Quantitative trait loci mapping of freezing tolerance and photosynthetic acclimation to cold in winter two‐ and six‐rowed barley

Photoacclimation (PA) and freezing tolerance (FT) have been identified as closely related traits, due to common mechanisms of environmental control. In this study, diversity array technology (DArT) was used for identification of the quantitative trait loci (QTL) of FT and PA in winter barley. Simple sequence repeat (SSR) and single nucleotide polymorphism (SNP) markers were subsequently used to saturate QTL regions. Two F₂ mapping populations were created, for two‐rowed (P44) and six‐rowed barley (CaP). Different regions of the genome were responsible for differences in traits between parents in these two populations. Eleven QTLs were identified in the P44 population, including five typical for FT and PA, on chromosomes 2H, 3H and 7H. In the CaP population, only one QTL connected with PA and 10 connected with FT were found on all chromosomes except 2H. Our results demonstrate that different sets of markers should be applied in marker‐assisted selection for FT in two‐ and six‐rowed barley, as several loci determine FT at the level of biparental crosses.     

大麦遗传多样性及连锁不平衡分析

为了合理评价引进种质资源,为大麦基因发掘及育种组合配置提供依据,选用分布于全基因组的64个SSR标记,对221份大麦材料进行了基因型分析。共检测到192个等位变异,变幅为2~7个;基因频率变异范围为0.0090~0.9729,平均0.3333;全部位点的基因多样性变化范围在0.0528~0.7807,平均0.4813;多态性信息含量(PIC)变异范围在0.0514~0.7464,平均0.4113。供试材料间遗传相似系数变幅为0.4844~0.9792,平均0.7023。221份材料被划分成两大群7个亚群,国内地方品种与1份北京品种为一大群,国内育种品种与所有国外引进品种为另一群。遗传结构分析与聚类结果基本一致,两大类群间的遗传距离为0.3358,且第二大群多样性比第一大群丰富。2016个SSR位点成对组合中,不论共线性组合还是非共线性组合,都存在一定程度的连锁不平衡(LD)。D′统计概率(P<0.01)支持的LD成对位点830个,占全部位点组合的41.2%,D′平均值为0.4,整体LD水平较高。栽培品种的LD水平高于地方品种,且现代遗传改良的目标性状集中于2H、4H、6H和7H染色体。     

Ribosomal DNA spacer-length polymorphisms in three samples of wild and cultivated barleys and their relevance to the origin of cultivated barley

This study was conducted to provide additional data for evaluating two important issues surrounding the origin of cultivated barley: (i) the level of genetic diversity of the two‐rowed wild barley from Tibet, and (ii) the distribution of rDNA allele 104 in wild and cultivated barleys in the Occidental region. A total of 198 accessions consisting of three distinct samples were used: 82 entries of two‐rowed wild barley from Tibet, 57 accessions of two‐rowed wild barley from 8 countries with a broad range of representation of two‐rowed wild barley in the world, and 59 landrace accessions from four countries representing a part of the barley‐growing areas in the Middle East. These were assayed for rDNA spacer‐length variants (slvs). In all, 27 rDNA space length pheno types were detected, from which 10 slvs were identified as alleles at the two rDNA loci. The two‐rowed wild barley samples from Tibet had the lowest level of genetic variation as evaluated by rDNA polymorphism. Together with results of previous studies, the two wild forms (two‐rowed and six‐rowed) from Tibet could not account for the large genetic diversity observed in the cultivated barley of this region, suggesting that Tibet is unlikely a centre of origin for cultivated barley. In samples from the Occidental region, allele 104 of Rm2 was very rare in wild barley, but occurred at the highest frequency in cultivated barley, while the reverse is the case for allele 107, which is consistent with previous results. The implications of such a contrasting distribution of these rDNA alleles between wild and cultivated barleys in the origin and evolution of cultivated barley were discussed.     

