Segregation analysis indicates that Puroindoline b-2 variants 2 and 3 are allelic in Triticum aestivum and that a revision to Puroindoline b-2 gene symbolization is indicated

Genetic and kernel texture relationships between Puroindoline b-2 variants 2 and 3 have not been fully established in wheat (Triticum aestivum L.). Here, 480 F₂ plants, derived from three hard spring wheat populations were used to test the segregation of Puroindoline b-2 (Pinb-2) variants 2 and 3. Chi-square analysis indicated that Pinb-2 variants 2 and 3 in all three F₂ populations segregated as a single bi-allelic locus, with segregation ratios fitting a 1:2:1 ratio. Using 448 of the 480 plants derived from these three F₂ populations, the average SKCS hardness index of plants homozygous for Pinb-2 variant 2 vs. those homozygous for variant 3 was not significantly different (67.5 vs. 67.9). Results indicated that plants with Pina-D1b/Pinb-D1a were on average 10.0 Single Kernel Characterization System (SKCS) hardness index units harder than those carrying the Pina-D1a/Pinb-D1b haplotype. In conclusion, Pinb-2 variants 2 and 3 are allelic and exert little effect on kernel texture in hard-kernel T. aestivum germplasm. Further, the designation of Pinb-2v2 and Pinb-2v3 should be changed to Pinb-B2a and Pinb-B2b, respectively. We propose that Pinb-2 variants 1 and 4 of Chinese Spring be designated Pinb-D2a and Pinb-A2a, respectively.     

Development of simple and co-dominant PCR markers to genotype puroindoline a and b alleles for grain hardness in bread wheat (Triticum aestivum L.)

Grain hardness is one of the most important quality characteristics of cultivated bread wheat (Triticum aestivum L.). A large deletion in the puroindoline a (Pina) gene or single nucleotide polymorphisms (SNPs) in the puroindoline b (Pinb) gene results in hard grain texture. So far, nine Pina alleles (Pina-D1a–Pina-D1b, Pina-D1k–Pina-D1q) and seventeen Pinb alleles (Pinb-D1a–Pinb-D1g, Pinb-D1p–Pinb-D1ab) have been identified in bread wheat. The major Pina and Pinb alleles identified in hard wheat cultivars are Pina-D1b, Pinb-D1b, Pinb-D1c and Pinb-D1d. In this study, a three-primer PCR system was employed to develop nine co-dominant STS markers for genotyping Pina-D1a and Pina-D1b, whereas temperature-switch (TS) PCR was used to develop six co-dominant SNP markers for genotyping the Pinb-D1a, Pinb-D1b, Pinb-D1c and Pinb-D1d alleles. These STS and TS-PCR markers were used to verify the grain hardness genotype of 100 wheat cultivars. The reliability and genotyping accuracy of TS-PCR markers were confirmed through sequencing of PCR products and a comparison with previously published results. Therefore, STS and TS-PCR markers offer a simple, cost-effective and reliable method for high-throughput genotyping Pina and Pinb alleles to select grain hardness in wheat quality breeding programs and for wheat market classification.     

The Pinb-2 genes in wheat comprise a multigene family with great sequence diversity and important variants

The puroindoline genes Pina-D1 and Pinb-D1 located at the Ha locus on chromosome 5D of common wheat are considered the most important genetic determinants of grain hardness. The recent identification of Pinb-2 genes on group 7 chromosomes emphasises the need for detailed analysis of the genetics of this important trait. This study focussed on the analysis of Pinb-2 genes from accessions of hexaploid, tetraploid and diploid wheat, to address key questions related to their diversity and possible roles. Extensive DNA sequence heterogeneity was identified in the form of single nucleotide polymorphisms (SNPs), leading to seventeen reproducible haplotypes, of which thirteen are new. The results confirmed the known groups Pinb-2v1 to Pinb-2v5, identified a new group Pinb-2v6, and showed that the Pinb-2 genes comprised a small multigene family, at least in some genomes. The putative proteins exhibited changes at the important tryptophan-rich domain as well as basic and hydrophobic residues. A new Pina-D1 allele (at Ha locus) was also identified, designated Pina-D1t, with a premature stop codon at the TRD. Additionally, peptides designed on PINB-2 proteins displayed activity against bacteria and phytopathogenic fungi. The data strongly support the Pinb-2 genes being functionally relevant to roles including influencing grain texture.     

