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 20 chromosomes 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.

Improving plant resistance to Verticillium wilt (VW), which causes massive losses in Gossypium hirsutum, is a global challenge.  Crop plants need to efficiently allocate their limited energy resources to maintain a balance between growth and defense.  However, few transcriptional regulators specifically respond to Verticillium dahliae and the underlying mechanism has not been identified in cotton.  In this study, we found that the that expression of most R2R3-MYB members in cotton is significantly changed by V. dahliae infection relative to the other MYB types.  One novel R2R3-MYB transcription factor (TF) that specifically responds to V. dahliae, GhMYB3D5, was identified.  GhMYB3D5 was not expressed in 15 cotton tissues under normal conditions, but it was dramatically induced by V. dahliae stress.  We functionally characterized its positive role and underlying mechanism in VW resistance.  Upon V. dahliae infection, the up-regulated GhMYB3D5 bound to the GhADH1 promoter and activated GhADH1 expression.  In addition, GhMYB3D5 physically interacted with GhADH1 and further enhanced the transcriptional activation of GhADH1.  Consequently, the transcriptional regulatory module GhMYB3D5-GhADH1 then promoted lignin accumulation by improving the transcriptional levels of genes related to lignin biosynthesis (GhPAL, GhC4H, Gh4CL, and GhPOD/GhLAC) in cotton, thereby enhancing cotton VW resistance.  Our results demonstrated that the GhMYB3D5 promotes defense-induced lignin accumulation, which can be regarded as an effective way to orchestrate plant immunity and growth. 

The cereal cyst nematode, Heterodera avenae, is one of the most economically important pathogens impacting the worldwide production of cereals and is widely distributed in more than 16 regions in China.  The present study used the numbers of nematodes inside the plant roots to evaluate the resistance/susceptibility of different subpopulations of barley Hordeum vulgare (QH2R, QH6R and TB2R) to H. avenae under field and pot conditions.  Nematode development in two highly resistant varieties was also evaluated by in vivo experiment and microscopic observation.  Analyses of 186 selected varieties showed the numbers of susceptible varieties identified with the number of females/cysts per plant (NFP) method were significantly higher than those identified with the Pf/Pi ratio (PPR) method, which indicated that the NFP method rather than the PPR method is more reliable to evaluate the resistance of barley.  The field and pot experiment results indicated that the QH2R subpopulation had lower females/cysts numbers than QH6R and TB2R subpopulations, and eight HR varieties (Sunong 7617, Sunong 7635, Dongyuan 87-14, Rudong 14-46, Rudong 87-57, Rudong 87-8-45, Rudong 88-14-2, and Rudong 88-67-1) were identified in QH2R, with the NFP numbers below 4.2.  Further microscopic observation of nematode development suggested that H. avenae often penetrated less into highly resistant varieties (Sunong 7635 and Dongyuan 87-14) and more frequently failed to develop into females than the susceptible barleys.  The promising resistant varieties identified in the present research might be helpful for breeders to develop CCN-resistant cultivars and control H. avenae populations effectively at low costs.

Pod shattering is an important domesticated trait which can cause great economic loss of crop yield in cultivated soybean.  In this study, we utilized two recombinant inbred line populations (RILs, CY, Huachun 2×Wayao; GB, Guizao 1×B13) to identify quantitative trait loci (QTLs) associated with pod shattering in soybean across multiple environments.  A total of 14 QTLs for pod shattering were identified in the two RIL populations, which had LOD scores ranging from 2.64 to 44.33 with phenotypic variance explanation (PVE) ranging from 1.33 to 50.85%.  One QTL qPS16-1, located on chromosome 16, included a well-known functional gene Pod dehiscence 1 (Pdh1) that was reported previously.  Ten new putative QTLs were validated in two RIL populations, and their LOD scores were between 2.55 and 4.24, explaining 1.33 to 2.60% of the phenotypic variation.  Of which four novel QTLs (qPS01-1, qPS03-2, qPS05-1, and qPS07-1) could be detected in two environments where nine genes had specific changes in gene expression.  Although the nine genes may have significant effects on pod shattering of soybean, their detailed functions still need to be further explored in the future.  The results of this study will facilitate a better understanding of the genetic basis of the pod shattering-resistant trait and benefit soybean molecular breeding for improving pod shattering resistance