The KL system in wheat permits homoeologous crossing over between closely related chromosomes

The Chinese wheat landrace Kaixianluohanmai(KL)expresses the ph-like phenotype.A major QTL,QPh.sicau-3A(syn.phKL),responsible for this effect has been mapped to chromosome arm 3AL.This study presents some characteristics of homoeologous pairing and recombination induced by phKL.In KL haploids,the level of homoeologous pairing was elevated relative to Ph1 Chinese Spring(CS)haploids.There was a clear preference for A–D pairing and less frequent for A–B and B–D,reflecting the higher levels of affinity between genomes A and D in wheat.The characteristics of pairing were affected by temperature and magnesium ion supplementation.The suitability of phKL for chromosome engineering was tested on three pairs of homoeologues:2Sv-2B,2Sv-2D,and 2RL-2BL.The recombination rates were 1.68%,0.17%,and 0%,respectively.The phKL locus in KL induced a moderate level of homoeologous chromosome pairing and recombination when the Ph1 locus of wheat was present,both in wheat haploids and hexaploids.The Ph1-imposed criteria for chromosome pairing and crossing over were relaxed to some degree,permitting homoeologous crossing over but only between closely related chromosomes;there was no crossing over between more differentiated chromosomes.Therefore,the phKL system(QPh.sicau-3A)can be a useful tool in chromosome engineering of wheat to transfer genes from closely related species with the benefit of reduced genomic chaos generated by the ph1b mutation.

Identification of the target genes of AhTWRKY24 and AhTWRKY106 transcription factors reveals their regulatory network in Arachis hypogaea cv.Tifrunner using DAP-seq

WRKY transcription factors(TFs)have been identified as important core regulators in the responses of plants to biotic and abiotic stresses.Cultivated peanut(Arachis hypogaea)is an important oil and protein crop.Previous studies have identified hundreds of WRKY TFs in peanut.However,their functions and regulatory networks remain unclear.Simultaneously,the AdWRKY40 TF is involved in drought tolerance in Arachis duranensis and has an orthologous relationship with the AhTWRKY24 TF,which has a homoeologous relationship with AhTWRKY106 TF in A.hypogaea cv.Tifrunner.To reveal how the homoeologous AhTWRKY24 and AhTWRKY106 TFs regulate the downstream genes,DNA affinity purification sequencing(DAP-seq)was performed to detect the binding sites of TFs at the genome-wide level.A total of 3486 downstream genes were identified that were collectively regulated by the AhTWRKY24 and AhTWRKY106 TFs.The results revealed that W-box elements were the binding sites for regulation of the downstream genes by AhTWRKY24 and AhTWRKY106 TFs.A gene ontology enrichment analysis indicated that these downstream genes were enriched in protein modification and reproduction in the biological process.In addition,RNA-seq data showed that the AhTWRKY24 and AhTWRKY106 TFs regulate differentially expressed genes involved in the response to drought stress.The AhTWRKY24 and AhTWRKY106 TFs can specifically regulate downstream genes,and they nearly equal the numbers of downstream genes from the two A.hypogaea cv.Tifrunner subgenomes.These results provide a theoretical basis to study the functions and regulatory networks of AhTWRKY24 and AhTWRKY106 TFs.

Genome-wide identification and transcriptome profiling reveal great expansion of SWEET gene family and their wide-spread responses to abiotic stress in wheat (Triticum aestivum L.)

The Sugars Will Eventually be Exported Jransporter(SWEET)gene family,identified as sugar transporters,has been demonstrated to play key roles in phloem loading,grain filling,pollen nutrition,and plant-pathogen interactions.To date,the study of SWEET genes in response to abiotic stress is very limited.In this study,we performed a genome-wide identification of the SWEET gene family in wheat and examined their expression profiles under mutiple abiotic stresses.We identified a total of 105 wheat SWEET genes,and phylogenic analysis revealed that they fall into five clades,with clade V specific to wheat and its closely related species.Of the 105 wheat SWEET genes,59%exhibited significant expression changes after stress treatments,including drought,heat,heat combined with drought,and salt stresses,and more up-regulated genes were found in response to drought and salt stresses.Further hierarchical clustering analysis revealed that SWEET genes exhibited differential expression patterns in response to different stress treatments or in different wheat cultivars.Moreover,different phylogenetic clades also showed distinct response to abiotic stress treatments.Finally,we found that homoeologous SWEET genes from different wheat subgenomes exhibited differential expression patterns in response to different abiotic stress treatments.The genome-wide analysis revealed the great expansion of SWEET gene family in wheat and their wide participation in abiotic stress response.The expression partitioning of SWEET homoeologs under abiotic stress conditions may confer greater flexibility for hexaploid wheat to adapt to ever changing environments.

Molecular characterization and expression analysis of three homoeologous Ta14S genes encoding 14-3-3 proteins in wheat(Triticum aestivum L.)