Potential loss of unique genetic diversity in tomato landraces by genetic colonization of modern cultivars at a non-center of origin

We report the genetic diversity of tomato landraces from Myanmar, with reference to worldwide tomato accessions. Ten simple sequence repeat markers were screened and used to create diversity profiles of tomato germplasm. A total of 133 alleles were amplified from the germplasm investigated; alleles specific to landraces from Myanmar were also observed. Higher genetic diversity for the Myanmar landraces highlighted the broad genetic base of tomato germplasm. Principal component analysis showed that most of the Myanmar landraces were divergent from other accessions. The different approaches used to analyse landrace diversity documented the broader genetic base of germplasm from Myanmar, which is a non‐center of origin for tomato. Genetic diversity in the landraces may be attributable to diverse production systems used by different ethnic groups in Myanmar, ranging from natural hydroponics in eastern areas, to slash‐and‐burn fields in mountain areas and shifting cultivation in many parts of the country. The availability of uniform and high‐yielding cultivars/hybrids threatens the valuable landraces in Myanmar. We emphasize the need to evaluate tomato germplasm from Myanmar for different traits and sustainable use with simultaneous conservation.     

Evaluation of cultivated barley (Hordeum vulgare) germplasm for the presence of thermostable alleles of β-amylase

A cleaved amplified polymorphic sequence marker was used to detect the alleles Bmy‐Sd2H and Bmy‐Sd3 identifying highly thermostable isoforms of the enzyme b‐amylase, which improves fermentability during brewing. Among the 889 accessions of barley (Hordeum vulgare) investigated, and two accessions of H. spontaneum a total of 166 accessions were identified carrying the superior b‐amylase alleles. These thermostable alleles of b‐amylase were most frequently observed in six‐rowed varieties originating from Asia, especially Japan, with 61.9% of the accessions from Asia carrying the alleles of interest. Additional six‐rowed barleys carrying the relevant alleles were identified among accessions from America, Africa and the Near East. In the European varieties, the percentage of accessions with the alleles of interest was 5.1% with a strong predominance in two‐rowed spring barleys. A pedigree analysis identified the cross ‘Binder’ x ‘Gull’ as the main source of the thermostable b‐amylase alleles in European varieties. The data suggest that an improvement of malting quality in barley could be achieved by introduction of the Bmy1‐Sd2H and Bmy1‐Sd3 alleles into the European breeding programmes.     

Genetic diversity of Chinese Spring Soybean Germplasm Revealed by SSR Markers

To use, maintain and increase crop germplasm collections efficiently, it is important to assess the diversity of these collections. In this study, 1383 accessions of Chinese spring sowing soybean ( Glycine max ) were used for SSR analysis. In total, 1111 alleles were detected among these collections with an average number of alleles (NA) of 18.52 per locus. The genetic diversity index (PIC value) varied from 0.456 to 0.928 with an average of 0.815. Intensive breeding of cultivars have led to a decrease of genetic diversity. Random-repeated sampling within landraces of different geographical regions suggested that the ranking of both average NA and PIC values among different geographical regions were North spring soybean (Nsp) > South spring soybean (Ssp) > Northeast spring soybean (NEsp), but because of the uneven distribution of SSR variation patterns, the differences between them did not reach a significant level. There was a relationship between genetic distances and geographical distances among soybean populations from different regions, indicating a certain degree of geographical differentiation among Chinese soybean germplasm collections.     

High genetic diversity of Spanish common wheats as judged from gliadin alleles

Gliadin alleles were identified in 100 common wheat cultivars registered and/or grown in Spain during the last 40 years. A very high level of genetic polymorphism was found: in total, 103 allelic variants including one null‐allele were found at the six major Gli loci in the Spanish wheats studied. An average genetic diversity for these six loci was found to be higher (H=0.844) than in any group of wheat cultivars studied previously. Spanish wheats bred in Spain demonstrated even higher genetic diversity (H=0.868), probably because of the occurrence in this group of some landraces (local varieties) assumed to be strongly differentiated to fit local environments. The high level of genetic diversity of wheats grown in Spain was maintained by the introduction of distantly related wheat germplasm from different sources, especially from Italy and CIMMYT. A slight decrease of genetic diversity in recently registered cultivars might be caused by the excessive introduction of French wheats. Thirteen new alleles found in Spanish wheats were catalogued, including Gli‐D2w which encodes the first Gli‐D2‐controlledγ‐gliadin to be found.     

