A genetic linkage map in southern‐by‐spring oat identifies multiple quantitative trait loci for adaptation and rust resistance

We developed 178 recombinant inbred lines from a southern‐by‐spring oat population designated as “TxH.” These lines were genotyped to generate a high‐quality linkage map that resolved 6,902 markers into 21 linkage groups that matched closely with the latest hexaploid oat consensus map. Three major quantitative trait loci (QTLs) affecting heading date were found in locations that are consistent with known QTLs and candidate genes, and two other QTLs affecting heading date were found in novel locations. Five QTLs affecting plant height were found. Both sets of QTLs are responsible for transgressive segregation observed for these two traits. Four QTLs affecting resistance to crown rust, caused by the pathogen Puccinia coronata f. sp. avenae, were identified. Two of these QTLs are consistent with known clusters of rust resistance genes, while two may represent new locations of novel rust resistance genes. A complete set of SNP sequences suitable for generating markers for molecular selection is provided.     

Quantitative trait loci for quality and agronomic traits in two advanced backcross populations in oat (Avena sativa L.)

Using the advanced backcross quantitative trait loci (AB‐QTL) strategy, we successfully transferred and mapped valuable allelic variants from the high β‐glucan (BG) accession IAH611 (PI 502955), into the genome of cultivar ‘Iltis’. By backcrossing one BC₁F₁ plant to ‘Iltis’, we developed two BC₂F_2‐6 populations A and B, comprising 98 and 72 F₂‐individuals, respectively. Genotyping of BC₂F₂ individuals with predominantly AFLP markers resulted in 12 linkage groups with a map size of 455.4 cM for Population A and 11 linkage groups with a map size of 313.5 cM for Population B. Both populations were grown at three sites in Germany over a three‐year period. Individuals were then phenotyped for 13 traits including grain yield (YD) and β‐glucan content (BG). QTL analysis via stepwise regression detected a total of 33 QTLs, most of which were clustered in three linkage groups. Two dense linkage groups A1 and B13 were found to be putatively homologous to groups KO_6 and KO_11 of the ‘Kanota’/‘Ogle’ map, respectively.     

The development and use of microsatellite markers for genetic analysis and plant breeding with emphasis on bread wheat

In recent years, a variety of molecular markers, based on microsatellites or simple sequence repeats (SSRs) have become the markers of choice, thus necessitating their development and use in a variety of plant systems. In this review, the basic principles underlying different hybridization-based (oligonucleotide fingerprinting) and PCR based approaches (STMS, MP-PCR, AMP-PCR/ ISSR/ ASSR, RAMPs/ dRAMPs, SAMPL), making use of microsatellites, have been outlined. Different methods for enrichment of genomic libraries for microsatellites have also been outlined. Relevant literature on the subject, giving a summary of results obtained using each approach, has been reviewed and critically discussed. The review also includes a discussion on literature, which deals with the use of microsatellites in genome mapping, gene tagging, DNA fingerprinting, characterization of germplasm and cytogenetics research. Special emphasis has been laid on the genome of bread wheat, where the work done in the authors' own laboratory has also been briefly reviewed. This revised version was published online in July 2006 with corrections to the Cover Date.     

Comparative Study of CaMsrB2 Gene Containing Drought‐Tolerant Transgenic Rice (Oryza sativa L.) and Non‐Transgenic Counterpart

Concerns regarding the safety of transgenic foods have been raised because of possibility of undesirable effects development during genetic engineering. Analysis of phenotypic traits can increase the likelihoods of identifying those unintended effects in dietary composition of the GM crops. Objective of this study was to compare the transgenic lines with their non‐transgenic counterpart. Different vegetative and reproductive traits as well as antioxidant properties were considered to evaluate the transgenic (HV8 and HV23) lines containing CaMsrB2 gene and their non‐transgenic (Ilmi) parent line. Grain size and weight, seed germination, root length, root and shoot dry weight, length and width of flag leaf, plant height, and ligule, stamen and carpel length were not significantly different. Onset and completion of heading in each line occurred almost during the same period. The antioxidant properties in terms of DPPH (1,1‐diphenyl‐2‐picrylhydrazyl) radical scavenging activity and polyphenol content were not statistically different under same treatment condition. The results suggested that the transgenic rice lines containing CaMsrB2 gene were equivalent to their non‐transgenic counterpart without any visible unintended effects.     