The purpose of this study was to characterize Ta14 S homoeologs and assess their functions in wheat seed development.The genomic and c DNA sequences of three Ta14 S homoeologous genes encoding 14-3-3 proteins were isolated.Sequence analysis revealed that the three homoeologs consisted of five exons and four introns and were very highly conserved in the coding regions and in exon/intron structure,whereas the c DNA sequences were variable in the 5′ and 3′-UTR.The three genes,designated as Ta14S-2A,Ta14S-2B and Ta14S-2D,were located in homoeologous group 2 chromosomes.The polypeptide chains of the three Ta14 S genes were highly similar.These genes were most homologous to Hv14 A from barley.Real-time quantitative PCR indicated that the three Ta14 S genes were differentially expressed in different organs at different developmental stages and all exhibited greater expression in primary roots of 1-day-old germlings than in other tissues.Comparison of the expression patterns of the three homoeologous genes at different times after pollination also revealed that their expression was developmentally regulated.The transcription of Ta14S-2B was clearly higher during seed germination,whereas expressions of Ta14S-2A and Ta14S-2D were up-regulated at the beginning of seed imbibition(0–12 h),but declined thereafter.The results suggested that the three Ta14 S homoeologous genes have regulatory roles in seed development and germination.

Development and Identification of Triticum aestivum L.-Thinopyrum bessarabicum Lve Chromosome Translocations

With assistance of chromosome C-banding and genomic in situ hybridization (GISH) combinedwith meiotic analysis, five germplasms with homozygous wheat-Th. bessarabicum chromosometranslocations were developed and identified among BC1F5 progenies of the cross betweenT. aestivum cv. Chinese Spring and Chinese Spring-Th. bessarabicum amphiploid. Theselines included Tj01 and Tj02 (2n=44) containing a pair of wheat-Th. bessarabicumtranslocation chromosomes besides a pair of added Th. bessarabicum chromosomes, Tj03(2n=44) with a pair of added interspecific translocation chromosomes, Tj04 (2n=44)containing a pair of interspecific translocation chromosomes besides an added pair ofTh. bessarabicum chromosome arms and Tj05 (2n=46) containing a pair of interspecifictranslocation chromosomes besides two pairs of added intact alien chromosomes. Thebreakpoints of all the translocations were found to be not around centromere. Meanwhile,all the lines showed normal plant growth, development and fertility, while the translocationchromosomes transmitted regularly. The obtained translocations might be of use fortransferring elite genes from Th. bessarabicum into wheat.

An Integrated Genetic,Physical and Transcript Map of Homoeologous Chromosomes 12 and 26 in Upland Cotton(Gossypium hirsutum L.)

While Upland cotton(Gossypium hirsutum L.) represents 95% of the world production,its genetic improvement is hindered by the shortage of effective genomic tools and resources.The

Genome resources for the elite bread wheat cultivar Aikang 58 and mining of elite homeologous haplotypes for accelerating wheat improvement

Despite recent progress in crop genomics studies,the genomic changes brought about by modern breeding selection are still poorly understood,thus hampering genomics-assisted breeding,especially in polyploid crops with compound genomes such as common wheat(Triticum aestivum).In this work,we constructed genome resources for the modern elite common wheat variety Aikang 58(AK58).Comparative genomics between AK58 and the landrace cultivar Chinese Spring(CS)shed light on genomic changes that occurred through recent varietal improvement.We also explored subgenome diploidization and divergence in common wheat and developed a homoeologous locus-based genome-wide association study(HGWAS)approach,which was more effective than single homoeolog-based GWAS in unraveling agronomic trait-associated loci.A total of 123 major HGWAs loci were detected using a genetic population derived from AK58 and cs.Elite homoeologous haplotypes(HHs),formed by combinations of subgenomic homoeologs of the associated loci,were found in both parents and progeny,and many could substantially improve wheat yield and related traits.We built a website where users can download genome assembly sequence and annotation data for AK58,perform blast analysis,and run JBrowse.Our work enriches genome resources for wheat,provides new insights into genomic changes during modern wheat improve-.ment,and suggests that efficientmining of elite HHs can make a substantial contribuutionto genomics-assisted breeding in common wheat and other polyploid crops.

Development of T. aestivum L.eH. californicum Alien Chromosome Lines and Assignment of Homoeologous Groups of Hordeum californicum Chromosomes