利用功能标记揭示新疆小麦改良品种与地方品种的遗传变异

揭示新疆小麦改良品种与地方品种在主要农艺性状相关基因上的遗传变异对进一步改良和利用新疆育成品种具有重要意义。本研究利用52个功能标记对136份新疆小麦改良品种和地方品种分析发现, 与适应性相关的矮秆等位变异Rht-B1b和Rht-D1b、半冬性生长习性相关等位变异Vrn-D1b、T1BL·1RS易位系, 与品质相关的高脂肪氧化酶活性等位变异TaLox-B1a、低多酚氧化酶活性等位变异Ppo-D1a、低黄色素含量等位变异Psy-A1b以及与高粒重等位变异Hap-H (TaSus-2B)仅分布在改良品种中, 而且光周期不敏感等位变异Ppd-D1a (77.6%)、优质麦谷蛋白亚基Dx5+Dy10 (35.4%)和硬质等位变异Pin-D1b (25.0%), 以及高千粒重等位变异TaCwi-A1a (63.3%)、Hap-4A-T (Tacwi-4A) (33.8%)、Hap-5D-C (TaCWI-5D) (93.7%)、Hap-2 (TaGS1a) (77.9%)、TaGS-D1a (78.5%)、TaGS5-A1b (50.0%)和TaTGW6-A1a (92.1%)在改良品种中分布频率明显高于地方品种。大部分优异等位变异分布频率随着育种时期的推进呈现不连续性上升趋势。在适应性与品质相关基因方面, 春性改良品种的优异等位变异频率高于冬性改良品种。功能标记分析显示改良品种的遗传多样性高于地方品种。136份新疆小麦资源被聚为改良品种和地方品种两类, 改良品种被进一步聚为冬性和春性两类, 说明新疆改良品种与地方品种间存在明显的遗传差异。本研究鉴定的优异等位基因和等位基因组合为进一步改良新疆小麦品种提供了重要信息。     

Genetic diversity of barley cultivars grown in Spain, estimated by RFLP, similarity and coancestry coefficients

This study was conducted with the objective of characterizing the genetic variation among a representative set of 37 barley cultivars currently grown in Spain, using restriction fragment length polymorphism (RFLP) markers. Thirty-two RFLP probes, in combination with three restriction enzymes, were used to analyse polymorphism at the molecular level. Genetic distances (GD), based on RFLP band patterns, and coancestry coefficients (f), based on pedigree records, were calculated. Of the 95 clone-enzyme combinations analysed, 71 (74.7%) were polymorphic, representing 246 RFLP patterns. A cluster analysis of GD split the sample into five distinct germplasm groups that were consistent with the history of the cultivars (winter European, spring European, CIMMYT-ICARDA materials, the single cultivar ‘Dobla’ and Spanish local materials). The Spanish group was the most distinct one and had unique alleles at markers close to major loci determining phonological adaptation. The probes which best distinguished among groups were also identified. Genetic similarity estimates were moderately consistent with f (for cultivars with complete pedigrees). The implications for integration of diversity studies into breeding programmes are discussed.     

High level of natural variation in a groundnut (Arachis hypogaea L.) germplasm collection assayed by selected informative SSR markers

The ability to identify genetic variation is indispensable for effective management and use of genetic resources in crop breeding. Genetic variation among 189 groundnut ( Arachis hypogaea L.) accessions comprising landraces, cultivars, a mutant, advanced breeding lines and others (unknown genetic background) representing 29 countries and 10 geographical regions was assessed at 25 microsatellite or simple sequence repeat loci. A high number of alleles (265) were detected in the range of 3 (Ah1TC6G09) to 20 (Ah1TC11H06) with an average of 10.6 alleles per locus. The polymorphism information content value at these loci varied from 0.38 (Ah1TC6G09) to 0.88 (Ah1TC11H06) with an average of 0.70. A total of 59 unique alleles and 127 rare alleles were detected at almost all the loci assayed. Cluster analysis grouped 189 accessions into four clusters. In general, genotypes of South America and South Asia showed high level of diversity. Extraordinary level of natural genetic variation reported here provides opportunities to the groundnut community to make better decisions and define suitable strategies for harnessing the genetic variation in groundnut breeding.     