Genetic studies of powdery mildew resistance in common oat (avena sativa L.) I. Cultivars and breeding lines grown in Western Europe and North America

Common oat (Avena sativa L.) cultivars and breeding lines grown in Western Europe and North America were tested against twelve Erysiphe graminis f. sp. avenae mildew isolates collected in Germany and Denmark. These isolates were selected for their ability to produce differential response patterns permitting characterization of five oat mildew resistance (OMR) groups. From a total of 259 cultivars and lines tested 173 accessions showed susceptible responses, 48 accessions were characterized by susceptible or intermediate responses and 38 accessions revealed isolate-specific resistance response patterns. Eight cultivars and lines had resistance patterns of OMR group 1, six cultivars of OMR group 2, and eleven cultivars of OMR group 3. Two cultivars, each possessed resistance patterns corresponding to OMR groups 1 + 3 and 2 + 3 in combination, respectively. Three cultivars exhibited the response pattern of OMR group 3 in association with an additional unknown resistance. Eight cultivars and lines showed a resistance response pattern not yet detected in the documented OMR groups. This revised version was published online in July 2006 with corrections to the Cover Date.     

Genome‐Wide Identification of MicroRNAs Responsive to High Temperature in Rice (Oryza sativa) by High‐Throughput Deep Sequencing

MicroRNAs (miRNAs) are known to play important roles in plant growth and stress response. Heat stress is a severe abiotic stresses by adversely affecting plant growth and yield. To identify heat‐responsive miRNAs at the genome‐wide level in rice (Oryza sativa), we constructed two small RNA libraries from young panicles treated or not with heat conditions. Ion torrent sequencing of the two libraries identified 294 known miRNAs and 539 novel miRNAs. Differential expression analysis showed that 26 miRNAs were downregulated and 21 miRNAs were upregulated in response to heat stress. Among them, five heat‐responsive miRNAs, including miR162b, miR529a‐p5, PC‐5P‐62245‐9, miR171b and miR169n, were validated by quantitative real‐time polymerase chain reaction. A total of 44 target genes of the differentially expressed miRNAs were predicted. These target genes are most significantly overrepresented in the cell growth process. The results demonstrated that rice miRNAs play critical roles in the heat stress response. This study opens up a new avenue for understanding the regulatory mechanisms of miRNAs involvement in the heat stress response in rice.     

Grain-yield characteristics of oat lines surviving uniform and shuttle selection strategies

Summary Four selection strategies were used on four sets of oat lines to select for grain yield. Two of these used uniform environments whereby sequential selection of the high-yielding lines occurred in continuous high- or continuous low-productivity environments. These are referred to as high and low uniform selection strategies, respectively. The other two selection strategies were conducted by sequential selection of the high-yielding lines in alternating high- and low-productivity environments. They are referred to as high and low shuttle selection strategies, respectively, with high and low designating the productivity of the first environment in the sequence. After three or four cycles of selection, the surviving lines and a random sample from each set were evaluated for mean grain yield, grain yield response to improving environments, and stability of grain yield, in a range of environments typical of oat production on Iowa farms.Grain yield and regression response for all selection strategies, when calculated across all sets of lines, were significantly greater than corresponding values for random samples. Stability was unchanged. The uniform-high and uniform-low strategies gave the greatest and the smallest gains in mean grain yield, respectively, with the shuttle strategies giving intermediate gains. Shuttle selection in predominantly high-productivity environments increased grain yield more than shuttle selection in predominantly low-productivity environments. The uniform-strategy followed by the shuttle-high strategy identified entries with superior performance in high productivity environments. Increased gain in mean grain yield across all environments was associated with increased number of selection cycles conducted in high-productivity environments.Journal Paper No. J-15252 of the Iowa Agric. and Home Econ. Exp. Stn., Ames, Iowa 50011, USA. Project No. 2447.     

Continued response through seven cycles of recurrent selection for grain yield in oat (Avena sativa L.)

