Mapping of QTLs and candidate genes associated with multiple phenotypic traits for Huanglongbing tolerance in citrus

Huanglongbing(HLB)is the most devastating disease for citrus worldwide.Candidatus Liberibacter asiaticus(C Las),vectored by Asian citrus psyllid(ACP,Diaphorina citri Kuwayama),is the most common pathogen causing the disease.Commercial citrus varieties are highly susceptible to HLB,whereas trifoliate orange(Poncirus trifoliata)is considered highly tolerant to HLB.An F1 segregating population and their parent trifoliate orange and sweet orange,which had been exposed to intense HLB pressure for three years,was evaluated for disease symptoms,ACP colonization,C Las titer and tree vigor repeatedly for two to three years.Trifoliate orange and sweet orange showed significant differences for most of the phenotypic traits,and the F1 population exhibited a large variation.A high-density SNP-based genetic map with 1402 markers was constructed for trifoliate orange,which exhibited high synteny and high coverage of its reference genome.A total of 26 quantitative trait locus(QTLs)were identified in four linkage groups LG-t6,LG-t7,LG-t8 and LG-t9,of which four QTL clusters exhibit a clear co-localization of QTLs associated with different traits.Through genome-wide analysis of gene expression in response to C Las infection in‘Flying Dragon’and‘Larger-Flower DPI-50-7’trifoliate orange,85 differentially expressed genes were found located within the QTL clusters.Among them,seven genes were classified as defense or immunity protein which exhibited the highest transcriptional change after C Las infection.Our results indicate a quantitative genetic nature of HLB tolerance and identified candidate genes that should be valuable for searching for genetic solutions to HLB through breeding or genetic engineering.

OcBSA:An NGS-based bulk segregant analysis tool for outcross populations

Constructing inbred lines for self-incompatible species and species with long generation times is challenging,making the use of F1 outcross/segregating populations the main strategy for genetic studies of such species.However,there is a lack of dedicated algorithms/tools for rapid quantitative trait locus(QTL)mapping using the F1 populations.To this end,we have designed and developed an algorithm/tool called OcBSA specifically for QTL mapping of F1 populations.OcBSA transforms the four-haplotype inheritance problem from the two heterozygous diploid parents of the F1 population into the two-haplotype inheritance problem common in current genetic studies by removing the two haplotypes from the heterozygous parent that do not contribute to phenotype segregation in the F1 population.Testing of OcBSA on 1800 simulated F1 populations demonstrated its advantages over other currently available tools in terms of sensitivity and accuracy.In addition,the broad applicability of OcBSA was validated by QTL mapping using seven reported F1 populations of apple,pear,peach,citrus,grape,tea,and rice.We also used OcBSA to map the QTL for flower color in a newly constructed F1 population of potato generated in this study.The OcBSA mapping result was verified by the insertion or deletion markers to be consistent with a previously reported locus harboring the ANTHOCYANIN 2 gene,which regulates potato flower color.Taken together,these results highlight the power and broad utility of OcBSA for QTL mapping using F1 populations and thus a great potential for functional gene mining in outcrossing species.For ease of use,we have developed both Windows and Linux versions of OcBSA,which are freely available at:https://gitee.com/Bioinformaticslab/OcBSA.

Construction of high-density genetic linkage map of Pyropia yezoensis(Bangiales,Rhodophyta)and identifi cation of red color trait QTLs in the thalli

Pyropia yezoensis is an important macroalga because of its extensive global distribution and economic importance.Color is an important trait in the thalli of P.yezoensis,it is also an effective marker to identify the hybridization in genetic breeding.In this study,a high-density genetic linkage map was constructed based on high-throughput single nucleotide polymorphism(SNP)markers,and used for analyzing the quantitative trait loci(QTLs)of red color trait in the thalli of P.yezoensis.The conchospore undergoes meiosis to develop into an ordered tetrad,and each cell has a haploid phenotype and can grow into a single individual.Based on this theory,F1 haploid population was used as the mapping population.The map included 531 SNP markers,394.57 cM long on average distance of 0.74 cM.Collinear analysis of the genetic linkage map and the physical map indicated that the coverage between the two maps was 79.42%.Furthermore,QTL mapping identified six QTLs for the chromosomal regions associated with the red color trait of the thalli.The value of phenotypic variance explained(PVE)by an individual QTL ranged from 4.71%-63.11%.And QTL qRed-1-1,with a PVE of 63.11%,was considered the major QTL.Thus,these data may provide a platform for gene and QTL fine mapping,and marker-assisted breeding in P.yezoensis in the future.