Sequence variation in the barley genes encoding sucrose synthase I and sucrose phosphate synthase II,and its association with variation in grain traits and malting quality

Sequence diversity in the two barley (Hordeum vulgare L.) genes encoding sucrose synthase I (SSI) and sucrose phosphate synthase II (SPSII), both of which are involved in sucrose accumulation and grain filling, was studied by partial resequencing of eight reference genotypes and SNP analysis by pyrosequencing in a panel of 94 spring and 96 winter European barley varieties. The resequencing was based on two adjacent SSI fragments of size 880 and 820 bp, and a 2,322 bp SPSII fragment. In the SSI gene, 26 SNPs were present in the larger fragment, and 25 in the smaller one, and 11 of these were exploited to develop high-throughput SNP assays used for haplotype analysis. An association analysis based on either a general or a mixed linear model suggested that the predominant three haplotypes influenced certain components of both kernel and malting quality. However, the level of phenotype/haplotype association shown with the SPSII gene was rather low. SNP variation of SSI was used to map the locus to chromosome 7H.     

Localisation and combination of resistance genes against soil-borne viruses of barley (BaMMV,BaYMV) using doubled haploids and molecular markers

Barley yellow mosaic virus disease caused by different strains of BaYMV and BaMMV is a major threat to winter barley cultivation in Europe. Different resistance genes against these viruses have been mapped and suitable PCR-based markers have been developed. In this respect doubled haploid (DH) populations proved to be advantageous as they facilitate a repeated test for resistance against all agents of the barley yellow mosaic virus complex and besides this, dominant marker systems are as informative as co-dominant ones in DHs due to the lack of heterozygous genotypes. Using DH populations resistance genes rym4, rym5, rym11, rym13, rym15 and the BaYMV/BaYMV-2 resistance of the barley cultivar ‘Chikurin Ibaraki 1’ have been mapped. DHs are also well suited to pyramiding resistance genes against BaMMV and BaYMV. Since homozygous recessive genotypes are more frequent in DHs than in segregating F₂ populations, DHs can be efficiently used to create broad-spectrum resistance and to extend the usability of partly overcome resistance genes. Results from employing two different strategies for pyramiding, based on one and two DH-steps, respectively, combining three recessive resistance genes, i.e. rym4/rym5, rym9 and rym11, are presented. The faster strategy based on one haploidy step resulted in the identification of all three and two-way combinations of the respective resistance genes.     

Allelic variation for the rust resistance gene <Emphasis Type="Italic">Lr34</Emphasis>/<Emphasis Type="Italic">Yr18</Emphasis> in Canadian wheat cultivars

The wheat (Triticum aestivum L.) gene Lr34/Yr18 conditions resistance to leaf rust, stripe rust, and stem rust, along with other diseases such as powdery mildew. This makes it one of the most important genes in wheat. In Canada, Lr34 has provided effective leaf rust resistance since it was first incorporated into the cultivar Glenlea, registered in 1972. Recently, molecular markers were discovered that are either closely linked to this locus, or contained within the gene. Canadian wheat cultivars released from 1900 to 2007, breeding lines and related parental lines, were tested for sequence based markers caSNP12, caIND11, caIND10, caSNP4, microsatellite markers wms1220, cam11, csLVMS1, swm10, csLV34, and insertion site based polymorphism marker caISBP1. Thirty different molecular marker haplotypes were found among the 375 lines tested; 5 haplotypes had the resistance allele for Lr34, and 25 haplotypes had a susceptibility allele at this locus. The numbers of lines in each haplotype group varied from 1 to 140. The largest group was represented by the leaf rust susceptible cultivar “Thatcher” and many lines derived from “Thatcher”. The 5 haplotypes that had the resistance allele for Lr34 were identical for the markers tested within the coding region of the gene but differed in the linked markers wms1220, caISBP1, cam11, and csLV34. The presence of the resistance or susceptibility allele at the Lr34 locus was tracked through the ancestries of the Canadian wheat classes, revealing that the resistance allele was present in many cultivars released since the 1970s, but not generally in the older cultivars.     