Yield Responsiveness in Two- and Six-Rowed Barley Grown in Contrasting Nitrogen Environments

Two‐ and six‐rowed barley with different intrinsic ability to produce tillers and kernels per ear, would differ in responsiveness to nitrogen availability with environmental improvements. Two field experiments were carried out to elucidate how nitrogen supply (N₄₀ and N₁₅₀) affects yield and its components in two‐ and six‐rowed barley. High nitrogen increased aboveground dry matter at anthesis, by improving cumulative solar radiation intercepted by the crop, determining an increased dry‐matter production at maturity without changes in harvest index. In both barley types, variations in grain yield were explained by changes in kernels per unit land area rather than by differences in the average kernel weight. However, changes in the number of kernels were due to variations in the number of ears per m² in two‐rowed barley and the number of kernels per ear in six‐rowed barley. Ears per unit area showed a greater responsiveness in two‐ than in six‐rowed barley due to a higher nitrogen supply treatment, associated with their intrinsic higher tillering capacity, while the number of kernels per ear was more responsive in six‐ than in two‐rowed types. The fact that responses to nitrogen by the number of kernels per unit land area in two‐ and six‐rowed barley is better explained by different yield sub‐components, allows the speculation that the critical period for yield determination would differ between barley types.     

SSR-based genetic diversity assessment among Tunisian winter barley and relationship with morphological traits

For studying genetic diversity caused byselection for adaptation and end-use, 17microsatellites (SSR), representative ofthe barley genome, were used in 26 barley(Hordeum vulgare L.) accessions andcultivars in Tunisia. Theaccessions/cultivars originate fromdifferent geographic regions and are ofdifferent end-use. For the 15 polymorphicSSR, the mean number of alleles per locuswas 3.6 and the average polymorphisminformation content was 0.45. Clusteranalysis based on SSR data and onmorphological data clearly differentiatethe genotypes according to their type(local landraces vs. varieties), row-numberand end-use. The correlation between bothdiversity measures was highly significant(r = 0.25, p<10^-5) and thecorrespondence between the clustering basedon SSR and morphological data wasrelatively good. Our results show the largegenetic diversity of the Tunisian barleycultivars and the association of thisdiversity with adaptation traits.     

Genetic diversity and population structure of Indian melon (Cucumis melo L.) landraces with special reference to disease and insect resistance loci

This study was aimed to examine the genetic diversity and population structure of Indian melon landraces with special reference to disease and insect resistance loci. Thirty‐six simple sequence repeat (SSR) markers along with seven markers at disease and insect resistance loci were used for this purpose on a panel of 91 accessions available at Indian Institute of Horticultural Research, Bengaluru, India. Model‐based structure analysis revealed the presence of four groups that were consistent with the results of principal coordinate analysis (PCoA). The delineation of populations was mostly based on geography with improved varieties as a separate group. Ten accessions have been identified to possess beneficial alleles at all the selected disease resistance loci and shall be useful for incorporating multiple disease resistance after phenotypic validation. The results obtained in the current study demonstrate the importance of the Indian melon group as a valuable genetic reservoir and the need to plan strategies for its conservation and utilization in breeding programmes.     

西藏青稞冬春性鉴定及抽穗期多样性与稳定性分析

为提高青稞种质资源的利用效率并筛选优异杂交亲本,分别在西藏林芝和拉萨两地的春播和秋播环境下对1605份青稞种质资源进行冬春性鉴定和抽穗期多样性分析。设拉萨春播2个播期,即正常春播I和晚10 d春播II,以2个播期的抽穗期变化作为冬春性区别依据。结果表明,96.2%的西藏青稞地方品种为春性,在西藏3个生态区均有分布,冬性品种仅有3.8%,且主要分布在以林芝为主的藏东南生态区;抽穗期的Shannon-Wiener's多样性分析表明,春播条件下抽穗期多样性高于秋播,拉萨春播条件下抽穗期多样性最高,林芝春播次之,林芝秋播最低;在相同环境下,地方品种的多样性高于育成品种;在环境稳定性分析中, 368份春性地方品种和21份育成品种在不同环境中抽穗期较为稳定,其中康青3号在两地所有参试品种中抽穗期稳定性最高。本研究为全面理解西藏青稞资源的冬春性、抽穗期多样性和环境稳定性提供了参考,为广适应性青稞品种培育筛选出环境稳定性佳的亲本材料。     

