Karyotype establishment and development of specific molecular markers of Aegilops geniculata Roth based on SLAF-seq

The constant evolution of pathogens poses a threat to wheat resistance against diseases,endangering food security.Developing resistant wheat varieties is the most practical approach for circumventing this problem.As a close relative of wheat,Aegilops geniculata,particularly accession SY159,has evolved numerous beneficial traits that could be applied to improve wheat.In this study,we established the karyotype of SY159 by fluorescence in situ hybridization(FISH)using the oligonucleotide probes Oligo-pTa535 and Oligo-pSc119.2 and a complete set of wheat–Ae.geniculata accession TA2899 addition lines as a reference.Using specific-locus amplified fragment sequencing(SLAF-seq)technology,400 specific markers were established for detecting the SY159 chromosomes with efficiencies reaching 81.5%.The SY159-specific markers were used to classify the different homologous groups of SY159 against the wheat-Ae.geniculata addition lines.We used these specific markers on the 7Mg chromosome after classification,and successfully confirmed their suitability for studying the different chromosomes of SY159.This study provides a foundation for accelerating the application of SY159 in genetic breeding programs designed to improve wheat.

A likely paleo-autotetraploidization event shaped the high conservation of Nyssaceae genome

Scientific knowledge about the ancestral genome of core eudicot plant kingdom can potentially have profound impacts on both basic and applied research,including evolution,genetics,genomics,ecology,agriculture,forestry,and global climate.To investigate which plant conserves best the core eudicots common ancestor genome,we compared Arcto-Tertiary relict Nyssaceae and 30 other eudicot plant families.The genomes of Davidia involucrata(a known living fossil),Camptotheca acuminata and Nyssa sinensis,one per existent genus of Nyssaceae,were performed comparative genomic analysis.We found that Nyssaceae originated from a single Nyssaceae common tetraploidization event(NCT)-autotetraploidization 28-31 Mya after the core eudicot common hexaploidization(ECH).We identified Nyssaceae orthologous and paralogous genes,determined its chromosomal evolutionary trajectory,and reconstructed the Nyssaceae most recent ancestor genome.D.involucrata genome contained the entire seven paleochromosomes and 17 ECH-generated eudicot common ancestor chromosomes and was the slowest in mutation among the analyzed 42 species of 31 plant families.Combing both its high retention of paleochromosomes and its low mutation rate,D.involucrata provides the best case in conservation of the core eudicot paleogenome.

Repeated pregnancy losses with multiple aneuploidies and major genomic imbalance:A case report

Rationale:If one of the partners is having balanced autosomal translocation,it is usually observed that the offspring inherit either normal chromosomes,balanced translocation identical to one of the parent or unbalanced chromosomal rearrangements of the same parental chromosome having translocation.Concern:A unique case presented with history of 8 miscarriages for genetic counseling.The last abortus material evaluation showed monosomy of chromosome X(Turner syndrome)in all the analyzed cells.There was a history of infertility and also repeated second trimester abortions on the paternal side.On the maternal side,there was a history of intellectual disability.Diagnose:History of repeated abnormal pregnancy outcomes.Wife’s karyotype is normal;however,husband shows translocation between chromosome 4 and 22.Intervention:Peripheral blood sample around 3 mL was collected for karyotype.Embryo biopsy was done and DNA was extracted and processed for whole exome sequencing.Outcomes:Wife’s karyotype is normal and husband has translocation between chromosome 4 and 22.Surprisingly,the entire pregnancy outcome including embryo screening has different,complete or partial aneuploidies of chromosomes other than chromosome 4 and 22.Main lesson:Though the translocation in one of the parent is balanced,we have to think beyond traditional ways for evaluating a couple with repeated pregnancy loss as we cannot predict the errors at cell division.Option of in vitro fertilization and preimplantation genetic diagnosis in couples having balanced translocations should be discussed so that early intervention can prevent the agony of pregnancy loss.