Candidate markers for powdery mildew resistance genes from wild barley PI284752

PI284752, an accession of wild barley (Hordeum vulgare ssp. spontaneum) resistant to powdery mildew caused by Blumeria graminis f.sp. hordei, was studied with the aim of identifying genes involved in powdery mildew resistance. An F₂ population (456 plants) was established from a cross between the winter barley variety ‘Tiffany’ and PI284752. This cross demonstrated a two-locus model of resistance. Linkage analysis using polymorphic DNA markers was carried out on 180 plants. The RGH1a gene sequence from the Mla locus was used as a source for developing the RGH1aE2I2 marker. By interval mapping on chromosome 1HS, one resistance gene was found to be tightly linked with RGH1aE2I2 and it was found to be located 2 cM from GBMS062. In F₂ plants exhibiting resistance reaction type (RT) 0, specific DNA fragments for the RGH1aE2I2 marker were amplified. In plants with RT1 to RT2-3, the resistance was conferred exclusively by the second R gene that we identified, which is linked with Bmac0134 and GBMS247 on chromosome 2HS. The aforementioned markers may be valuable candidates for marker-assisted selection of resistant genotypes conferred by one or both genes.     

Understanding physiological and morphological traits contributing to drought tolerance in barley

Drought stress is a major limiting factor for crop production in the arid and semi‐arid regions. Here, we screened eighty barley (Hordeum vulgare L.) genotypes collected from different geographical locations contrasting in drought stress tolerance and quantified a range of physiological and agronomical indices in glasshouse trails. The experiment was conducted in large soil tanks subjected to drought treatment of eighty barley genotypes at three‐leaf stage and gradually brought to severe drought by withholding irrigation for 30 days under glasshouse conditions. Also, root length of the same genotypes was measured from stress‐affected plants growing hydroponically. Drought tolerance was scored 30 days after the drought stress commenced based on the degree of the leaf wilting, fresh and dry biomass and relative water content. These characteristics were related to stomatal conductance, stomatal density, residual transpiration and leaf sap Na, K, Cl contents measured in control (irrigated) plants. Responses to drought stress differed significantly among the genotypes. The overall drought tolerance was significantly correlated with relative water content, stomatal conductance and leaf Na⁺ and K⁺ contents. No significant correlations between drought tolerance and root length of 6‐day‐old seedling, stomatal density, residual transpiration and leaf sap Cl^? content were found. Taking together, these results suggest that drought‐tolerant genotypes have lower stomatal conductance, and lower water content, Na⁺, K⁺ and Cl^? contents in their tissue under control conditions than the drought‐sensitive ones. These traits make them more resilient to the forthcoming drought stress.     

Association analysis of five candidate genes with plant height and dry matter yield in perennial ryegrass

Five candidate genes LpIAA1, LpRUB1, LpBRI1, LpSHOOT1 and LpTB1 with putative function in plant architecture were allele sequenced in a panel of 96 diploid perennial ryegrass genotypes of diverse origin. The total length of the non‐redundant genomic DNA alignment was 5425 bp and revealed 270 polymorphic sites in total. A negative significant Tajima's D value was detected in LpTB1 gene, suggesting selection pressure for low‐frequency alleles in this gene. All 96 genotypes were evaluated for plant height and dry matter yield over two years. Marker–trait associations were calculated between polymorphic sites and both phenotypic traits. Three indels and three single nucleotide substitutions in LpTB1 gene were significantly (P < 0.05, q < 0.05) associated with plant height, while one indel was associated with dry matter yield. The results suggest putative role of LpTB1 gene in plant height determination in perennial ryegrass and provide means for target allele selection.     

QTL mapping for heading date,leaf area and chlorophyll content under cold and drought stress in two related recombinant inbred line populations (Japonica rice) and meta‐analysis

Rice is highly susceptible to drought and cold. The goal of this study was to identify the QTLs affecting the rice heading date (HD), leaf area (LA) and chlorophyll content (CC) under cold and drought stress. A total of twenty‐nine and thirty‐eight additive QTLs were detected from two crosses of ‘Dongnong422’/‘Kongyu131’ and ‘Xiaobaijingzi’/‘Kongyu131’, respectively. qHD1‐7‐1, qHD1‐7‐2, qHD1‐2‐1, qLA1‐7‐1, qLA1‐6‐3 and qCC1‐7‐1 show adaptive effects under cold treatment, while qHD2‐2‐3, qHD2‐2‐2, qLA2‐7‐3 and qCC2‐5‐1 were important for explaining the genetic mechanism during drought tolerance. Additionally, nine and five additive × environment interaction QTLs were detected for two RILs, respectively. RIL26 and RIL73 were two lines that are associated with cold and drought for HD. 339 QTLs related to HD, CC and LA of rice from database and our research were projected onto the genetic map. Nine cloned genes and nineteen homologous candidate genes related to HD, CC, cold tolerance and drought tolerance were mapped by meta‐analysis. These results lay the foundation for the fine mapping of QTLs related to HD, LA and CC for marker‐assisted selection.     