Long-term selection experiments provide germplasm to study the effects of selection in a closed population. Recurrent selection to enhance grain yield in oat has been ongoing at the University of Minnesota since 1968. The objectives of this study were: (i) estimate the GCA and SCA effects for three agronomic traits in the seventh cycle of selection, (ii) assess the effect of the current methods of selection on parental contribution and unselected traits, and (iii) determine the direct and indirect responses to seven cycles of recurrent selection for grain yield. Progeny of the Cycle 6 parents and parents for Cycles 0 through 7 were grown in two separate tests. Grain yield, heading date and plant height were evaluated in each test. Grain yield was increased by 21.7% after seven cycles of selection. Evaluation of Cycle 6 progeny showed that GCA effects were significant for all three traits studied, and SCA effects were significant only for grain yield. Four Cycle 6 parents did not have any progeny selected as Cycle 7 parents. Results from this study indicate that long term recurrent selection has continued to increase grain yield. Alternative selection strategies may be necessary to maintain the genetic variability in this population, particularly when improvement of secondary traits is required. This revised version was published online in August 2006 with corrections to the Cover Date.     

EST-derived microsatellites as a rich source of molecular markers for oats

Polymerase chain reaction-based microsatellite markers are valuable tools for molecular breeding because of their co-dominant inheritance and their applicability for high-throughput analysis. Being still very limited for oats, their number has to be increased significantly to cover the entire genome. For these purposes, a set of 7031 recently published expressed sequence tags (ESTs) was screened for microsatellites with dinucleotide, trinucleotide and tetranucleotide repeat motifs. Subsequent in silico analysis resulted in the development of 216 primer pairs for Avena EST-derived microsatellite loci ( AME ). Using a sample set of 12 oat lines, 107 of 195 functional primers could be assayed as polymorphic. The marker variability averaged out at three alleles per locus and a polymorphic information content (PIC) value of 0.42. This variability documents their suitability for molecular oat-breeding purposes. Finally, 51 of the AME loci could be placed within the known reference map of 'Kanota' × 'Ogle' that previously contained only 12 microsatellite loci. Thus, a remarkable enhancing of the number of mapped oat microsatellite loci could be achieved.     

Fine mapping of a day‐length‐sensitive dwarf gene in rice

Dwarf mutants are valuable and crucial resources for genetic research and crop breeding programme in rice. In this study, we identified a dwarf mutant derive from tissue culture, which exhibited a delayed heading date and dwarfism under long‐day growth conditions, suggesting the heading date of dwarf mutant was sensitive to day length. Based on 2000 F₂ mutant‐like individuals from the cross of the mutant and a Japonica var. ‘IRAT129’, the dwarf gene was finally narrowed into a 512‐kb region near the centromere on chromosome 9. According to the sequence analysis of a delimited region, 21 genes had base alternations either in promoters (15 SNPs) or in coding regions (6 InDels) among 73 annotated genes, and five genes were confirmed sequence alternations resulting from their expression mainly in the vegetative organs. Given to the RNAi plants of the five genes incapable to mimic dwarf and late heading date phenotype, the candidate gene remains to be identified by other genetic or molecular methods. Therefore, all these results give us informative foundation for the day‐length‐sensitive dwarf gene isolation.     

Sexual hybridization between Capsella bursa‐pastoris (L.) Medik (♀) and Camelina sativa (L.) Crantz (♂) (Brassicaceae)

The development of transgenic oilseed Camelina sativa (2n = 40) and the potential for hybridization with its weedy relative Capsella bursa‐pastoris (2n = 36) necessitates a careful evaluation of the reproductive compatibility between the species. Here, we conducted over 1800 crosses (emasculation and manual pollination) to examine the ability of 10 Canadian C. bursa‐pastoris (♀) accessions to hybridize with five accessions of C. sativa (♂). Seven hybrids were confirmed among 586 putative hybrids screened with species‐specific markers, indicating a hybridization rate of 1.5 hybrids per 10 000 ovules pollinated. All seven hybrids had intermediate DNA content compared to their parents, were morphologically distinct, had low (1.9%) pollen fertility and failed to produce selfed or backcrossed seed. Given the abundance of C. bursa‐pastoris along field margins, hybrids will likely be generated in the wild, but they will be unable to establish lineages unless fertility is restored. The large number of crosses and the diversity captured by the use of multiple accessions resulted in strong statistical power and a high degree of confidence in the estimated hybridization rate.     

