a interacted with GmTic20, GmTic40a, and GmTic40b in tobacco leaves. These results indicated that the GmTic110a gene plays an important role in chloroplast development.

Traits Expansion and Storage of Soybean Phenotypic Data in Computer Vision-Based Test.

Phenotypic traits of crops are an important basis for cultivating new crop varieties. Breeding experts expect to use artificial intelligence (AI) technology and obtain many accurate phenotypic data at a lower cost for the design of breeding programs. Computer vision (CV) has a higher resolution than human vision and has the potential to achieve large-scale, low-cost, and accurate analysis and identification of crop phenotypes. The existing criteria for investigating phenotypic traits are oriented to artificial species examination, among these are a few traits type that cannot meet the needs of machine learning even if the data are complete. Therefore, the research starts from the need to collect phenotypic data based on CV technology to expand, respectively, the four types of traits in the "Guide to Plant Variety Specificity, Consistency and Stability Testing: Soybean": main agronomic traits in field investigation, main agronomic traits in the indoor survey, resistance traits, and soybean seed phenotypic traits. This paper expounds on the role of the newly added phenotypic traits and shows the necessity of adding them with some instances. The expanded traits are important additions and improvements to the existing criteria. Databases containing expanded traits are important sources of data for Soybean AI Breeding Platforms. They are necessary to provide convenience for deep learning and support the experts to design accurate breeding programs.

GmPGL2, Encoding a Pentatricopeptide Repeat Protein, Is Essential for Chloroplast RNA Editing and Biogenesis in Soybean.

Chloroplast biogenesis and development are highly complex processes requiring interactions between plastids and nuclear genomic products. Pentatricopeptide repeat (PPR) proteins play an essential role in the development of chloroplasts; however, it remains unclear how RNA editing factors influence soybean development. In this study, a Glycine max pale green leaf 2 mutant (Gmpgl2) was identified with decreased chlorophyll contents. Genetic mapping revealed that a single-nucleotide deletion at position 1949 bp in the Glyma.05g132700 gene in the Gmpgl2 mutant, resulting in a truncated GmPGL2 protein. The nuclear-encoded GmPGL2 is a PLS-type PPR protein that localizes to the chloroplasts. The C-to-U editing efficiencies of rps16, rps18, ndhB, ndhD, ndhE, and ndhF were reduced in the Gmpgl2 mutant. RNA electrophoresis mobility shift assay (REMSA) analysis further revealed that GmPGL2 binds to the immediate upstream sequences at RNA editing sites of rps16 and ndhB in vitro, respectively. In addition, GmPGL2 was found to interact with GmMORF8, GmMORF9, and GmORRM6. These results suggest that GmPGL2 participates in C-to-U RNA editing via the formation of a complex RNA editosome in soybean chloroplasts.

Eight soybean reference genome resources from varying latitudes and agronomic traits.

Comparative analysis of multiple reference genomes representing diverse genetic backgrounds is critical for understanding the role of key alleles important in domestication and genetic breeding of important crops such as soybean. To enrich the genetic resources for soybean, we describe the generation, technical assessment, and preliminary genomic variation analysis of eight de novo reference-grade soybean genome assemblies from wild and cultivated accessions. These resources represent soybeans cultured at different latitudes and exhibiting different agronomical traits. Of these eight soybeans, five are from new accessions that have not been sequenced before. We demonstrate the usage of these genomes to identify small and large genomic variations affecting known genes as well as screening for genic PAV regions for identifying candidates for further functional studies.

GmNAP1 is essential for trichome and leaf epidermal cell development in soybean.

