Marker-assisted selection (MAS) and genomic selection (GS) breeding have greatly improved the efficiency of rice breeding.  Due to the influences of epistasis and gene pleiotropy, ensuring the actual breeding effect of MAS and GS is still a difficult challenge to overcome.  In this study, 113 indica rice varieties (V) and their 565 testcross hybrids (TC) were used as the materials to investigate the genetic basis of 12 quality traits and nine agronomic traits.  The original traits and general combining ability of the parents, as well as the original traits and mid-parent heterosis of TC, were subjected to genome-wide association analysis.  In total, 381 primary significantly associated loci (SAL) and 1,759 secondary SALs that had epistatic interactions with these primary SALs were detected.  Among these loci, 322 candidate genes located within or nearby the SALs were screened, 204 of which were cloned genes.  A total of 39 MAS molecular modules that are beneficial for trait improvement were identified by pyramiding the superior haplotypes of candidate genes and desirable epistatic alleles of the secondary SALs.  All the SALs were used to construct genetic networks, in which 91 pleiotropic loci were investigated.  Additionally, we estimated the accuracy of genomic prediction in the parent V and TC by incorporating either no SALs, primary SALs, secondary SALs or epistatic effect SALs as covariates.  Although the prediction accuracies of the four models were generally not significantly different in the TC dataset, the incorporation of primary SALs, secondary SALs, and epistatic effect SALs significantly improved the prediction accuracies of 5 (26%), 3 (16%), and 11 (58%) traits in the V dataset, respectively.  These results suggested that SALs and epistatic effect SALs identified based on an additive genotype can provide considerable predictive power for the parental lines.  They also provide insights into the genetic basis of complex traits and valuable information for molecular breeding in rice.

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. 

Ovulation is paramount for female animal fertility, necessitating a thorough understanding of its process and molecular underpinnings. This study aimed to delineate the goat ovary temporal dynamics of ovulation. Utilizing single-cell sequencing, we analyzed follicular fluid samples obtained at 0, 6, 12, 18, and 24 h post-hCG administration, identifying 4 cell types and 6 myeloid cell subtypes. We elucidated gene expression and functional changes in granulosa cells over the time course of ovulation. Notably, our study detected and confirmed immune cell infiltration at 6 h post-LH peak. Additionally, we observed significant cellular interactions between granulosa cells and macrophages, with granulosa cells expressing IL1RAP, COL4A1, COL4A2 implicated in immune cell regulation, while macrophages expressed EREG to facilitate oocyte maturation. Collectively, our investigation has established a comprehensive single-cell transcriptome atlas of the ovulating goat ovary for advancing exploration into ovulation mechanisms and developing therapies for ovulatory disorders.

Stripe rust caused by Puccinia striiformis f. sp. tritici (Pst) is a serious disease affecting wheat production in China.  Wheat cultivar Aikang 58 (AK58) has exhibited effective resistance to stripe rust since its release in 2005.  But the genetic basis of its stripe rust resistance remains unknown. Two genetic populations from the crosses of Avocet S/AK58 (128 recombinant inbred lines) and Kenong 9204/AK58 (1,042 F_2:3 families) were used to dissect the genetic basis of stripe rust resistance in AK58, respectively. In addition, Panel 1 consisting of 688 wheat accessions were used for genome-wide association study (GWAS) and sweep selection analysis to validate the presence of the resistance haplotype of the target region and Panel 2 consisting of 388 Chinese cultivars and breeding lines was genotyped using molecular markers to evaluate the prevalence and distribution of the resistant loci in AK58. The genetic populations were evaluated for stripe rust responses at Yangling and Guiyang over five cropping seasons (2017-2022) and genotyped using GBW16 K SNP array and KASP markers. Using quantitative trait loci (QTLs) analysis, seven QTL were detected on chromosome arms 1BL, 2BS, 2BL, 5BL and 7BL (three QTLs).  Among them, QYrak.nwafu-2BL identified as Yr5b conferred all-stage resistance to Pst race V32L; three QTL within the 7BL chromosome arm region 715.77-733.25 Mb based on Chinese Spring RefSeq v.2.1, were designated YrAK58.1, YrAK58.2 and YrAK58.3, respectively.  YrAK58.1 confirmed as Yr6, and YrAK58.2 conferred all-stage resistance to multiple Pst races and were also effective in field environments. YrAK58.3 contributed stable resistance in all field environments. The remaining QTL were environment-dependent with minor effect. GWAS and sweep selection analyses revealed specific genomic regions with artificial selection signals for the three QTL on chromosome arm 7BL in different breeding groups.  A haplotype combination of high-throughput molecular markers tightly flanking Yr6, YrAK58.2 and YrAK58.3 detected all three genes in 3.6% of entries in Panel 2. The same marker set can be used to further exploit the resistance gene combination in breeding programs.