Efficient development of Haynaldia villosa chromosome 6VS‐specific DNA markers using a CISP‐IS strategy

Development of effective molecular markers linked to Pm21 deriving from Haynaldia villosa is critical for wheat breeding of powdery mildew resistance. In this study, we designed 12 pairs of conserved‐intron scanning primers (CISPs), using intron‐containing conserved genes located on the short arm of Brachypodium distachyon chromosome 3 (3BdS) aligned with cDNA or expressed sequence tags (ESTs) of Triticeae crops. Of 12 CISP primer pairs, 11 amplified DNA both in H. villosa and in wheat, and four displayed H. villosa chromosome 6VS‐specific polymorphisms. Six non‐polymorphic DNAs were further sequenced for designing internal primers, and five additional 6VS‐specific markers were obtained. Of the total nine 6VS‐specific co‐dominant markers, six could effectively trace Pm21 in F₂ population derived from the hybrid between the T6AL.6VS line and ‘Yangmai 158’. This study demonstrated that Brachypodium genomic information could be powerfully utilized to develop molecular markers in H. villosa or other Triticeae species.     

The introgression of characters of the wild oat Avena magna (2n=4x=28) into the cultivated oat A. sativa (2n=6x=42)

Summary A study of derivatives from the hybrid Avena sativa × A. magna backcrossed to A. sativa clearly indicate that it is possible to introduce characters of the wild oat into the cultivated oat. Progeny with improved grain characters and crude protein content of the groat have been isolated and their use as breeding material is discussed.     

Chromosomal location of genes for resistance to powdery mildew in cultivated oat (Avena sativa L.). 1. Gene Eg-3 in the cultivar 'Mostyn'

The cultivar 'Mostyn' of hexaploid oat ( Avena sativa L.) possesses a dominant gene conferring resistance to powdery mildew caused by Erysiphe graminis avenae. The resistance gene, designated Eg -3, was derived from the wild oat Avena sterilis L. var. ludoviciana. Monosomic analysis revealed that this gene was located on chromosome 17, which corresponds to the missing chromosome in the 'Kanota' monosomic line Kl1. This chromosome is associated with the homoeologous group 1 of the Triticeae.     

Genetic dissection of vitamin E content in rice (Oryza sativa) grains using recombinant inbred lines derived from a cross between 'Zhenshan97B' and 'Nanyangzhan'

Vitamin E (VE) is an important nutritional trait in rice grains. In order to dissect the genetic basis underlying VE content, a recombinant inbred lines population derived from 'Zhenshan 97B' and 'Nanyangzhan' was used for quantitative trait locus (QTL) analysis. Totally, 29 QTLs for six VE traits were identified in 2 consecutive years. Among those, five QTLs repeatedly detected in two years formed a cluster on chromosome 2, which was responsible for all five VE isomers. OsγTMT, the gene encoding γ‐tocopherol methyltransferase in rice, was located to the same region and treated as the candidate gene. Sequence analysis of alleles from two parents revealed many polymorphisms, including 19 single nucleotide polymorphisms (SNPs) and two insert/deletions (Indels) in the promoter region, two nonsynonymous SNPs in exons, and 25 SNPs and an Indel in introns. Besides, a QTL for δ‐tocotrienol and two QTLs for α‐tocopherol were repeatedly detected on chromosome 5 and 8, respectively, all three regions carrying no homologous genes involved in VE biosynthesis. These results could be useful in development of rice lines displaying desirable VE content.     

Morphological and molecular diversity of Nordic oat through one hundred years of breeding

Summary Genetic diversity in microsatellites and development of agronomical characters in Nordic oat cultivars (Avena sativa) from the 20th century, ranging from landraces to new cultivars, were studied. A clear development in agronomical characters has taken place in this period: Straw length has been reduced, harvest index has increased and heading date has declined. The persistent oat breeding effort in the northern part of the region was indicated by the data, since cultivars from this region showed higher harvest index. Also adaptation to shorter summers was apparent in cultivars from the most northern part of the area. When comparing cultivars released after 1940 to the landraces, the loss of diversity revealed for the agronomical characters was also indicated by the molecular data. This indicates that a more general loss of diversity has taken place in the period, possibly due to random factors during the breeding process (bottleneck effect). The reduction in diversity revealed by recent cultivars at an agronomical as well as a molecular level emphasises the importance of implementing a conservation strategy for older material in order to secure genetic diversity for future oat breeding efforts.     