Molecular mapping of genes involved in root hair formation in barley

In the presented study, the existing AFLP and SSR maps of barley were used to find chromosomal position of four genes controlling different stages of root hair development. Four barley mutants were used in the analysis: the root hairless mutant rhl1.b, mutant rhp1.b with root hair development blocked at the initial bulge formation, mutant rhi1.a with irregular pattern of sparsely located root hairs and mutant rhs1.a with very short root hairs. Each mutant was crossed with parents of ‘Steptoe’/‘Morex’ mapping population and F₂ progenies of crosses: mutant × ‘Steptoe’ and mutant × ‘Morex’ were analyzed for segregation of root hair phenotype and polymorphic AFLP and SSR markers. It was possible to map all the analyzed genes on barley chromosomes: rhl1 gene on the short arm of chromosome 7H, rhp1 gene on chromosome 1H, rhs1 locus in the pericentromeric region of chromosome 5H and rhi1 gene on the long arm of chromosome 6H. Subsequently, the Bulk Segregant Analysis and AFLP technique were used for saturation of the identified regions with new markers. The joint maps were constructed using as common points the SSR markers located in the target regions. Linkage maps of the regions around the four genes involved in the root hair formation in barley were composed of 8–11 markers and spanned over 16.1–49.0 cM. The distances between localized genes and the closest markers ranged from 1.0 to 3.8 cM. The identified chromosomal locations of genes can be used for their fine mapping and future map-based cloning.     

A method for testing drought tolerance in <Emphasis Type="Italic">Fragaria</Emphasis> based on fast screening for water deficit response and use of associated AFLP and EST candidate gene markers

Drought stress is one of the most important environmental factors that limit plant growth and development, thus reducing yield. The objective of the present research was to correlate the genetic structure of different Fragaria genotypes, as assessed by Expressed Sequence Tag (EST) and Amplified Fragment Length Polymorphism (AFLP) markers, and plant responses to drought stress. Firstly, physiological parameters related to the plant response to drought stress such as leaf relative water content (RWC) and water losing rate (WLR) were measured. WLR and RWC were compared for 20 cultivars of the octaploid Fragaria × ananassa, two ecotypes of the diploid species F. vesca and one octaploid species F. chiloensis. These parameters could discriminate genotypes showing a contrasting response to water stress. Secondly, AFLP and ESTs were compared in terms of their information content and efficiency in the study of genetic diversity and relationships among these 23 Fragaria genotypes. To evaluate the genetic basis for the observed variation in the measured physiological parameter, the effect of specific AFLP/EST loci on WLR and RWC for the different Fragaria genotypes was quantified by Kruskal–Wallis analysis. By Mantel testing, the hierarchical clustering of the Fragaria genotypes based on associated EST or AFLP markers was compared to the observed eco-physiological relevant grouping. A better discriminating capacity for associated markers was noted, enabling a functional marker selection approach to screen the strawberry gene pool for drought tolerance. Correlation of EST markers to leaf RWC and WLR enforces them as potential candidate genes in control of plant responses to drought stress in Fragaria sp.     

Molecular assessment of genetic diversity in winter barley and its use in breeding

Summary During the last decades extensive progress has been achieved in winter barley breeding with respect to both, yield and resistance to fungal and viral diseases. This progress is mainly due to the efficient use of the genetic diversity present within high yielding adapted cultivars and – with respect to resistance – to the extensive evaluation of genetic resources followed by genetic analyses and introgression of respective genes by sexual recombination. Detailed knowledge on genetic diversity present on the molecular level regarding specific traits as well as on the whole genome level may enhance barley breeding today by facilitating efficient selection of parental lines and marker assisted selection procedures. In the present paper the state of the art with respect to virus diseases, i.e. Barley mild mosaic virus, Barley yellow mosaic virus, and Barley yellow dwarf virus is briefly reviewed and first results on a project aiming on a genome wide estimation of genetic diversity which in combination with data on yield and additional agronomic traits may facilitate the detection of marker trait associations and a more efficient selection of parental genotypes are presented. By field tests of 49 two-rowed and 64 six-rowed winter barley cultivars the genetic gain in yield for the period 1970–2003 was estimated at 54.6 kg ha⁻¹ year⁻¹ (r² = 0.567) for the six-rowed cultivars and at 37.5 kg ha⁻¹ year⁻¹ (r² = 0.621) for the two-rowed cultivars. Analysis of 30 SSRs revealed a non-homogenous allele distribution between two and six-rowed cultivars and changes of allele frequencies in relation to the time of release. By PCoA a separation between two and six-rowed cultivars was observed but no clear cut differentiation in relation to the time of release. In the two-rowed cultivars an increase in genetic diversity (DI) from older to newly released cultivars was detected.     