黑龙江省大豆遗传结构及遗传多样性分析

利用22个表型性状和60个微卫星(simple sequence repeat, SSR)位点对黑龙江省140份代表性种质(78份地方品种和62份育成品种)进行分析, 根据UPGMA (unweighted pair group method with arithmetic mean)和Model-base对SSR数据进行遗传结构划分。结果表明, 参试品种可分为2大类群, 第II类群的各项多样性指标均高于第I类群, 2个类群遗传距离为0.2427;PCO结果显示这2个类群分布在不同区域, 这与地理来源和育成年代密切有关。依据品种类型分为育成品种和地方品种两组, 后者的各项多样性指标均高于前者, 两组间的遗传距离为0.1131。依据表型数据的PCO分析表明, 分布区域与品种类型有关, 与SSR结构分类的结果吻合度低, 两组品种主要在3个主成分的6个表型性状上有所不同。它们不是2个相对独立的遗传群体, 根据分子标记和表型分类各有特点;建议在种质遗传多样性研究中将分子数据和表型数据结合起来。     

Genetic diversity and population structure of wild and cultivated barley from West Asia and North Africa

Population structure and relationships within and among 185 accessions of wild (Hordeum vulgare ssp. spontaneum) and cultivated barley (H. v. ssp. vulgare) from five countries in the West Asia and North Africa (WANA) region were studied using 36 simple sequence repeat (SSR) markers. The accessions were divided into subspecies/origin (S/O)‐groups and marker results were analysed in relation to genetic diversity and genetic structure. Wild barley from WANA was found to be highly diverse. The landraces from different countries of the Near East showed genetic diversity that was nearly as high as the wild barley from the same country. Further analyses showed that wild barley from Palestine/Israel represented the group with the highest diversity and the most complex structure. However, this group was distantly related to the cultivated barley in WANA, while the wild barley from the rest of the WANA region was closely related to the cultivated WANA barley. The high diversity and the close relationship to the wild barley make the WANA landraces an interesting genetic resource for both conservation and exploitation.     

Field variation in a tetraploid progeny derived by selfing a Solanum commersonii (+) S. tuberosum somatic hybrid: A multivariate analysis

A phenotypic diversity index (PDI) was calculated using 10 agronomiccharacteristics recorded in 90 accessions of 2-row spring barleys and 29accessions of 6-row spring barleys grown in the Nordic Region. The PDIranged from 0.0308 to 0.6245 in 2-row barley accessions and from0.0314 to 0.7016 in 6-row barley accessions. The average PDIs were0.2178 and 0.2438 in 2-row and 6-row barley germplasm, which confirmsthat some older cultivars were parents of newer cultivars. The lowest PDIwas between accessions with the same name, which suggest that irrespectiveof their market source, they were the same cultivars. The largest PDI rangesin 2-row barley cultivars within the same country or release decade werecorrelated to the number of accessions in the respective cluster, whichsuggests that phenotypic diversity in this germplasm depends on the numberof cultivars included in the cluster. However, this association was not alwaysobserved in 6-row barley cultivars. The most distinct 2-row cultivars wereArla and Akka from Sweden, whereas Sigur and Tampa from Iceland werethe most distinct 6-row cultivars as determined by both PDI and averagelinkage cluster analysis. This analysis also confirm that the 2-row barleyaccessions Jenny, Triumph, and Vega, which were obtained from twodistinct market sources, and the 6-row barley accessions under the nameAgneta (but from three market sources) were the same. The analysis ofvariance of the PDI indicates that 6-row germplasm may be clusteredaccording to their geographical origin or decade of release, but this was notobserved in 2-row barley germplasm. This research demonstrates theadvantage of PDI to assess variation among breeding pools.     