Association of Puroindoline b-B2 variants with grain traits,yield components and flag leaf size in bread wheat (Triticum aestivum L.) varieties of the Yellow and Huai Valleys of China

A total of 169 wheat (Triticum aestivum L.) varieties (landraces and cultivars) were used to asses the relationship between Puroindoline D1 alleles and Puroindoline b-B2 variants and grain hardness, other grain traits, yield components, and flag leaf size. Results indicated that the average SKCS hardness of Pinb-B2v3 varieties was significantly greater than that of Pinb-B2v2 varieties within the soft Puroindoline D1 haplotype sub-group. Conversely, no statistically significant difference was obtained for SKCS hardness between varieties with the Pinb-B2v3 vs. Pinb-B2v2 alleles within the two hard Puroindoline D1 haplotypes (Pinb-D1b and Pinb-D1p sub-groups). Therefore, the Puroindoline b-B2 gene may have a bigger impact on soft wheat varieties than hard. Across all varieties, thousand-kernel weight, grain weight per spike, grain diameter, grain number per spike, flag leaf width and area of Pinb-B2v3 varieties were significantly greater than those possessing Pinb-B2v2. These results indicated that the Pinb-B2v3 allele was associated with preferable grain yield traits compared to the Pinb-B2v2 allele in bread wheat. This study provides evocative information for better understanding the molecular and genetic basis of wheat grain yield.     

A new puroindoline b mutation present in Chinese winter wheat cultivar Jingdong 11

Kernel hardness is one of the most important characteristics in determining utilization and marketing of bread wheat. Genes coding for puroindoline a and b (PINA and PINB) were located at the Ha locus and designated as Pina-D1 and Pinb-D1, respectively. The coding sequence of the Pinb gene in a Chinese winter wheat cultivar Jingdong 11 (Triticum aestivum L.) was amplified with polymerase chain reaction (PCR), and the obtained 447-bp fragment sequenced from two strands, and compared with the eight known Pinb alleles. The results showed that Jingdong 11 possessed a new Pinb allele not reported previously, and was designated as Pinb-D1q. It is characterized by a single base T to G substitution, which results in a tryptophan to leucine substitution (TGG to TTG) at position 44 and is most likely the cause of hard grain texture in Jingdong 11. The characterization of Pinb-D1 alleles would be helpful in manipulating grain hardness of bread wheat in breeding programs.     

Association analysis of Puroindoline-D1 and Puroindoline b-2 loci with 13 quality traits in European winter wheat (Triticum aestivum L.)

Grain hardness, a major determinant influencing end-use quality of common wheat, is mainly controlled by Puroindoline a-D1 (Pina-D1) and Puroindoline b-D1 (Pinb-D1) genes. Recently, additional puroindoline genes, designated Puroindoline b-2 (Pinb-2), were described. This study examined frequencies of Pin-D1 alleles and Pinb-2 variants in 94 West European wheat genotypes and assessed their association with 13 quality traits considering population and family structure. The survey was completed by analyzing the Grain softness protein-1 gene. Results indicated sequence variation only for Pinb-D1 and Pinb-B2 genes. Pinb-D1b was the predominant hard allele. Pinb-B2v3-1 was the most common Pinb-2 variant, followed by a newly discovered variant Pinb-B2v3-5. Association mapping carried out in the whole sample population showed that Pinb-D1 alleles were associated with 11 quality traits, whereas Pinb-B2 variants were only associated with semolina extraction. Considering only the panel of hard wheat genotypes, variation for flour ash content, sedimentation value, gluten index and loaf volume was found to be associated with Pinb-D1 mutations suggesting that different Pinb-D1 mutations might have particular effects on quality traits. Our study indicated that Pinb-D1d was associated with inferior sedimentation value, gluten index and loaf volume, for which reason this mutation should be disregarded in breeding for quality wheat.     

