A novel variation of TaGW2-6B increases grain weight without penalty in grain protein content in wheat (Triticum aestivum L.).

Yield and quality are two crucial breeding objects of wheat therein grain weight and grain protein content (GPC) are two key relevant factors correspondingly. Investigations of their genetic mechanisms represent special significance for breeding. In this study, 199 F2 plants and corresponding F2:3 families derived from Nongda3753 (ND3753) and its EMS-generated mutant 564 (M564) were used to investigate the genetic basis of larger grain and higher GPC of M564. QTL analysis identified a total of 33 environmentally stable QTLs related to thousand grain weight (TGW), grain area (GA), grain circle (GC), grain length (GL), grain width (GW), and GPC on chromosomes 1B, 2A, 2B, 4D, 6B, and 7D, respectively, among which QGw.cau-6B.1, QTgw.cau-6B.1, QGa.cau-6B.1, and QGc.cau-6B.1 shared overlap confidence interval on chromosome 6B. This interval contained the TaGW2 gene playing the same role as the QTLs, so TaGW2-6B was cloned and sequenced. Sequence alignment revealed two G/A SNPs between two parents, among which the SNP in the seventh exon led to a premature termination in M564. A KASP marker was developed based on the SNP, and single-marker analysis on biparental populations showed that the mutant allele could significantly increase GW and TGW, but had no effect on GPC. Distribution detection of the mutant allele through KASP marker genotyping and sequence alignment against databases ascertained that no materials harbored this allele within natural populations. This allele was subsequently introduced into three different varieties through molecular marker-assisted backcrossing, and it was revealed that the allele had a significant effect on simultaneously increasing GW, TGW, and even GPC in all of three backgrounds. Summing up the above, it could be concluded that a novel elite allele of TaGW2-6B was artificially created and might play an important role in wheat breeding for high yield and quality. Supplementary Information: The online version contains supplementary material available at 10.1007/s11032-024-01455-y.

Rhnull phenotype in an Indian patient due to a novel c.1138 + 2 t > a mutation in the RHAG gene.

BACKGROUND: The Rh system is an extremely important RBC antigen system with over 50 antigens, 5 of which (D, C, E, c and e) are considered most clinically significant. The rare Rhnull phenotype can result from mutations in the RHD and RHCE genes or the RHAG gene that affects their expression. This is a case report of the second type. CASE REPORT: This case reports a multiparous lady who had to be evaluated for a panreactive antibody. The discrepancy was first identified at the centre she reported to. A thorough immunohematological workup was performed at a second reference laboratory. Suspecting Rhnull phenotype, a third referral (molecular typing) was requested at International Blood Group Reference Laboratory (IBGRL), Bristol. RESULTS: A novel RHAG null allele (c.1138+2t>a), causing a Rhnull phenotype was identified. The antibody was most likely an anti-Rh 29 antibody. CONCLUSION: The novel c.1138+2 t > a mutation in the RHAG gene causing the Rhnull phenotype and development of a pan reacting antibody(ies) made the patient's pregnancy challenging. Confirmation of the diagnosis, an important step in her management, required use of both serological immunohematology and molecular techniques.

One novel single nucleotide polymorphism c.424A>G on A1.02 allele in ABO glycosyltransferases leads to Aweak phenotype.

BACKGROUND: The dysfunction of the ABO glycosyltransferase (GT) enzyme, which is caused by mutations in the ABO gene, can lead to weak ABO phenotypes. In this study, we have discovered a novel weak ABO subgroup allele and investigated the underlying mechanism to causing its Aweak phenotype. MATERIALS AND METHODS: The ABO phenotyping and genotyping were performed by serological studies and direct DNA sequencing of ABO gene. The role of the novel single nucleotide polymorphism (SNP) was evaluated by 3D model, predicting protein structure changes, and in vitro expression assay. The total glycosyltransferase transfer capacity in supernatant of transfected cells was examined. RESULTS: The results of serological showed the subject was Aweak phenotype. A novel SNP c.424A > G (p. M142V) based on ABO*A1.02 was identified, and the genotype of the subject was AW-var/O.01 according to the gene analysis. In silico analysis showed that the SNP c.424A > G on the A allele may change the local conformation by damaging the hydrogen bonds and reduce the stability of GT. In vitro expression study showed that SNP p.M142V impaired H to A antigen conversion, although it did not affect the generation of A glycosyltransferase (GTA). CONCLUSIONS: One novel AW allele was identified and the SNP c.424A > G (p.M142V) can cause the Aweak phenotype through damaging the hydrogen bonds and reducing stability of the GTA.

Identification of a novel variant c.761C>T on ABO*B.01 gene in ABO glycosyltransferases associated with Bweak phenotype.

BACKGROUND AND OBJECTIVES: ABO antigens are produced from H antigen by the activity of glycosyltransferase enzyme encoded by the ABO gene. Variants in the ABO gene can produce a weak ABO phenotype. In this study, we identify a novel ABO*BW allele and investigate the underlying mechanism leading to the Bweak phenotype. MATERIALS AND METHODS: The ABO phenotype and genotype of the sample were determined using serological and direct DNA sequencing methods. We assessed the impact of the novel variant by three-dimensional modelling to predict protein stability changes (ΔΔG), and carried out an in vitro expression assay. The total glycosyltransferase transfer capacity in the supernatant of transfected cells was also examined. RESULTS: Serological analysis confirmed the Bweak phenotype in the subject, and gene sequencing identified a novel variant c.761C>T (p.A254V) on the ABO*B.01 allele, resulting in a BW-var/O.01.02 genotype. In silico analysis suggested that the p.A254V variant on the B allele may reduce the stability of glycosyltransferase B (GTB), as indicated by the ΔΔG values. In vitro expression studies showed that the variant p.A254V impaired H to B antigen conversion, although it did not affect the expression of GTB. CONCLUSION: We identified a novel BW allele and demonstrated that the variant c.761C>T (p.A254V) can cause the Bweak phenotype by reducing the stability of GTB.