Identification and marker‐assisted introgression of QTL conferring resistance to bacterial leaf blight in cowpea (Vigna unguiculata (L.) Walp.)

Bacterial leaf blight (BLB), caused by Xanthomonas axonopodis pv. vignicola (Xav), is widespread in major cowpea [Vigna unguiculata (L.) Walp.] growing regions of the world. Considering the resource poor nature of cowpea farmers, development and introduction of cultivars resistant to the disease is the best option. Identification of DNA markers and marker‐assisted selection will increase precision of breeding for resistance to diseases like bacterial leaf blight. Hence, an attempt was made to detect QTL for resistance to BLB using 194 F_2 : 3 progeny derived from the cross ‘C‐152’ (susceptible parent) × ‘V‐16’ (resistant parent). These progeny were screened for resistance to bacterial blight by the leaf inoculation method. Platykurtic distribution of per cent disease index scores indicated quantitative inheritance of resistance to bacterial leaf blight. A genetic map with 96 markers (79 SSR and 17 CISP) constructed from the 194 F₂ individuals was used to perform QTL analysis. Out of three major QTL identified, one was on LG 8 (qtlblb‐1) and two on LG 11 (qtlblb‐2 and qtlblb‐3). The PCR product generated by the primer VuMt337 encoded for RIN2‐like mRNA that positively regulate RPM1‐ and RPS2‐dependent hypersensitive response. The QTL qtlblb‐1 explained 30.58% phenotypic variation followed by qtlblb‐2 and qtlblb‐3 with 10.77% and 10.63%, respectively. The major QTL region on LG 8 was introgressed from cultivar V‐16 into the bacterial leaf blight susceptible variety C‐152 through marker‐assisted backcrossing (MABC).     

Genetic structure of putative heterotic populations of alfalfa

Semi‐hybrids between genetically distant alfalfa (Medicago sativa subsp. sativa) populations may display heterosis whose extent is affected by the structure of genetic diversity across populations. This study aimed to assess the genetic diversity across three putative heterotic populations, one Italian, one Egyptian and one of semi‐erect germplasm from Eastern Europe, Canada and Spanish Mielga (EECM population). Each population was bred from ten parents after various selection cycles. Fifteen genotypes per population were characterized by 20 polymorphic SSR markers. The among‐population variance was over eightfold smaller than the average within‐population variance (2.05 vs. 17.24) and accounted for 10.6% of the total variation. G’_ST = .090 across markers indicated modest population differentiation. Various diversity measures, multidimensional scaling, and cluster analysis of the genetic structure indicated that the Italian population was more distant from the EECM population than the Egyptian one. The EECM and Egyptian populations were the most distant geographically and genetically. EECM displayed widest intrapopulation variation, accordingly to its constitutive geographical diversity. In conclusion, this study indicates modest genetic differentiation between alfalfa populations even for geographically distant germplasm.     

The first genetic linkage map of crape myrtle (Lagerstroemia) based on amplification fragment length polymorphisms and simple sequence repeats markers

Lagerstroemia (crape myrtle) are famous ornamental plants with large pyramidal racemes, long flower duration and diverse colours. Genetic maps provide an important genomic resource of basic and applied significance. A genetic linkage map was developed by genotyping 192 F₁ progeny from a cross between L. caudata (female) and L. indica (‘Xiang Xue Yun’) (male) with a combination of amplification fragment length polymorphisms (AFLP) and simple sequence repeats (SSR) markers in a double pseudo‐testcross mapping strategy. A total of 330 polymorphic loci consisting of 284 AFLPs and 46 SSRs showing Mendelian segregation were generated from 383 AFLP primer combinations and 150 SSR primers. The data were analysed using JoinMap 4.0 (evaluation version) to construct the linkage map. The map consisted of 20 linkage groups of 173 loci (160 AFLPs and 13 SSRs) covering 1162.1 cM with a mean distance of 10.69 cM between adjacent markers. The 20 linkage groups contained 2–49 loci and ranged in length from 7.38 to 163.57 cM. This map will serve as a framework for mapping QTLs and provide reference information for future molecular breeding work.