Gene expression analysis of four WIR1-like genes in floret tissues of European winter wheat after challenge with <Emphasis Type="Italic">G. zeae</Emphasis>

Fusarium head blight (FHB) is a highly destructive disease of wheat and other cereals which causes serious mycotoxin contaminations of grain. A number of molecular mapping studies led to the detection of QTL with small to moderate effects on FHB resistance in European winter wheat. Genes involved in the defence reaction of these genotypes remain largely unknown. WIR1 (wheat induced resistance 1) genes have been shown to be upregulated in cereals during attack of various fungal pathogens; however, their role in resistance is ambiguous. In this study, the expression of three WIR1 genes and a gene with high sequence similarity to WIR1 was investigated in European winter wheat genotypes after inoculation with Giberella zeae. Floret tissues of four winter wheat genotypes (Dream, Lynx, G16-92, Hussar) were challenged with G. zeae conidia or water (control) and sampled six times during 0–96 h after inoculation. Quantitative real-time PCR showed that all four genes were highly upregulated in the resistant genotypes compared to the susceptible ones. WIR1b and a gene with sequence similarity to WIR1 genes mapped to chromosome 5DS in the G16-92/Hussar mapping population. Two genes annotated as WIR1a mapped in the interval of a FHB resistance QTL on chromosome 7BS in the Dream/Lynx mapping population. These could be considered possible candidate genes for quantitative FHB resistance.     

Genetic variability among sugarcane genotypes based on polymorphisms in sucrose metabolism and drought tolerance genes

Target region amplification polymorphism (TRAP) markers were used to estimate the genetic similarity (GS) among 53 sugarcane varieties and five species of the Saccharum complex. Seven fixed primers designed from candidate genes involved in sucrose metabolism and three from those involved in drought response metabolism were used in combination with three arbitrary primers. The clustering of the genotypes for sucrose metabolism and drought response were similar, but the GS based on Jaccard’s coefficient changed. The GS based on polymorphism in sucrose genes estimated in a set of 46 Brazilian varieties, all of which belong to the three Brazilian breeding programs, ranged from 0.52 to 0.9, and that based on drought data ranged from 0.44 to 0.95. The results suggest that genetic variability in the evaluated genes was lower in the sucrose metabolism genes than in the drought response metabolism ones.     

Breeding drought tolerant cowpea: constraints,accomplishments, and future prospects

This review presents an overview of accomplishments on different aspects of cowpea breeding for drought tolerance. Furthermore it provides options to enhance the genetic potential of the crop by minimizing yield loss due to drought stress. Recent efforts have focused on the genetic dissection of drought tolerance through identification of markers defining quantitative trait loci (QTL) with effects on specific traits related to drought tolerance. Others have studied the relationship of the drought response and yield components, morphological traits and physiological parameters. To our knowledge, QTLs with effects on drought tolerance have not yet been identified in cowpea. The main reason is that very few researchers are working on drought tolerance in cowpea. Some other reasons might be related to the complex nature of the drought stress response, and partly to the difficulties associated with reliable and reproducible measurements of a single trait linked to specific molecular markers to be used for marker assisted breeding. Despite the fact that extensive research has been conducted on the screening aspects for drought tolerance in cowpea only very few—like the ‘wooden box’ technique—have been successfully used to select parental genotypes exhibiting different mechanisms of drought tolerance. Field and pot testing of these genotypes demonstrated a close correspondence between drought tolerance at seedling and reproductive stages. Some researchers selected a variety of candidate genes and used differential screening methods to identify cDNAs from genes that may underlie different drought tolerance pathways in cowpea. Reverse genetic analysis still needs to be done to confirm the functions of these genes in cowpea. Understanding the genetics of drought tolerance and identification of DNA markers linked to QTLs, with a clear path towards localizing chromosomal regions or candidate genes involved in drought tolerance will help cowpea breeders to develop improved varieties that combine drought tolerance with other desired traits using marker assisted selection.

