Development of Oligo-GISH kits for efficient detection of chromosomal variants in peanut

Oligo probe staining is a low-cost and efficient chromosome identification technique.In this study,oligo genomic in situ hybridization(Oligo-GISH)technology was established in peanut.Peanut A and B subgenome-specific interspersed repeat(IR)oligo probe sets were developed based on clustering and electronic localization of tandem repeat sequences in the reference genome of Tifrunner.The OligoGISH kit was then used to perform staining of 15 Arachis species.The A-subgenome probe set stained the chromosomes of A-and E-genome Arachis species,the B-subgenome probe set stained those of B-,F-,K-,and E-genome species,and neither set stained those of H-genome species.These results indicate the relationships among the genomes of these Arachis species.The Oligo-GISH kit was also used for batch staining of the chromosomes of 389 seedlings from the irradiated M1generation,allowing 67 translocation and deletion lines to be identified.Subsequent Oligo-FISH karyotyping,FISH using single-copy probe libraries,and trait investigation identified seven homozygous chromosomal variants from the M3generation and suggested that there may be genes on chromosome 4B controlling seed number per pod.These findings demonstrate that the IR probe sets and method developed in this study can facilitate research on distant hybridization and genetic improvement in peanut.

QTL mapping of quality traits in peanut using whole-genome resequencing

Oil and protein content and fatty acid composition are quality traits in peanut.Elucidating the genetic mechanisms underlying these traits may help researchers to obtain improved cultivars by molecular breeding.Whole-genome resequencing of a recombinant inbred population of 318 lines was performed to construct a high-density linkage map and identify QTL for peanut quality.The map,containing 4561 bin markers,covered 2032 c M with a mean marker density of 0.45 c M.A total of 110 QTL for oil and protein content,and fatty acid composition were mapped on the 18 peanut chromosomes.The QTL q A05.1 was detected in four environments and showed a major phenotypic effect on the contents of oil,protein,and six fatty acids.The genomic region spanned by q A05.1,corresponding to a physical interval of approximately 1.5 Mb,contains two SNPs polymorphic between the parents that could cause missense mutations.The two SNP sites were employed as KASP markers and validated using lines with extremely high and low oil contents.These sites may be useful in the marker-assisted breeding of peanut cultivars with high oil contents.

Identification of a stable major QTL for fresh-seed germination on chromosome Arahy.04 in cultivated peanut(Arachis hypogaea L.)

Fresh-seed germination(FSG)impairs peanut production,especially in areas where the peanut harvest season coincides with rainy weather.Developing FSG-resistant cultivars by molecular breeding is expected to mitigate yield loss and quality impairment caused by FSG.However,the genetic control of FSG awaits elucidation.In this study,FSG at 1,3,5,7,and 9 days post-imbibition in three environments were tested,and quantitative-trait loci(QTL)associated with FSG were mapped in a peanut recombinant inbred line population by leveraging existing high-density peanut genetic maps.Of 24 QTL identified in 13 linkage groups,qFSGA04 was a stable major QTL on linkage group 04(LG04).It was consistently detected in five germination stages and three environments.By designing and validating DNA markers in the confidence interval of qFSGA04,we identified one single-nucleotide polymorphism and one In Del closely associated with FSG that could be used as linked markers for FSG resistance in peanut breeding.

RMT-Based Urban Traffic Cross-Correlation Analysis and Its Application on Traffic Incident Impact Analyses

Cross-correlating traffic flow data at different intersections in an urban transportation network is important for understanding the collective behavior of constituents in a complex system and for predicting the risk of network-wide congestion. In this work, a Random Matrix Theory (RMT) based method is used to describe the collective behavior from massive traffic data sets. Nonrandom correlations between traffic flow series recorded in the Beijing road network occur both with and without detrending. The effect of the traffic load on the correlation patterns of network-wide traffic flows is analyzed using the RMT analysis of a simulated data set collected from Paramics. The RMT analysis is also used to evaluate the impact of incidents on the network-wide traffic status. Cluster analysis is used to find the largest cluster in the network which indicates the critical congestion caused by the incident. All the results show that RMT analyses are an effective method for investigating systematic interactions in urban transportation systems.

Molybdenum and cadmium co-induce necroptosis through Th1/Th2 imbalance-mediated endoplasmic reticulum stress in duck ovaries

Cadmium(Cd)and excess molybdenum(Mo)pose serious threats to animal health.Our previous study has determined that Cd and/or Mo exposure can cause ovarian damage of ducks,while the specific mechanism is still obscure.To further investigate the toxic mechanism of Cd and Mo co-exposure in the ovary,forty 8-day-old female ducks were randomly allocated into four groups for 16 weeks,and the doses of Cd and Mo in basic diet per kg were as follows:control group,Mo group(100 mg Mo),Cd group(4 mg Cd),and Mo+Cd group(100 mg Mo+4 mg Cd).Cadmium sulfate 8/3-hydrate(CdSO_(4)·8/3H_(2)O)and hexaammonium molybdate((NH_(4))_(6)Mo_(7)O_(24)·4H_(2)O)were the origins of Cd and Mo,respectively.At the 16th week of the experiment,all ovary tissues were collected for the detection of related indexes.The data indicated that Mo and/or Cd induced trace element disorders and Th1/Th2 balance to divert toward Th1 in the ovary,which activated endoplasmic reticulum(ER)stress and then provoked necroptosis through triggering RIPK1/RIPK3/MLKL signaling pathway,and eventually caused ovarian pathological injuries and necroptosis characteristics.The alterations of above indicators were most apparent in the joint group.Above all,this research illustrates that Mo and/or Cd exposure can initiate necroptosis through Th1/Th2 imbalance-modulated ER stress in duck ovaries,and Mo and Cd combined exposure aggravates ovarian injuries.This research explores the molecular mechanism of necroptosis caused by Mo and/or Cd,which reveals that ER stress attenuation may be a therapeutic target to alleviate necroptosis.