Naturally occurring anti-PP1PK in a Chinese individual with p phenotype: A case based on compound heterozygosity including one novel allele.

BACKGROUND: The null phenotype in P1PK blood group, known as "p," is extremely rare in the whole world. Individuals of p phenotype spontaneously form anti-PP1PK isoantibody. Here, we report a case of p phenotype with naturally occurring anti-PP1PK isoantibodies in a Chinese individual. STUDY DESIGN AND METHODS: Serology tests, containing alloantibodies screening and identification, were conducted to demonstrate the phenotype in P1PK blood group. The genotype of A4GALT gene was identified by haplotypes separation and sequencing. RESULTS: The serological assay demonstrated the p phenotype of the proband, presenting with 1:64 titer of anti-PP1PK . The sequencing data revealed a compound heterozygote consisting of A4GALT*P1.01 with c.343A>T and a novel allele based on A4GALT*01N.05 with an addition polymorphism c.100G>A. The sequence of the novel allele has been submitted to GenBank and the accession number OM912503 was assigned. CONCLUSION: Our study demonstrates a case of naturally occurring anti-PP1Pk in a Chinese individual with p phenotype, which is based on compound heterozygosity including one novel allele. As the proband is a young lady, monitoring the titer of anti-PP1PK and early initiation of medical intervention are essential after her pregnancy.

Utility of next-generation sequencing methods to identify the novel HLA alleles in potential stem cell donors from Chinese Marrow Donor Program.

The human leucocyte antigen (HLA) is the most polymorphic region of the human genome. Compared with Sanger-sequencing-based typing (SBT) methods, next-generation sequencing (NGS) has significantly higher throughput and depth sequencing characteristics, having dramatic impacts on HLA typing in clinical settings. Here, we performed NGS technology with Ion Torrent S5 platform to evaluate the potential four novel HLA alleles detected in five donors from Chinese Marrow Donor Program (CMDP, Shaanxi Province) during routine Sanger SBT testing. We also predicted the highest estimated relative frequency novel allele-bearing haplotypes according to their phenotypes and HaploStats database. NGS assays, as it provided the phase-defined and complete sequencing information, undoubtedly increase novel allele identification which will greatly enrich HLA database and provide more information for donor selection.

Identification of a novel HLA-A*02:06:01:02 allele in a Chinese individual by sequence-based typing.

The new HLA-A*02:06:01:02 allele differs from HLA-A*02:06:01 by a C→G substitution in Intron 1.

Identification of a novel allele: DQB1*06:127 in Hispanic sisters.

Newly identified allele, HLA-DQB1*06:127, differs from DQB1*06:02:01 by the single nucleotide substitution 426C-A at codon 110 in exon 3.

Identification of a novel HLA allele, HLA-A* 24:02:90, in a Han Chinese individual.

HLA-A*24:02:09 shows one nucleotide difference from HLA-A*24:02:01:01 at position 408 in exon 3 (codon 112 GGG>GGC).

A new HLA-B*39 allele, HLA-B*39:01:15, discovered in a Taiwanese rheumatoid arthritis patient.

The new allele B*39:01:15 differs from B*39:01:01 by a point mutation at position 315 (G>T) of exon 2.

Characterization of the novel HLA-C*08:01:09 allele identified in a Chinese Han individual.

HLA-C*08:01:09 allele differs from HLA-C*08:01:01 at nt735 C>T in exon 4.

Identification of a novel HLA-B*40 allele, HLA-B*40:210, in a Chinese individual.

The newly detected HLA-B*40:210 allele has two nucleotide changes in exon 2 compared to B*40:49 allele.

HLA-DRB1*11:106, a variant of HLA-DRB1*11, discovered in a Chinese bone marrow donor.

HLA-DRB1*11:106 has 1 nucleotide change from HLA-DRB1*11:01:01 at nucleotide 155 (G → A).

Identification of a novel HLA-B*40 variant allele, B*40:301, by sequence-based typing.

The new allele, HLA-B*40:301 differs from B*40:01:02 by one nucleotide substitution at codon 239 (AGA → AAA).

Identification of a novel HLA-B*40 allele, HLA-B*40:229, in a Chinese individual.

The novel HLA-B*40:229 allele shows one nucleotide difference from B*40:02:01 in exon 2 at nucleotide position 97 (C → T).

A single nucleotide replacement in exon 2 produces a novel HLA-C*01:02 variant, HLA-C*01:02:34.

HLA-C*01:02:34 differs from HLA-C*01:02:01 by a single nucleotide replacement in codon 43.

Identification of the novel KIR3DL1*079 allele from a southern Chinese Han individual.

The novel KIR3DL1*079 allele differs from KIR3DL1*0150201 by a single mutation at CDS nt1119 G>T.

Characterization of a novel HLA-B allele (HLA-B*18:108) by intron-exon sequencing of the HLA-B locus.

HLA-B*18:108 has two nucleotide changes from B*18:01:01:02 at nt 430 where A → G and nt 431 where G → A.