Hordeum californicum （2n = 2x = 14, HH） is resistant to several wheat diseases and tolerant to lower nitrogen. In this study, a molecular karyotype of H. californicum chromosomes in the Triticum aestivum L. cv. Chinese Spring （CS）-H. californicum amphidiploid （2n = 6x = 56, AABBDDHH） was established. By genomic in situ hybridization （GISH） and multicolor fluorescent in situ hybridization （FISH） using repetitive DNA clones （pTa71, pTa794 and pSc119.2） as probes, the H. californicum chromosomes could be differentiated from each other and from the wheat chromosomes unequivocally. Based on molecular karyotype and marker analyses, 12 wheat--alien chromosome lines, including four disomic addition lines （DAH1, DAH3, DAH5 and DAH6）, five telosomic addition lines （MtH7L, MtHIS, MtH1L, DtH6S and DtH6L）, one multiple addition line involving H. californicum chromosome H2, one disomic substitution line （DSH4） and one translocation line （TH7S/1BL）, were identified from the progenies derived from the crosses of CS-H. californicum amphidiploid with common wheat varieties. A total of 482 EST （expressed sequence tag） or SSR （simple sequence repeat） markers specific for individual H. californicum chromosomes were identified, and 47, 50, 45, 49, 21, 51 and 40 markers were assigned to chromosomes H1, H2, H3, H4, H5, H6 and H7, respectively. According to the chromosome allocation of these markers, chromosomes H2, H3, H4, H5, and H7 of H. californicum have relationship with wheat homoeologous groups 5, 2, 6, 3, and 1, and hence could be designated as 5Hc, 2He, 6Hc, 3Hc and 1Hc, respectively. The chromosomes H1 and H6 were designated as 7Hc and 4Hc, respectively, by referring to SSR markers located on rye chromosomes.

Diverse transcriptional patterns of homoeologous recombinant transcripts in triploid fish(Cyprinidae)

Homoeologous recombination(HR),the exchange of homoeologous chromosomes,contributes to subgenome adaptation to diverse environments by producing various phenotypes.However,the potential relevance of HR and innate immunity is rarely described in triploid cyprinid fish species.In our study,two allotriploid genotypes(R_(2)C and RC_(2)),whose innate immunity was stronger than their inbred parents(Carassius auratus red var.and Cyprinus carpio L.),were obtained from backcrossing between male allotetraploids of C.auratus red var.×C.carpio L.and females of their two inbred parents,respectively.The work detected 140 HRs shared between the two triploids at the genomic level.Further,transcriptions of 54 homoeologous recombinant genes(HRGs)in R_(2)C and 65 HRGs in RC_(2) were detected using both Illumina and PacBio data.Finally,by comparing expressed recombinant reads to total expressed reads in each of the genes,a range of 0.1%-10% was observed in most of the 99-193 HRGs,of which six recombinant genes were classified as"response to stimulus".These results not only provide a novel way to predict HRs in allopolyploids based on cross prediction at both genomic and transcriptional levels,but also insight into the potential relationship between HRs related to innate immunity and adaptation of the triploids and allotetraploids.

The Battle to Sequence the Bread Wheat Genome:A Tale of the Three Kingdoms

In the year 2018,the world witnessed the finale of the race to sequence the genome of the world’s most widely grown crop,the common wheat.Wheat has been known to bear a notoriously large and complicated genome of a polyploidy nature.A decade competition to sequence the wheat genome initiated with a single consortium of multiple countries,taking a conventional strategy similar to that for sequencing Arabidopsis and rice,became ferocious over time as both sequencing technologies and genome assembling methodologies advanced.At different stages,multiple versions of genome sequences of the same variety(e.g.,Chinese Spring)were produced by several groups with their special strategies.Finally,16 years after the rice genome was finished and 9 years after that of maize,the wheat research community now possesses its own reference genome.Armed with these genomics tools,wheat will reestablish itself as a model for polyploid plants in studying the mechanisms of polyploidy evolution,domestication,genetic and epigenetic regulation of homoeolog expression,as well as defining its genetic diversity and breeding on the genome level.The enhanced resolution of the wheat genome should also help accelerate development of wheat cultivars that are more tolerant to biotic and/or abiotic stresses with better quality and higher yield.

The allopolyploid B. juncea genome uncovered differential homoeolog gene expression influencing selection

With the long-term support by the National Natural Science Foundation of China,Ministry of Agriculture,and Science and Technology Department of Zhejiang Province,the research team led by Prof.Zhang Mingfang(张明方)at Zhejiang University,assembled an allopolyploid B.juncea genome and uncovered differential homoeolog gene expression influencing selection,which was published in Nature

Evolutionary divergence of subgenomes in common carp provides insights into speciation and allopolyploid success

Hybridization and polyploidization have made great contributions to speciation,heterosis,and agricultural production within plants,but there is still limited understanding and utilization in animals.Subgenome structure and expression reorganization and cooperation post hybridization and polyploidization are essential for speciation and allopolyploid success.However,the mechanisms have not yet been comprehensively assessed in animals.Here,we produced a high-fidelity reference genome sequence for common carp,a typical allotetraploid fish species cultured worldwide.This genome enabled in-depth analysis of the evolution of subgenome architecture and expression responses.Most genes were expressed with subgenome biases,with a trend of transition from the expression of subgenome A during the early stages to that of subgenome B during the late stages of embryonic development.While subgenome A evolved more rapidly,subgenome B contributed to a greater level of expression during development and under stressful conditions.Stable dominant patterns for homoeologous gene pairs both during development and under thermal stress suggest a potential fixed heterosis in the allotetraploid genome.Preferentially expressing either copy of a homoeologous gene at higher levels to confer development and response to stress indicates the dominant effect of heterosis.The plasticity of subgenomes and their shifting of dominant expression during early development,and in response to stressful conditions,provide novel insights into the molecular basis of the successful speciation,evolution,and heterosis of the allotetraploid common carp.