Reduced height alleles (Rht) and Hagberg falling number of wheat

Near-isogenic lines varying for alleles for reduced height (Rht) and photoperiod insensitivity (Ppd-D1) in cv. Mercia (2005/6–2010/11; rht (tall), Rht-B1b, Rht-D1b, Rht-B1c, Rht8c+Ppd-D1a, Rht-D1c, Rht12) and cvs Maris Huntsman and Maris Widgeon (2007/8–2010/11; rht (tall), Rht-B1b, Rht-D1b, Rht-B1c, Rht-B1b+Rht-D1b, Rht-D1b+Rht-B1c) were compared at one field site, but within different systems (‘organic’, O, 2005/6–2007/8 v. ‘intensive’, I, 2005/6–2010/11). Further experiments at the site (2006/7–2008/9) compared 64 lines of a doubled-haploid (DH) population [Savannah (Rht-D1b) × Renesansa (Rht-8c+Ppd-D1a)]. Gibberellin (GA) insensitive dwarfing alleles (Rht-B1b; Rht-B1c; Rht-D1b; Rht-D1c) could reduce α-amylase activity and/or increase Hagberg falling number (HFN) but effects depended greatly on system, background and season. Only Rht-B1c increased grain dormancy despite producing plants taller than Rht-D1c. The GA-sensitive Rht8c+Ppd-D1a in Mercia was associated with reduced HFN but analysis of the DH population suggested this was more closely linked with Ppd-D1a, rather than Rht8c. The GA-sensitive severe-dwarfing allele Rht12 was associated with reduced HFN. Instability in HFN over season tended to increase with degree of dwarfing. There was a negative association between mean grain weight and HFN that was in addition to effects of Rht and Ppd-D1 allele.     

Development and characterization of a Triticum aestivum-H. villosa T5VS•5DL translocation line with soft grain texture

The Hardness locus on the short arm of chromosome 5D is the main determinant of grain texture in bread wheat. The Pina and Pinb genes are tightly linked at this locus, and the soft kernel texture phenotype results when both genes are present and encode the wild-type puroindoline proteins PINA and PINB. In this study a compensating T5VS•5DL Triticum aestivum-Haynaldia villosa translocation line, NAU415, was characterized by chromosome C-banding, genomic in situ hybridization and molecular markers. Single Kernel Characterization System (SKCS) analysis and scanning electron microscopy indicated that NAU415 had soft endosperm although it lacked the wheat Pina-D1a and Pinb-D1a genes, suggesting the presence of functional Pin gene orthologs on chromosome 5VS. Using a PCR approach, Pina-related (designated Dina) and Pinb-related (Dinb) genes in H. villosa and NAU415 were identified and sequenced. The nucleotide and predicted amino acid sequences showed close similarities to the wild-type puroindolines of T. aestivum cv. Chinese Spring. The tryptophan-rich regions of both Dina and Dinb showed a sequence change from lysine-42 to arginine, a feature that may have an effect on grain texture. The potential of T5VS•5DL translocation line as a source of genes that may be used for modulation of endosperm texture and other valuable traits in wheat breeding is discussed.     

甘肃冬小麦品种(系)面粉品质性状相关基因分析

为了解甘肃省近20年育成的106份冬小麦品种(系)中加工品质性状相关基因分布情况,用22个分子标记对供试材料的HMW-GS、LMW-GS、面粉色泽及籽粒硬度等品质性状相关基因进行了分析。结果发现,供试品种(系)的HMW-GS相关基因中,在Glu-A1位点检测到34份品种(系)含有AxNull,频率为32.08%;在Glu-B1位点检测到Bx7+By8和Bx14+By15共2种基因组合,分别占17.92%和25.47%;在Glu-D1位点检测到11份品种(系)含有Dx5+Dy10,占10.38%。对LMW-GS鉴定结果显示,29份品种(系)含Glu-A3d基因,分布频率为27.36%。HMW-GS和LMW-GS亚基组合中,含有4个、3个和2个位点优质亚基基因组合的品种(系)分别占0.94%、8.49%和3.77%。对面粉色泽相关基因Ppo-A1、Ppo-D1、Psy-A1、Lox-B1和TaPod-A1位点的检测发现,优异等位变异占比分别为39.62%、50.94%、31.13%、30.19%和38.68%。对籽粒硬度相关基因检测发现,在Pina、Pinb和Pinb-2等位变异位点的检测...     