Clinical manifestations and the prenatal diagnosis of trisomy 7 mosaicism:Two case reports

BACKGROUND The clinical manifestations of trisomy 7 mosaicism are diverse and nonspecific,so prenatal diagnosis is very difficult.CASE SUMMARY Two pregnant women with abnormal prenatal screening results were included.One was a 22-year-old woman(G1P0).At 31st week of gestation,ultrasound revealed that the posterior horn of the left lateral ventricle was 10 mm and the right renal pelvis had a separation of 7 mm.The other pregnant woman was 33 years old(G2P1L1A0),and her fetus was found to have a cardiac malformation at the 24th week of gestation.Copy number variation sequencing,whole-exome sequencing and karyotype analysis were carried out after amniocentesis,and both fetuses were diagnosed with trisomy 7 mosaicism.After parental counseling,one woman continued the pregnancy,and the other woman terminated the pregnancy.CONCLUSION In trisomy 7 mosaicism,the low proportion of trisomy does not lead to abortion,but can result in abnormal fetal development,which can be detected via ultrasound.Therefore,clinicians need to pay more attention to various aspects of fetal growth and development,combining with imaging,cellular,molecular genetics and other methods to perform comprehensive evaluations of fetuses to provide more reliable genetic counseling for pregnant women.

A likely autotetraploidization event shaped the Chinese mahogany(Toona sinensis)genome

Chinese mahogany(Toona sinensis) is of considerable medical and economic importance, and its genome has been deciphered. However, the process underlying its polyploidy is unclear, and the chromosomal evolutionary trajectory is poorly understood. Here, by reanalysing the T.sinensis genome, we found evidence of a tetraploidization event(T. sinensis special tetraploidization, TST) that occurred approximately 15-17 million years ago(MYA) after the core eudicot-common hexaploidization(ECH or gamma) event. We characterized the synonymous nucleotide substitution rates(Ks values) of collinear genes and found that T. sinensis genes affected by the TST evolve at a slower rate than Acer yangbiense genes. Furthermore, we identified homologous genes related to polyploidization and speciation and constructed multiple alignments with different reference genomes. Notably, the significant balance of gene retention and loss characterized in the two TST-derived subgenomes suggests an autopolyploid nature of the TST. Moreover, we deduced the chromosomal karyotypes of the two subgenomes and identified 7chromosomal fusions that have shaped the T. sinensis genome;more information is available on a newly constructed karyotype platform(http://www.cgrpoee.top/Toona_sinensis/index.html). The T. sinensis genome preserves the ancestral chromosome structure of dicotyledons well and could serve as a good reference for understanding genomic changes in other Meliaceae and Sapindales plants. In addition, we verified that tandem duplication and the ECH have promoted the expansion of terpene synthase(TPS) genes;conversely, the TST seems to have inhibited expansion of these genes. This present effort has clarified the polyploidy events of the T. sinensis genome, filled gaps in the history of karyotype evolution, and laid a solid foundation for further genomic studies in the Meliaceae research community and beyond.

Unique Roberts syndrome with bilateral congenital glaucoma: A case report

BACKGROUND Congenital glaucoma associated with Roberts syndrome(RS)is an unusual and unique condition.No previous report describes this association.A multidisciplinary approach including molecular studies were conducted to reach the final diagnosis.CASE SUMMARY We present a rare case of a 1-wk-old male with RS associated with bilateral congenital glaucoma,left ectopic kidney,and left-hand rudimentary digits.A comprehensive approach was applied by which bilateral non-penetrating glaucoma surgery was performed with good control of intraocular pressure for more than 6 mo.Cytogenetic and molecular testing were conducted and revealed normal measurements.CONCLUSION This report described a case of a male baby with clinical features of RS but with a negative molecular analysis,presenting with left-hand rudimentary digits,bilateral congenital glaucoma,and left ectopic kidney.To the best of our knowledge,this is the first case reported with phocomelia,bilateral congenital glaucoma,and unilateral ectopic kidney.

Confusing finding of quantitative fluorescent polymerase chain reaction analysis in invasive prenatal genetic diagnosis:A case report

BACKGROUND Quantitative fluorescent polymerase chain reaction(QF-PCR)is a rapid prenatal diagnostic method for abnormalities on chromosomes 21,18,and 13 and sex chromosomal aneuploidy.However,the value of QF-PCR in diagnosing chromosomal structural abnormalities is limited.In this article,we report a confusing QF-PCR finding in a pregnant woman who underwent amniocentesis.CASE SUMMARY The short tandem repeat marker AMXY(Xp22.2/Yp11.2)located on the sex chromosome exhibited a trisomic biallelic pattern,indicating that the karyotype of the fetus might be 47,XYY.Chromosome analysis performed on cultured amniocytes showed a normal male karyotype of the fetus.Copy number variation sequencing confirmed a 500 kb duplication at Yp11.2-Yp11.2(chrY:6610001_7110000)and a 250 kb duplication at Yp11.2-Yp11.2(chrY:7110001_7360000).CONCLUSION In conclusion,the comprehensive application of different methods could achieve a higher detection rate and accuracy for the prenatal diagnosis of chromosomal disorders through chromosomal testing.