KEY MESSAGE: Map-based cloning revealed that two novel soybean distorted trichome mutants were due to loss function of GmNAP1 gene, which affected the trichome morphology and pavement cell ploidy by regulating actin filament assembly. Trichomes increase both biotic and abiotic stress resistance in soybean. In this study, Gmdtm1-1 and Gmdtm1-2 mutants with shorter trichomes and bigger epidermal pavement cells were isolated from an ethyl methylsulfonate mutagenized population. Both of them had reduced plant height and smaller seeds. Map-based cloning and bulked segregant analysis identified that a G-A transition at the 3' boundary of the sixth intron of Glyma.20G019300 in the Gmdtm1-1 mutant and another G-A transition mutation at the 5' boundary of the fourteenth intron of Glyma.20G019300 in Gmdtm1-2; these mutations disrupted spliceosome recognition sites creating truncated proteins. Glyma.20G019300 encodes a Glycine max NCK-associated protein 1 homolog (GmNAP1) in soybean. Further analysis revealed that the GmNAP1 involved in actin filament assembling and genetic information processing pathways during trichome and pavement cell development. This study shows that GmNAP1 plays an important role in soybean growth and development and agronomic traits.

GmPGL1, a Thiamine Thiazole Synthase, Is Required for the Biosynthesis of Thiamine in Soybean.

Thiamine is an essential cofactor in several enzymatic reactions for all living organisms. Animals cannot synthesize thiamine and depend on their diet. Enhancing the content of thiamine is one of the most important goals of plant breeding to solve the thiamine deficiency associated with the low-thiamin staple crops. In this study, a Glycine max pale green leaf 1 (Gmpgl1) mutant was isolated from the EMS mutagenized population of soybean cultivar, Williams 82. Map-based cloning of the GmPGL1 locus revealed a single nucleotide deletion at the 292th nucleotide residue of the first exon of Glyma.10g251500 gene in Gmpgl1 mutant plant, encoding a thiamine thiazole synthase. Total thiamine contents decreased in both seedlings and seeds of the Gmpgl1 mutant. Exogenous application of thiazole restored the pale green leaf phenotype of the mutant. The deficiency of thiamine in Gmpgl1 mutant led to reduced activities of the pyruvate dehydrogenase (PDH) and pyruvate decarboxylase (PDC), and decreased contents of six amino acids as compared to that in the wild type plants. These results revealed that GmPGL1 played an essential role in thiamine thiazole biosynthesis.

The Soybean Laccase Gene Family: Evolution and Possible Roles in Plant Defense and Stem Strength Selection.

Laccase is a widely used industrial oxidase for food processing, dye synthesis, paper making, and pollution remediation. At present, laccases used by industries come mainly from fungi. Plants contain numerous genes encoding laccase enzymes that show properties which are distinct from that of the fungal laccases. These plant-specific laccases may have better potential for industrial purposes. The aim of this work was to conduct a genome-wide search for the soybean laccase genes and analyze their characteristics and specific functions. A total of 93 putative laccase genes (GmLac) were identified from the soybean genome. All 93 GmLac enzymes contain three typical Cu-oxidase domains, and they were classified into five groups based on phylogenetic analysis. Although adjacent members on the tree showed highly similar exon/intron organization and motif composition, there were differences among the members within a class for both conserved and differentiated functions. Based on the expression patterns, some members of laccase were expressed in specific tissues/organs, while some exhibited a constitutive expression pattern. Analysis of the transcriptome revealed that some laccase genes might be involved in providing resistance to oomycetes. Analysis of the selective pressures acting on the laccase gene family in the process of soybean domestication revealed that 10 genes could have been under artificial selection during the domestication process. Four of these genes may have contributed to the transition of the soft and thin stem of wild soybean species into strong, thick, and erect stems of the cultivated soybean species. Our study provides a foundation for future functional studies of the soybean laccase gene family.

Evolution and Expression Divergence of the CYP78A Subfamily Genes in Soybean.