Novel allelic variants encoded at the Glu-D3 locus in bread wheat

Low-molecular weight glutenin subunits (LWM-GS) are important components of wheat (Triticum aestivum L.) gluten, with important effects on end-use quality. The LMW-GS are encoded at Glu-3 loci (Glu-A3, Glu-B3 and Glu-D3, on the short arms of chromosomes 1A, 1B and 1D), each of which exhibits extensive allelic variation. Each locus encodes numerous LMW-GS, some of which have similar electrophoretic mobilities, making it difficult to distinguish among Glu-3 loci. Alleles of the Glu-D3 locus of bread wheat are considered the most problematic to assign. To date, six Glu-D3 alleles, designated a, b, c, d, e and f, have been reported. We report five previously undescribed alleles (g, h, i, j and k), and describe a method for characterizing them using a combination of SDS-PAGE and multiplexed PCR-based DNA markers. This method could be used for accurate identification of Glu-D3 alleles, permitting the estimation of the effects of these alleles on end-use quality and the selection of desirable alleles and allelic combinations in wheat breeding.     

黄淮麦区（南片）小麦粒重基因 TaGS-D1和 TaCwi-A1等位变异检测及效应分析

小麦粒重是影响小麦产量的重要因素,为了解小麦粒重基因 TaGS-D1和 TaCwi-A1及其等位变异在黄淮麦区（南片）新育成小麦品种（系）中的分布情况,以94份黄淮麦区（南片）新育成小麦品种（系）为试验材料,利用功能标记GS7D、CWI22和CWI21对试验材料中 TaGS-D1和 TaCwi-A1位点的等位变异进行检测,并分析了不同等位基因以及等位基因组合与粒重之间的关系。结果表明,在 TaGS-D1位点,共检测到 TaGS-D1a和 TaGS-D1b两种等位基因,分布频率分别为80.85%和19.15%,含有 TaGS-D1a等位基因的小麦材料的粒重显著高于含有 TaGS-D1b等位基因的材料;在 TaCwi-A1位点,共检测到 TaCwi-A1a和 TaCwi-A1b两种等位基因,分布频率分别为67.02%和32.98%,含有 TaCwi-A1a等位基因的小麦材料的粒重显著高于含有 TaCwi-A1b等位基因的材料;在 TaGS-D1和 TaCwi-A1位点,共检测到 TaGS-D1a/TaCwi-A1a、 TaGS-D1a/TaCwi-A1b、 TaGS-D1b/TaCwi-A1a和 TaGS-D1b/TaCwi-A1b四种等位基因组合,分布频率分别为56.38%、24.47%、10.64%和8.51%,含有 TaGS-D1a/TaCwi-A1a等位基因组合的小麦材料的粒重显著高于具有其余三种等位基因组合的材料,含有 TaGS-D1b/TaCwi-A1b等位基因组合的小麦材料的粒重显著低于具有其余三种等位基因组合的材料。     

江苏淮北地区小麦品种资源籽粒硬度基因等位变异的KASP检测

为了解江苏淮北地区小麦品种资源的籽粒硬度概况及硬度基因型分布规律,以74份近年来江苏淮北地区所育品种(系)和38份来自黄淮其他麦区的常用亲本为材料,采用单籽粒谷物硬度测试仪、KASP标记检测技术和基因扩增及测序技术对其SKCS硬度值及硬度基因型进行鉴定。硬度检测结果表明,供试小麦品种(系)硬度变化范围较大,但硬质麦的比例最大,为70.5%。与常用亲本相比,江苏淮北地区育成品种中软质麦比例较高,为34.3%,但在高代品系中软质麦比例下降到20.5%。基因型检测结果表明,在Puroindoline-D1位点,供试品种(系)中共检测到4种基因型,即野生型(Pina-D1a/Pinb-D1a)、Pina-D1b、Pinb-D1b和Pinb-D1p,其频率依次为25.0%、2.7%、67.9%和4.5%。其中,野生型和Pinb-D1p主要分布在江苏淮北地区。不同硬度基因型的硬度值也存在差异,其中以Pina-D1b基因型的硬度值最高,野生型(Pina-D1a/Pinb-D1a)硬度值最低,Pinb-D1b和Pinb-D1p两硬质类型的籽粒硬度没有显著性差异。在Pinb-2位点,供试品种(系)中共检测到25份材料为Pinb-B2b基因型,包含21份硬质麦、2份混合麦和2份软质麦,其平均硬度值为63.8。     

