Mapping and identification of QTLs for seed fatty acids in soybean(Glycine max L.)

Soybean is one of the most important sources of vegetable oil.The oil content and fatty acid ratio have attracted significant attention due to their impacts on the shelf-life of soybean oil products and consumer health.In this study,a high-density genetic map derived from Guizao 1 and Brazil 13 was used to analyze the quantitative trait loci of palmitic acid(PA),stearic acid(SA),oleic acid(OA),linoleic acid(LA),linolenic acid(LNA),and oil content(OC).A total of 54 stable QTLs were detected in the genetic map linkage analysis,which shared six bin intervals.Among them,the bin interval on chromosome 13(bin106-bin118 and bin123-bin125)was found to include stable QTLs in multiple environments that were linked to OA,LA,and LNA.Eight differentially expressed genes(DEGs)within these QTL intervals were determined as candidate genes according to the combination of parental resequencing,bioinformatics and RNA sequencing data.All these results are conducive to breeding soybean with the ideal fatty acid ratio for food,and provide the genetic basis for mining genes related to the fatty acid and oil content traits in soybean.

Genetic Diversity of Wild Soybeans from Some Regions of Southern China Based on SSR and SRAP Markers

There are rich annual wild soybean (Glycine soja) resources in Southern China, which are the progenitor of cultivated soybean. To evaluate the genetic diversity and differentiation of G. soja in Southern China, we analyzed allelic profiles of 141 annual wild soybean accessions from Southern China and 8 core wild soybean accessions fromNorthern Chinaby using 41 simple sequence repeat (SSR) markers and 18 Sequence-related amplified polymorphism (SRAP) primer combinations. The 41 SSR markers produced a total of 421 alleles (10.27 per locus) with a mean of gene diversity of 0.825 (Simpson index) and 1.987 (Shannon-weaver index). The 18 SRAP primer combinations detected a total of 90 polymorphism bands (5 per primer combination) with a mean of gene diversity of 0.918 (Shannon-weaver index). SSR and SRAP markers detected 43 and 5 rare alleles in 149 wild soybeans, respectively. The wild soybeans from Fujian province showed the highest genetic diversity with Shannon-weaver index of 1.837 (by SSR) and 0.803 (by SRAP), and the highest allelic richness with an average of 8.8 alleles per locus and the most number of rare alleles of 0.68 per locus based on SSR data. An analysis of Molecular Variance (AMOVA) analysis showed that significant variance did exist amongHunan,Fujian, Guangxi andNorthern Chinasubpopulations based on SSR and SRAP data. The unweighted pair-group method of the arithmetic average (UPGMA) cluster analysis indicated that the wild soybeans fromFujianprovince occurred in different clusters based on both SSR and SRAP data. The above results indicated thatFujianprovince could be the major center of genetic diversity for annual wild soybean inSouthern China. In addition, Mantle test showed there was a weak positive linear correlation (r = 0.25) between SSR and SRAP analysis in the study.

Fine mapping of an adult-plant resistance gene to powdery mildew in soybean cultivar Zhonghuang 24

Powdery mildew(PM),caused by the fungus Microsphaera diffusa,causes severe yield losses in soybean[Glycine max(L.)Merr.]under suitable environmental conditions.Identifying resistance genes and developing resistant cultivars may prevent soybean PM damage.In this study,analysis of F_(1),F_(2),and F8:11 recombinant inbred line(RIL)populations derived from the cross between Zhonghuang 24(ZH24)and Huaxia 3(HX3)indicated that adult-plant resistance(APR)to powdery mildew in the soybean cultivar(cv.)ZH24 was controlled by a single dominant locus.A high-density genetic linkage map of the RIL population was used for fine mapping.The APR locus in ZH24 was mapped to a 281-kb genomic region on chromosome 16.Using 283 susceptible plants of another F2 population,the candidate region was finemapped to a 32.8-kb genomic interval flanked by the markers InDel14 and Gm16_428.The interval harbored five genes,including four disease resistance(R)-like genes,according to the Williams 82.a2.v1 reference genome.Quantitative real-time PCR assays of candidate genes revealed that the expression levels of Glyma.16g214300 and Glyma.16g214500 were changed by M.diffusa infection and might be involved in disease defense.Rmd_B13 showed all-stage resistance(ASR)to PM in soybean cv.B13.An allelism test in the F2 segregating population from the cross of ZH24 × B13 suggested that the APR locus Rmd_ZH24 and the ASR locus Rmd_B13 may be allelic or tightly linked.These results provide a reference marker-assisted selection in breeding programs.

Identification of long InDels through whole genome resequencing to fine map qIF05-1 for seed isoflavone content in soybean(Glycine max L. Merr.)