Gene expression divergence is an important evolutionary driving force for the retention of duplicate genes. In this study, we identified three CYP78A subfamily genes in soybean, GmCYP78A70, GmCYP78A57 and GmCYP78A72, which experienced different duplication events. GmCYP78A70 was mainly expressed in leaf tissue and the vegetative phase, whereas GmCYP78A57 was mainly expressed in floral tissue and seed, i.e., the reproductive phase. Expression of GmCYP78A72 could be detected in all the tissues and phases mentioned above. The expression levels of GmCYP78A70 and GmCYP78A57 in different soybean cultivars showed positive correlations with leaf size and 100-seed weight, respectively. The population genetics analysis indicated that the three genes had experienced different selective pressures during domestication and improved breeding of soybean. Deciphering the function of this subfamily of genes may well prove useful to breeders for improving soybean's agronomic traits.

GmILPA1, Encoding an APC8-like Protein, Controls Leaf Petiole Angle in Soybean.

Leaf petiole angle (LPA) is an important plant architectural trait that affects canopy coverage, photosynthetic efficiency, and ultimately productivity in many legume crops. However, the genetic basis underlying this trait remains unclear. Here, we report the identification, isolation, and functional characterization of Glycine max Increased Leaf Petiole Angle1 (GmILPA1), a gene encoding an APC8-like protein, which is a subunit of the anaphase-promoting complex/cyclosome in soybean (Glycine max). A gamma ray-induced deletion of a fragment involving the fourth exon of GmILPA1 and its flanking sequences led to extension of the third exon and formation of, to our knowledge, a novel 3'UTR from intronic and intergenic sequences. Such changes are responsible for enlarged LPAs that are associated with reduced motor cell proliferation in the Gmilpa1 mutant. GmILPA1 is mainly expressed in the basal cells of leaf primordia and appears to function by promoting cell growth and division of the pulvinus that is critical for its establishment. GmILPA1 directly interacts with GmAPC13a as part of the putative anaphase-promoting complex. GmILPA1 exhibits variable expression levels among varieties with different degrees of LPAs, and expression levels are correlated with the degrees of the LPAs. Together, these observations revealed a genetic mechanism modulating the plant petiole angle that could pave the way for modifying soybean plant architecture with optimized petiole angles for enhanced yield potential.

Genetic analysis and QTL detection of reproductive period and post-flowering photoperiod responses in soybean.

Reproductive period (RP) is an important trait of soybean [Glycine max (L.) Merr.] It is closely related to yield, quality and tolerances to environmental stresses. To investigate the inheritance and photoperiod response of RP in soybean, the F(1), F(2), and F(2:3) populations derived from nine crosses were developed. The inheritance of RP was analyzed through the joint segregation analysis. It was shown that the RP was controlled by one major gene plus polygenes. 181 recombinant inbred lines (RILs) generated from the cross of Xuyong Hongdou × Baohexuan 3 were further used for QTL mapping of RP under normal conditions across 3 environments, using 127 SSR markers. Four QTLs, designated qRP-c-1, qRP-g-1, qRP-m-1 and qRP-m-2, were mapped on C1, G and M linkage groups, respectively. The QTL qRP-c-1 on the linkage group C1 showed stable effect across environments and explained 25.6, 27.5 and 21.4% of the phenotypic variance in Nanjing 2002, Beijing 2003 and Beijing 2004, respectively. Under photoperiod-controlled conditions, qRP-c-1, and two different QTLs designated qRP-l-1 and qRP-o-1, respectively, were mapped on the linkage groups L and O. qRP-o-1 was detected under SD condition and can explained 10.70% of the phenotypic variance. qRP-c-1 and qRP-l-1 were detected under LD condition and for photoperiod sensitivity. The two major-effect QTLs can explain 19.03 and 19.00% of the phenotypic variance, respectively, under LD condition and 16.25 and 14.12%, respectively, for photoperiod sensitivity. Comparative mapping suggested that the two major-effect QTLs, qRP-c-1 and qRP-l-1, might associate with E8 or GmCRY1a and the maturity gene E3 or GmPhyA3, respectively. These results could facilitate our understanding of the inheritance of RP and provide information on marker-assisted breeding for high yield and wide adaptation in soybean.