Waxy endosperm accompanies increased fat and saccharide contents in bread wheat (Triticum aestivum L.) grain

The contents of fat, starch, pentosan, fructan, β-glucan and several mono- and oligosaccharides in grain were evaluated to find out the possible effects of the Wx-D1 gene of bread wheat using two sets of near-isogenic waxy and non-waxy lines and two low-amylose mutant lines with a common genetic background of Kanto 107. These materials have two non-functional Wx-A1b and Wx-B1b alleles in common. Waxy near-isogenic lines with a non-functional Wx-D1d allele showed consistently increased contents of fat, total fructan, β-glucan, glucose, fructose, sucrose, 1-kestose, 6-kestose, neokestose, nystose and bifurcose compared with non-waxy lines with a functional Wx-D1a allele throughout three growing/harvest seasons. Starch and total pentosan contents were inconsistently influenced by the allelic status of the Wx-D1 locus, while water-soluble pentosan and raffinose contents were not affected. The compositional changes of a low-amylose mutant line with an almost non-functional Wx-D1f allele were closely similar to those of waxy near-isogenic lines, while significantly different changes were barely observed in another low-amylose mutant line with a partly functional Wx-D1g allele in two seasons. These results showed that the Wx-D1 gene has pleiotropic effects on the fat and saccharide contents of bread wheat grain.     

Development of STS markers and establishment of multiplex PCR for Glu-A3 alleles in common wheat (Triticum aestivum L.)

Low-molecular-weight glutenin subunits (LMW-GS) play a key role in determining the processing quality of the end-use products of common wheat. The objectives of this study were to identify genes at Glu-A3 locus, develop the STS markers, and establish multiplex PCR with the STS markers for Glu-A3 alleles. Gene-specific PCR primers were designed to amplify six near-isogenic lines (NILs) and Glenlea with different Glu-A3 alleles (a, b, c, d, e, f and g) defined by the protein electrophoretic mobility. Three Glu-A3 genes with complete coding sequence were cloned, designated as GluA3-1, GluA3-2 and GluA3-3, respectively. Seven dominant allele-specific STS (sequence tagged sites) markers were designed based on the SNPs (single nucleotide polymorphisms) among different allelic variants for the discrimination of the Glu-A3 protein alleles a, b, c, d, e, f and g. Four multiplex PCRs were established including Glu-A3b + Glu-A3f, Glu-A3d + Glu-A3f, Glu-A3d + Glu-A3g, and Glu-A3b + Glu-A3e. These markers and multiplex-PCR systems were validated on 141 CIMMYT wheat varieties and advanced lines with different Glu-A3 alleles, confirming that they can be efficiently used in marker-assisted breeding.     

New insights into high-molecular-weight glutenin subunits and sub-genomes of the perennial crop Thinopyrum intermedium (Triticeae)

Intermediate wheatgrass (Thinopyrum intermedium) is a perennial crop that possesses desirable agronomic traits and provides environmental services, e.g., reducing soil erosion, nitrate leaching and inputs of energy and pesticide. Thus, intermediate wheatgrass is currently being domesticated as a perennial grain crop. However, the genetic information for molecular breeding is quite limited. Here we report a molecular analysis of high-molecular-weight glutenin subunits (HMW-GS) in intermediate wheatgrass using gene cloning and protein biochemistry. Five HMW-GS genes were isolated from individual intermediate wheatgrass plants: two x-type genes TiHGS1 and TiHGS4, and three y-type genes TiHGS2, TiHGS3 and TiHGS5. Among them, TiHGS5 was novel and possessed an additional cysteine residue at the N-terminal domain or repetitive domain. Sequence alignments showed that TiHGS1 and TiHGS2 genes shared high identities (>96%) with the Glu-1Dx and Glu-1Dy genes, respectively, in common wheat and Aegilops species, TiHGS3 with HMW-GS genes from Dasypyrum or Pseudoroegneria, and TiHGS4 and TiHGS5 with HMW-GS genes from Thinopyrum elongatum. This work provides substantial new insights into the gene compositions and protein profiles of HMW-GS in intermediate wheatgrass, and also gives evidence about the genome components of intermediate wheatgrass.     