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TaMyb2-Ⅱ基因在普通小麦(Triticum aestivum L.)及其近缘种中的单核苷酸多态性分析

以39份抗旱性不同的普通小麦、5份A基因组材料、4份拟斯卑尔脱山羊草（Aegilops speltoides）、6份粗山羊草（Aegilops tauschii）和2份四倍体小麦,分析TaMyb2基因的核苷酸序列长度多态性和单核苷酸多态性,及其与抗旱性的关系。结果发现,TaMyb2在A基因组材料中无目标片段扩增,在其他材料中检测到Ⅰ、Ⅱ、Ⅲ 3种类型序列。经详细分析,TaMyb2-Ⅱ序列长1 606 bp,在供试材料77 088 bp的核苷酸序列中包括34个单核苷酸变异,其中26个SNP,8个InDel,二者出现的频率分别为1/2 965 bp和1/9 636 bp,编码区π值（0.00055）小于非编码区的π值（0.00185）, 说明编码区的遗传变异小于非编码区的遗传变异。从SNP水平上分析,发现普通小麦与其D基因组供体种粗山羊草及四倍体小麦的亲缘关系较近,与B基因组供体种拟斯卑尔脱山羊草的亲缘关系较远。48份材料的TaMyb2-Ⅱ序列共分为18个单倍型（haplotype）,其中haplotype 2、3、5、6、8、9均为旱地栽培的普通小麦品种,说明普通小麦TaMyb2-Ⅱ的这几个haplotype结构可能与抗旱性有关。     

Tolerance to paraquat is correlated with the traits associated with water stress tolerance in segregating F2 populations of barley and wheat

To identify scorable marker traits that can be used in cereal breeding programs for selecting drought tolerant individuals, we investigated the correlation among the drought-associated traits in two F₂ populations derived from the crosses made between drought tolerant and sensitive barley and wheat parental genotypes. The parental genotypes of these crosses also differed by at least three other traits – paraquat tolerance, leaf size, and the relative water content. These three traits were scored in two F₂populations of 80 individuals for each barley and wheat cross. Analysis of results indicated that the enhanced tolerance to paraquat was correlated with reduced leaf size and increased relative water content, two traits associated with water stress phenotypes of the drought tolerant barley and wheat parents. Our results suggested that the selection based on paraquat tolerance istechnically less demanding and thus useful for rapid screening of individuals for enhanced drought tolerance in segregating populations. This revised version was published online in August 2006 with corrections to the Cover Date.     

Novel molecular marker associated with Tm2a gene conferring resistance to tomato mosaic virus in tomato

Tomato mosaic virus (ToMV) is an important Tobamovirus that causes significant crop losses. Resistance to the ToMV is conferred by the genes Tm1, Tm2 and Tm2^a. Among these three genes, Tm2^a confers resistance to most strains of the ToMV. Screening of genetic lines under field conditions based on phenotype is time‐consuming and challenging due to concerns associated with stability of the virus and its potential transmission to other plants. Tightly linked molecular markers associated with resistance genes can improve selection efficiency and avoid these problems. This study developed a PCR‐based marker based on restriction site differences from Tm2^a locus‐specific sequences, which was found to be useful in identifying the resistant and susceptible genotypes and was consistent with phenotypic data. The marker is a codominant cleaved amplified polymorphic sequence (CAPS) marker producing 270‐ and 600‐bp DNA fragments from resistant genotypes and an 870‐bp fragment from susceptible genotypes when digested with HaeIII restriction enzyme. This novel marker can be useful for tomato breeders to screen progeny from segregating populations for ToMV resistance.     

Identification and characterization of seedling and adult plant resistance to Puccinia hordei in Chinese barley germplasm

Leaf rust of barley, caused by Puccinia hordei, occurs in all barley‐growing regions of Australia causing significant yield losses under epidemic conditions. The development and use of resistant cultivars are the most economical and environmentally sustainable method to control leaf rust which in turn relies on ongoing efforts to identify and characterize new sources of resistance. The aim of this study was to postulate known genes and/or identify new sources of resistance to P. hordei. Fifty‐two genotypes were assessed at the seedling and adult plant growth stages. On the basis of multipathotype tests, 39 genotypes lacked detectable seedling resistance, and nine were postulated to carry the genes Rph2, Rph4, Rph12 and Rph19 singly. Four genotypes carried uncharacterized seedling resistance; however, the gene(s) present in each were ineffective to at least one of the pathotypes used. Field tests at the adult plant growth stage revealed the presence of adult plant resistance (APR) in 12 genotypes. Tests of allelism and marker analysis indicated that resistance genes present in these genotypes were independent of the APR gene Rph20.     