The genetic diversity of old and modern Siberian varieties of common spring wheat as determined by microsatellite markers

The objective of this study was to assess genetic diversity within old and modern common spring wheat (Triticum aestivumL.) varieties cultivated in Siberia and to find out whether old Siberian varieties could be a potential source for genetic diversity in modern wheat breeding in Siberia. A set of 54 varieties was analysed using 22 wheat microsatellite markers (WMS), determining 23 loci located on 19 different chromosomes. In total, 151 alleles were detected with an average of 6.6, ranging from three to 11 alleles per locus. The average genetic diversity value (polymorphic information content) was 0.70. WMS located in the B genome produced more alleles per locus (7.6) compared with WMS located in the A (6.0) and D (6.0) genomes. Genetic similarity values between varieties ranged from 0.19 to 0.96 and were used to produce a dendrogram. With a few exceptions the varieties studied were clustered in two nearly equal groups consisting of predominantly old (released before 1960) and modern (released in 1960‐90s) varieties, respectively. Genetic diversity values within these two groups were similar with 0.60 and 0.58, respectively. The numbers of group‐specific alleles were 34 and 29, respectively. A significant variation in frequencies of 79 shared alleles was observed. The results obtained by using genomic microsatellite sequences demonstrated that breeding has not resulted in a decrease in the genetic diversity in Siberian spring wheat. However, significant quantitative and qualitative changes in allelic frequencies of different loci were detected. It may be suggested, that old Siberian common spring wheat varieties are a potential basis for genetic diversity in modern wheat breeding in Siberia.     

Regional patterns of microsatellite diversity in Ethiopian tetraploid wheat accessions

This study was conducted to assess regional patterns of diversity of Ethiopian tetraploid wheat accessions and to identify areas of diversity that can be used as source of new germplasm for developing high yielding and stable varieties. A collection of 133 Ethiopian tetraploid wheat accessions and eight introduced cultivars was analysed using 29 wheat microsatellite markers. A total of 383 alleles were detected with an average value of 13.14 alleles per locus. Relatively more alleles were observed in the B genome than in the A genome. Gene diversity indices ranged from 0.08 to 0.95, with a mean value of 0.72. Accessions collected from the same region were pooled and the number of alleles and gene diversity were calculated over the 29 simple sequence repeats for each region. Higher numbers of alleles were detected in the Shewa region (8.72), followed by Tigray (5.86) and Hararghe (5.76). The highest average gene diversity value was found in Shewa (0.65), followed by Gondar (0.64). No significant correlation was observed between geographic distance and genetic distance. Out of 383 different alleles detected, 93 (24.4%) were observed to be region‐specific. Region‐specific alleles were found across all chromosomes except for Xgwm752, Xgwm155 and Xgwm148. Genetic similarity coefficients were estimated for all the possible 55 pairs of regional comparisons and they ranged from 0.16 to 0.52, with a mean value of 0.50. All provinces were differentiated in the UPGMA cluster diagram.     

Genetic diversity among elite Bulgarian barley varieties evaluated by RFLP and RAPD markers

Genetic variation among five elite winter barley cultivars (H. vulgare L.) currently grown in Bulgaria was assessed at the molecular level using restriction fragment length polymorphism (RFLP) and randomly amplified polymorphic DNA (RAPD) markers. The present study sampled RFLPs in four well characterized multigene families in barley: the seed storage protein loci; the 18S, 5.8S and 26S ribosomal DNA loci; the loci coding for 5S ribosomal RNA and the loci coding subunit α of ATP-A complex in the mitochondrial genome. RFLPs were detected in three out of five investigated chromosomal loci in the barley cultivars studied. RAPD assay using arbitrary 10-base primers was applied to generate amplified length polymorphic markers in barley. Overall a total of 15 polymorphic phenotypes were found among the studied barley cultivars by using 11 out of 25 tested primers. All RAPDs were considered as dominant genetic markers except for two, where PCR and Southern blot analysis indicated the presence of codominant amplification products. Five RAPD polymorphisms in F₁ and F₂ progenies of the cross between Alpha and Obzor were inherited in Mendelian fashion. The determined values for the genetic variation proved a high genetic similarity among the tested cultivars. Genetic similarity (GS) calculated from RFLP and RAPD data ranged from 0.888 to 0.997 with a mean GS – 0.933. This revised version was published online in July 2006 with corrections to the Cover Date.