Variation in Friabilin Composition as Determined by A-PAGE Fractionation and PCR Amplification, and its Relationship to Grain Hardness in Bread Wheat

A-PAGE fractionation of starch granule proteins from 63 bread wheat cultivars with contrasting grain texture characteristics revealed two prominent polypeptides and three minor ones, approximately 15 kDa in size. These proteins were found to be encoded by genes on the short arm of chromosome 5D. The two major friabilin components were assumed to correspond to puroindolines a and b (pinA and pinB), as suggested by PCR amplification of genes coding for pinA, glycine-type or serine-type pinB. Two electrophoretic patterns for pinA (presence vs absence) and three patterns for pinB were obtained by A-PAGE. In cultivars with pinA (allele Pina-D1a), pinB was found to be encoded by wild-type Pinb-D1a, serine-type Pinb-D1b or by the novel glycine-type b1 allele. Cultivars lacking pinA (allele Pina-D1b) were shown to contain eitherPinb-D1a or the novel b2 allele, both alleles coding for glycine-type pinB. The intensity of pinB in A-PAGE gels was found to be associated with grain hardness as determined by the SKCS method. Cultivars lacking pinA had the highest SKCS values, suggesting that both pinA and pinB may affect grain texture. In the presence of pinA, cultivars with wild-type allelePinb-D1a had soft grain texture, whereas those with alleles Pinb-D1b or b1 showed increased grain hardness. It is suggested that allele b1 affects the interaction of pinB with starch granules because of a sequence mutation different from the glycine-to-serine change.     

Effect of the grain protein content locus Gpc-B1 on bread and pasta quality

Grain protein concentration (GPC) affects wheat nutritional value and several critical parameters for bread and pasta quality. A gene designated Gpc-B1, which is not functional in common and durum wheat cultivars, was recently identified in Triticum turgidum ssp. dicoccoides. The functional allele of Gpc-B1 improves nitrogen remobilization from the straw increasing GPC, but also shortens the grain filling period resulting in reduced grain weight in some genetic backgrounds. We developed isogenic lines for the Gpc-B1 introgression in six hexaploid and two tetraploid wheat genotypes to evaluate its effects on bread-making and pasta quality. In common wheat, the functional Gpc-B1 introgression was associated with significantly higher GPC, water absorption, mixing time and loaf volume, whereas in durum wheat, the introgression resulted in significant increases in GPC, wet gluten, mixing time, and spaghetti firmness, as well as a decrease in cooking loss. On the negative side, the functional Gpc-B1 introgression was associated in some varieties with a significant reduction in grain weight, test weight, and flour yield and significant increases in ash concentration. Significant gene × environment and gene × genotype interactions for most traits stress the need for evaluating the effect of this introgression in particular genotypes and environments.     

Pins基因等位变异对磨粉品质和新疆拉面加工品质的影响

为了探讨新疆冬小麦品种Pins基因等位变异对小麦磨粉品质和新疆拉面加工品质的影响，对109份新疆冬小麦品种的籽粒硬度及其Pins基因等位变异、磨粉品质和新疆拉面加工品质进行测定，初步分析了新疆冬小麦品种资源籽粒硬度Pins基因的分布规律以及不同 Pins基因等位变异对籽粒硬度、磨粉品质和新疆拉面加工品质的影响。结果表明，新疆冬小麦品种属硬质麦类型，Pins基因型以 Pina-D1a、 Pinb-D1b和 Pina-D1a/ Pinb-D1b为主， Pins突变类型及Pins突变基因型组合类型小麦的籽粒硬度均显著高于野生型， Pinb-D1a基因型小麦的籽粒硬度最低，L^*值和a^*值最高，b^*值最低； Pinb-D1ab基因型小麦的吸水率最高。不同Pins基因型组合中，野生型小麦的籽粒硬度、b^*值和吸水率最低； Pina-D1a/ Pinb-D1aa的出粉率最高， Pina-D1a/ Pinb-D1ab的灰分含量最低，吸水率最高。Pins基因及其基因型组合对新疆拉面加工品质无直接影响，主要通过对灰分、面粉色泽和吸水率等磨粉品质的作用对新疆拉面产生间接影响。优质新疆拉面品种中，Pinb基因突变对新疆拉面加工品质的影响大于Pina基因突变，育种中应优先选择Pinb 基因突变型材料，其中 Pina-D1a/ Pinb-D1b可以作为重点选择的基因型组合。