Correlation between Reasons for Prescription and Karyotype Results in Patients Referred for Suspected Chromosomal Abnormalities

Karyotype prescription is based on clinical signs (or reasons for karyotype prescription) which are phenotypic manifestations associated with chromosomal abnormalities. The aim of this study was to establish a correspondence between karyotype indications and their results in patients. This was a retrospective study that was carried out in the Histology-Embryology-Cytogenetics laboratory of the University Hospital of Cocody-Abidjan from 2014 to 2019. 58 patient files were identified and included the indication or reason for prescribing a constitutional karyotype and the biological result obtained. An individual data sheet was used to collect the data. 17 reasons for prescription were identified and divided into 2 groups. Sexual ambiguity was the most frequent reason (29.3%). The first group (G1) represented the 10 reasons for which the karyotype results were normal. The second group (G2) corresponded of the 7 motives with normal or abnormal karyotype results. Several anomalies were listed according to these reasons: inversions, mosaics (anomalies of number and structure) and trisomy 21. The last was the most frequent chromosomal anomaly (69.24%). It was found in several reasons for karyotype prescription: malformations, neurological disorders, suspected trisomy and cardiac pathology. Several factors could explain these results, among which are the limits of the karyotype and the non-genetic causes that can induce these abnormal phenotypes. Complementary examinations to the karyotype are molecular cytogenetic techniques, notably fluorescence in situ hybridization (FISH) and array comparative genomic hybridization (Array-CGH).

Possible genetic reproductive isolation between two tilapiine genera and species:Oreochromis niloticus and Sarotherodon melanotheron

Successful crossbreeding between Oreochromis niloticus and Sarotherodon melanotheron to produce a commercial hybrid has been difficult.The karyotypes and isoenzyme of these two species and their reciprocal hybrids（O.niloticus ♀ × S.melanotheron ♂,S.melanotheron ♀ × O.niloticus ♂,the last not included in the isoenzyme study） were investigated via metaphase chromosomes obtained from head kidney cells and electropherogram of lactate dehydrogenase（LDH） isoenzymes from the liver,kidney,white muscle,heart,and eye balls.The diploid chromosome number（2n=44） and the fundamental number（NF=50） of the four tilapia genotypes were the same.However,the karyotype of O.niloticus had three pairs of sub-metacentric（sm）,twelve pairs of sub-telocentric（st）,and seven pairs of telocentric（t） chromosomes,while S.melanotheron had one pair of metacentric（m）,two pairs of sm,12 pairs of st,and seven pairs of t chromosomes.The reciprocal hybrids both showed a mixed karyotype range between their parents：0.5 pair of m,2.5 pairs of sm,12 pairs of st,and seven pairs of t chromosomes.In view of the electropherogram of isozymes,only the LDH of the kidney showed significant clear bands,with five bands in O.niloticus,three bands in S.melanotheron,and duplicated six bands in the hybrids.The bands varied depending on their activities and mobilities.We considered that the differences in karyotype and isoenzyme were related to the genetic mechanism for post-mating isolation,and provided some additional basic genetic background of their taxonomy.

Studies on the Karyotype of Two Species in Orius Wolff (Hemiptera: Heteroptera: Anthocoridae)

The karyotype of two Chinese species in Orius were studied in male germ cells prepared on air dried slides stained with Giemsa. It is reported that two species have 24 chromosomes in diploid and X Y sex chromosomal mechanism. But the beha vior of chromosomes during meiosis between two species is different. Which show in the arrangment and location of the X chromosome and autosome at the late diakinesis as well as metaphase stage respectively and so on. These characteristics may be used in ta xonomy among species of Orius .