Soybean seed isoflavones are a type of secondary metabolites that can provide health and nutrition benefits for humans. In our previous study, a stable quantitative trait locus(QTL) qIF05-1 controlling the seed isoflavone content in soybean was detected on chromosome(Chr.) 05 in a recombinant inbred line(RIL) population from a cross of Huachun 2×Wayao. In this study, the parental lines were re-sequenced using the Illumina Solexa System with deep coverage. A total of 63,099 polymorphic long insertions and deletions(InDels)(≥15 bp)were identified between the parents Huachun 2 and Wayao. The InDels were unevenly distributed on 20chromosomes of soybean, varying from 1,826 in Chr. 12 to 4,544 in Chr. 18. A total of 10,002 long InDels(15.85% of total) were located in genic regions, including 1,139 large-effect long InDels which resulted in truncated or elongated protein sequences. In the qIF05-1 region, 68 long InDels were detected between the two parents. Using a progeny recombination experiment and genotype analysis, the qIF05-1 locus was mapped into a 102.2 kb genomic region, and this region contained 12 genes. By RNA-seq data analysis, genome sequence comparison and functional validation through ectopic expression in Arabidopsis thaliana, Glyma.05G208300(described as GmEGL3), which is a basic helix-loop-helix(bHLH) transcription factor in plants, emerged as the most likely confirmed gene in qIF05-1. These long InDels can be used as a type of complementary genetic method for QTL fine mapping, and they can facilitate genetic studies and molecular-assisted selection breeding in soybean.

Modulation of evening complex activity enables north-to-south adaptation of soybean

Soybean,a typical short-day crop,is sensitive to photoperiod,which is a major limiting factor defining its north-to-south cultivation range.The long-juvenile(LJ)trait is controlled primarily by the J locus which has been used for decades by soybean breeders to delay flowering and improve grain yield in tropical regions.The J gene encodes an ortholog of the Arabidopsis Evening Complex(EC)component EARLY FLOWERING 3(ELF3).To identify modifiers of J,we conducted a forward genetic screen and isolated a mutant(eoj57)that in combination with j has longer flowering delay compared with j single mutant plants.Map-based cloning and genome re-sequencing identified eoj57(designated as GmLUX2)as an ortholog of the Arabidopsis EC component LUX ARRHYTHMO(LUX).To validate that GmLUX2 is a modifier of J,we used trans-complementation and identified a natural variant allele with a similar phenotype.We also show that GmLUX2 physically interacts with GmELF3a/b and binds DNA,whereas the mutant and natural variant are attenuated in both activities.Transcriptome analysis shows that the GmLUX2-GmELF3a complex co-regulates the expression of several circadian clock-associated genes and directly represses E1 expression.These results provide mechanistic insight into how GmLUX2-GmELF3 controls flowering time via synergistic regulation of gene expression.These novel insights expand our understanding of the regulation of the EC complex,and facilitate the development of soybean varieties adapted for growth at lower latitudes.

A Single Nucleotide Deletion in J Encoding GmELF3 Confers Long Juvenility and Is Associated with Adaption of Tropic Soybean

Wild soybean is a typical short-day plant that begins flowering when the days are shorter than its critical photoperiod, Soybean was domesticated in the temperate region of East Asia at the relatively high latitude, and the breeding and release of soybean varieties have historically centered on mid- and high-latitude temperate regions. Low-latitude areas with tropical and sub- tropical climates were previously considered unsuitable for soy- bean production because most temperate soybean varieties ex- hibited precocious flowering and early maturity and suffered from low yields.

Natural variation of GmFATA1B regulates seed oil content and composition in soybean

Soybean(Glycine max) produces seeds that are rich in unsaturated fatty acids and is an important oilseed crop worldwide. Seed oil content and composition largely determine the economic value of soybean. Due to natural genetic variation, seed oil content varies substantially across soybean cultivars. Although much progress has been made in elucidating the genetic trajectory underlying fatty acid metabolism and oil biosynthesis in plants, the causal genes for many quantitative trait loci(QTLs) regulating seed oil content in soybean remain to be revealed. In this study, we identified Gm FATA1B as the gene underlying a QTL that regulates seed oil content and composition, as well as seed size in soybean. Nine extra amino acids in the conserved region of Gm FATA1B impair its function as a fatty acyl–acyl carrier protein thioesterase, thereby affecting seed oil content and composition. Heterogeneously overexpressing the functional Gm FATA1B allele in Arabidopsis thaliana increased both the total oil content and the oleic acid and linoleic acid contents of seeds. Our findings uncover a previously unknown locus underlying variation in seed oil content in soybean and lay the foundation for improving seed oil content and composition in soybean.

GmRmd1 encodes a TIR-NBS-BSP protein and confers resistance to powdery mildew in soybean

Dear editor,Powdery mildew(PMD)is a widespread,fungal-borne disease that impacts crop yield worldwide.In soybean,PMD is caused by the fungal pathogen,Microsphaera diffusa.The most efficient and economic strategy for PMD management with minimal environmental impact is through the deployment of resistance genes(Dangl et al.,2013;Hafeez et al.,2021).Although resistant genes against PMD have been identified in some crops,identification of those in soybean remains elusive.Several independent reports have consistently mapped the PMD-resistance locus to the end of Chr 16(Kang and Mian,2010;Jun et al.,2012;Jiang et al.,2019),however,the underlying gene that confers PMD resistance in soybean has yet to be cloned.Identification of the resistance-to-M.diffusa 1(Rmd1)gene is critical for the breeding of resistant soybean varieties,and thus control of PMD in this important crop.