Development of two new molecular markers specific to cytoplasmic male sterility in tuber mustard (<Emphasis Type="Italic">Brassica juncea</Emphasis> var. <Emphasis Type="Italic">tumida</Emphasis> Tsen et Lee)

A novel and stable cytoplasmic male sterility CMS line of tuber mustard has been bred by subsequent backcrosses for 10 years. Two specific markers atpA and orf220 were cloned and partially characterized in our previous study (Zhang et al. 2003). In this study, two new molecular markers, orf256 and orf305/orf324, have been isolated and identified. The orf256 gene size was found to be 825 bp in CMS line and a 1,357 bp in its maintainer line. Sequence analysis indicated that the orf256 gene was an entire coding sequence and downstream of the cox1 gene. Interestingly, the 906 bp fragment, which contains part of the sequence of orf222, nad5 and orf139 genes, was found to be inserted from the 451st bp of 5′-flank of the 1,357 bp fragment. In the same way, the orf324 gene was isolated from CMS line and orf305 gene from its maintainer line. Both of them are entire coding sequences, upstream from nad3 and rps12 gene, and co-transcribed with the nad3 and rps12 genes. In addition, two molecular markers, orf256 and orf324/orf305, have been successfully converted into the SCAR markers. Subsequently, ORF256, ORF324, ORF305 protein and ORF256-M-431 fragment are predicated to contain signal peptide sequences, and ORF220 was predicated to contain signal anchor sequence. RFLP analysis results revealed that all of the molecular markers exhibited polymorphisms. Northern blot analysis indicated that the expression level of these genes in CMS line is higher than that of the maintainer line. In the mass, all of these genes are expressed lower in the leaf than that of floral organs between the CMS line and its maintainer line. The difference in expression pattern of different mitochondrial specific marker genes suggests that the abundance of mitochondrial proteins is differentially regulated in the organ/tissue development in tuber mustard. Results of this study also provide some novel and useful clues to explore the biological function of these specific marker genes in the tuber mustard.     

Haplotype analysis of <Emphasis Type="Italic">Viviparous</Emphasis>-<Emphasis Type="Italic">1</Emphasis> gene in CIMMYT elite bread wheat germplasm

Pre-harvest sprouting (PHS) greatly reduces the quality and economic value of wheat grain. In this study, a total of 168 International Maize and Wheat Improvement Center (CIMMYT) wheat germplasm lines were examined to characterize the haplotypes of Vp-1A, Vp-1B and Vp-1D, which are located on the long arms of chromosomes 3A, 3B and 3D, respectively. Among them, five new alleles of Vp-1Aa (the wild allele) were identified on chromosome 3A, and designated as Vp-1Ab, Vp-1Ac, Vp-1Ad, Vp-1Ae and Vp-1Af, respectively. The main difference between Vp-1Aa and the newly identified alleles was in the numbers of CTT repeats located in the third intron, but Vp-1Af also had 6 and 2 bp deletions at positions 2860–2865 bp and 2880–2881 bp, and possessed five SNPs within the same intron region. In the Vp-1B locus, several alleles (Vp-1Ba, Vp-1Bb, Vp-1Bc, Vp-1Bd, Vp-1Be and Vp-1Bf) have already been identified. In the present material only two, the already known allele Vp-1Bc, and a new one, designated as Vp-1Bg, were detected. Compared with Vp-Ba, Vp-1Bg had additional insertion of TCC at position 2372 bp and a 9 bp change from CTGCATC AC to GCATCAGTG at 2417–2425 bp. However, no polymorphism was detected in Vp-1D. The frequencies of Vp-1Aa Vp-1Ab, Vp-1Ac, Vp-1Ad, Vp-1Ae, and Vp-1Af were 65, 10, 11, 4, 5 and 5%, respectively. For Vp-1B, 155 out of the 168 lines were Vp-1Bc; the remaining 13 were Vp-1Bg. Analyses of the germination index (GI) and abscisic acid (ABA) sensitivity showed that genotypes with Vp-1Ab or Vp-1Af showed higher PHS resistance than the ones with other alleles, suggesting that they might be valuable for CIMMYT breeding program or germplasm introduction. The results presented here will underpin the introduction of germplasm from CIMMYT and the improvement of PHS resistance, both in CIMMYT and elsewhere.