Morphological Difference and Karyotype of Pelteobagrus fulvidraco in Dongting Lake Water System

[Objective] The research aimed to study the morphological characteristics and karyotype of Pelteobagrus fulvidraco in Dongting Lake water system.[Method] By using the conventional biological morphometry,PHA and colchicine injection method in vivo,the morphological characteristics and karyotype of P.fulvidraco in Yuanshui River and Lishui River of Dongting Lake were analyzed.[Result] In three ratio traits including standard length/head length,standard length/caudal peduncle depth,head length/snout length,P.fulvidraco of Yuanshui River and Lishui River had significant differences（P0.05）.However,the number and karyotype of their chromosomes were same.The chromosome number was 2n = 52,and the karyotype formula was 20M＋12SM＋10ST＋10T.The number of chromosome arm was 84.[Conclusion] The research result had certain theoretical guidance significance for the protection and utilization of wild P.resource in Dongting Lake water system.

Studies on the Karyotype of Three Species in the Genus Orius Wolff (Hemiptera:Anthocoridae)

Karyotype of 3 species of the genus Orius Wolff were firstly studied using the Giemsa staining and squashing slides method in male germ cell. It is reported that number of chromosome and system of sex chromosome of haploid chromosome complement of these species is n=11A＋X （Y） in the first meiotic stage. However, the behavior of chromosomes among the species are different distinctly, thus cytotaxonomic character can be adopted to the identification among the three species.

Karyotype Analysis of Lycium ruthenicum Murr.

Karyotype analysis of Lycium ruthenicum Murr. was carried out in this study. The results showed that the chromosome number was 2n=2x=24; the arm index was 48; the ratio of the longest chromosome to the shortest one was 1.31; the proportions of chromosomes with arm ratio higher than 2 was 0.08; the asymmetry index was 57.02; the karyotype type was 2A; and the karyotype formula was 2n=-24=20m＋4sm.

The Karyotype of Chi-lin Fish(Varicorhinus macrolepis) from Taishan Mountain

[Objective] The paper was to study the karyotype of Chi-lin fish （Varicorhi- nus macrolepis） from Taishan mountain. [Method] The chromosome number and karyotype of an endemic Chi-lin fish were studied using the head kidney cells. [Re- sult] The diploid chromosome number （2n） of Chi-lin fish was 50, and the karyotype of V. macrolepis was 2n=50,16m＋14sm＋20t, NF =80. No sex-chromosome was found in Chi-lin fish. [Conclusion] A detailed karyotype of this endemic cyprinid fish of Taishan Mountain was established for the first time in this study.

Research on the Karyotype and Evolution of Drosophila melanogaster Species Group

Mitotic metaphase chromosomes of 34 species of Drosophila melanogaster species group were examined. Certain new karyotypes were described for the first time, and their evolutionary and interspecific genetic relationships among 8 subgroups of D. melanogaster species group were analyzed systematically. The results were as follows. The basic karyotype of elegans subgroup was type A. The karyotypes of eugracilis subgroup, melanogaster subgroup, and ficusphila subgroup were all type C. The karyotypes of takahashii subgroup and suzukii subgroup were both type C and type D. The montium subgroup had six kinds of karyotypes types B, C, C＇, D, D＇, and E. The ananassae subgroup had three kinds of karyotypes： types F, G, and H. Thus, the melanogaster species group was classified into five pedigrees based on the diversity of these karyotypes： 1） elegans; 2） eugracilis-melanogasterficusphila; 3） takkahashii-suzukii; 4） montium; 5） ananassae. The above-mentioned results in karyotypic evolution were consistent with those of DNA sequence analysis reported by Yang except for the elegans subgroup and this subgroup was considered as the ancestral subgroup. Karyotype analysis of the same drosophila from different isofemale lines indicated that the same Drosophila from different places showed karyotypic variation which might be due to different geographical environment and evolutionary degree or interaction between the two factors.

Chromosomal Karyotypes of Fragaria Plants

[Objective]This study was to analyze the karyotypes of wild diploid strawberry species,so as to provide basis for revealing the ori- gins,evolvement and genetic breeding of strawberry. [Method] Four diploid strawberry species including Fragaria gracilis A. Los,Fragaria nilgerrensis Schidl,Fragaria pentaphylla A. Los. and Fragaria vesca L. were used as experimental materials to analyze their chromosomal kary- otypes. [Result]The karyotype formula for strawberry species tested was as follows： 2n =2x =14 =10m ＋2sm ＋2m＊ for F. gracilis A. Los, belonging to type 1B; 2n =2x =14 =14m for F. nilgerrensis Schidl,belonging to type 1A; 2n =2x =14 =12m ＋2sm for F. pentaphylla A. Loz. , belonging to type 1A; 2n =2x =14 =14m for F. vesca L. ,belonging to type 1A. Karyotype analysis showed that karyotypic asymmetry degree of the four species was F. gracilis A. Los. F. pentaphylla A. Loz. F. vesca L. F. nilgerrensis Schidl. [Conclusion] The evolution order of these four species was probably F. gracilis A. Los. ,F. pentaphylla A. Loz. ,F. vesca L. ,F. nilgerrensis Schidl.

Karyotype Study on Scilla scilloides (Lindl.) Druce in Yantai

[Objective] The aim of this study was to investigate the chromosome number and the karyotype of Scilla scilloides in Yantai.[Method]Root tips of Scilla scilloides were pretreated by 8-hydroxyquinoline,then fixed,dissociated and stained for slice production.The chromosome number was analyzed by microscopic examination,and then cells with good chromosomal morphology and dispersal chromosome were studied by microscopic photos.[Result]The somatic chromosome number of Scilla scilloides in Yantai was 2n=16+1Bs,while the karyotype formula was K(2n)=2x=16+1Bs=6m+4sm(2SAT)+4st+2t+1Bs and the karyotype classification was "3B" type.[Conclusion]Karyotype comparison,division of cell type and evolution of Scilla scilloides in Yantai are discussed,which provides basis for cytogenetics,evolutionary genetics,modern taxonomy and genetic breeding.

Comparative study of the chromosome karyotypes of two species of grasshoppers in Megaulacobothrus Caudell (Orthoptera: Acridoidea)

The chromosome karyotypes of Chorthippus （Megaulacobothrus） aethalinus （Zubovsky） and Ch. （M.） chinensis Tarbinsky were compared. Results show that the chromosome numbers of the two species fit 2n （♂） = 17 = 16 ＋ XO, in which three pairs of autosomal and sex chromosomes were terminal chromosomes, and the other five pairs of autosomes were metacentric chromosomes. These are diagnosis characters for Chorthippus. However, these two species can be distinguished by the different chromosome formula （CF） and the relative length （RL）. The CF in Ch. （M.） aethalinus is K （2n, ♂） = 6m ＋ 11t = 6L ＋ 6M ＋ 4S ＋ XO, whereas that of Ch. （M.） chinensis is K （2n, ♂） = 6m ＋ 11t = 6L ＋ 8M ＋ 2S ＋ XO. In addition, we also found that the relative lengths of sex chromosomes in the two species were different from each other. The sex-chromosome of Ch. （M.） aethalinus is located at the fifth position and its relative length is 8.33% whereas that of Ch. （M.） chinensis is at the eighth position and its relative length is 5.53%. These results show that significantly different genetic features exist for the two species of Chorthippus.

A new species in the genus Hedotettix Bolivar(Orthoptera: Tetrigidae), including chromosome karyotype, from the western Yunnan Province in China

A new species, Hedotettix nujiangensis Zheng sp. nov., is described. The chromosome complement of H. nujiangensis consists of 2n （♂） = 13. Sex determination is XO. All chromosomes are telocentric （T） and the sex chromosome is the fourth element in size. Type specimens are deposited at Southwest Forestry University.

Chromosomes and Karyotypes of Three Seagrass Species of Hydrocharitaceae

[Objective] This study aimed to investigate the chromosomes and karyotypes of three seagrass species of hydrocharitaceae-Enhalus acoroides, Thalassia hemprichii and Halophila minor collected from Li’an Lagoon, Hainan Province, China. [Method] The root-tips of E. acoroides, T. hemprichii and the axillary buds of H. minor were selected as the materials in this study. The conventional crushing method was used to prepare the slice specimens of chromosomes, and the karyotypes of the three species were analyzed. [Result] The chromosome numbers of E. acoroides, T. hemprichii and H. minor were 2n=18, 18, 28, respectively. The karyotype formulas were K （2n）=18= 12m＋6sm, K（2n）=18=12m＋6sm and K（2n）=28=16m＋8sm＋4st, respectively. According to the standard of Stebbins, the karyotypes of E. acoroides and T. hemprichii were 2A, and that of H. minor was 2B. There was no B chromosome and satellite in these three species. [Conclusion] According to the comparison on the karyotypes of this three species, E. acoroides and T. hemprichii are similar in karyotypes to each other, indicating that there is close, inter-relationship between E. acoroides and T. hemprichii.