Wild Introgression Research Articles

Validation of yield-enhancing quantitative trait loci from a low-yielding wild ancestor of rice

A set of introgression lines (ILs) containing chromosomal segments from O. rufipogon (IRGC 105491), a wild relative of O. sativa, in the genetic background of an elite US variety, cv. Jefferson, was developed to confirm the performance of six yield-enhancing quantitative trait loci (QTL). Fifty BC3F3 ILs containing homozygous O. rufipogon introgressions at each of the target QTL regions, and as few background introgressions as possible, were selected for evaluation of yield and 14 yield-related traits in field studies conducted over 2 years at four locations in the southern USA. Performance of the IL families was compared with three commercial inbreds and one hybrid variety. IL families carrying introgressions from the low-yielding wild parent at the QTL yld2.1 and yld6.1 yielded 27.7 and 26.1 % more than Jefferson, respectively. IL yld2A, which possesses yld2.1, also performed well under alternate wetting and drying conditions in two field locations. After the first year of field trials, 10 of the top-performing BC3F4 families, representing five of the QTL targets, were genotyped with an Illumina 1,536 assay to define the size and location of the wild introgressions. BC3F4 families with the fewest background introgressions were backcrossed to Jefferson and selfed. The resulting BC4F2 families were screened with targeted single nucleotide polymorphism assays to identify individuals carrying homozygous introgressions across the target QTL. Twelve ILs, representing each of the six QTL targets, have been submitted to the Genetic Stocks Oryza Collection for studies on transgressive variation and as interspecific pre-breeding lines.

Identification of a leaf-rust resistance gene in species of Aegilops L., synthetic forms, and introgression lines of common wheat

DNA samples of wild relatives, synthetic forms, and introgression lines of common wheat (Triticum aestivum L.) were genotyped with diagnostic molecular markers that are linked to the leaf-rust resistance genes Lr9, Lr35, and Lr47. The Lr9 gene was identified in Aegilops umbellulata and Lr35 and Lr47 were identified in Ae. speltoides. The synthetic forms Avrolata and Avrodes, in which the genomes of Ae. umbellulata and Ae. speltoides, respectively, replaced the wheat D genome, contain the Lr9 and Lr35 genes. The genomes of the introgression lines that were developed using Ae. umbellulata lack Lr9. The Lr35 gene is present in one of the introgression lines that was derived from Avrodes. Some of the wild relatives and the introgression lines may contain additional leaf-rust resistance genes.

Validation for root‐related quantitative trait locus effects of wild origin in the cultivated background of barley (Hordeum vulgare L.)

With 4 figures and 2 tablesAbstractExtensive root system plays a major role in plant’s ability to tolerate water deficit conditions. Recently, quantitative trait locus (QTL) effects of wild origin associated with natural variation of root parameters were detected on the distal arm of chromosome 5H using 301 BC2DH lines of a cross between spring barley cultivar ‘Scarlett’ and the wild barley accession ISR42‐8. Here, we report the validation of these QTL effects in the near isogenic background of ‘Scarlett’ by using introgression lines (ILs; S42IL‐126 and S42IL‐176) of the targeted region. S42IL‐126 encompasses a single wild introgression on chromosome 5H, reaching out from 145.57 to 200.12 cM, whereas S42IL‐176 harbours a major introgression on chromosome 5H from 154.37 to 234.98 cM along with three minor introgressions on chromosomes 1H, 2H and 3H. S42IL‐126, S42IL‐176, ‘Scarlett’ and ISR42‐8 were evaluated for the root‐related traits; root dry weight (RDW), root volume (RV), root length and the associated traits; shoot dry weight and change in tiller number during drought stress (ΔTIL). The phenotypic evaluations revealed contrasting root systems in both parents where ISR42‐8 inherited highly extensive fibrous roots with respect to ‘Scarlett’. Both ‘Scarlett’ and S42IL‐126 developed smaller roots and showed no variation in root parameters, indicating that the wild introgression present in S42IL‐126 does not contain QTL alleles for the above‐mentioned root traits. On the contrary, S42IL‐176 revealed remarkable trait increases in RDW, RV and ΔTIL, which are similar to the donor parent ‘ISR42‐8’. The trait increases in S42IL‐176 are presumably due to the presence of exotic alleles at the QTLs QRDW.S42IL‐1, QRV.S42IL‐1 and QΔTIL.S42IL‐1. The comparison of phenotypic data and overlapping introgressions between S42IL‐126 and S42IL‐176 suggests that these QTLs reside on chromosome 5H in the interval between 200.12 and 234.98 cM. On the basis of the magnitude of QRDW.S42IL‐1, QRV.S42IL‐1 and QΔTIL.S42IL‐1, it is likely that these QTL effects are also linked to extra introgressions of S42IL‐176 present on chromosomes 1H where a QTL effect for RDW was also detected previously at the corresponding region of the wild introgression. In future, a follow‐up study with segregating offspring which are derived from S42IL‐176 will help to ultimately quantify and map the identified QTLs. On the basis of our QTL study, S42IL‐176 can be used for positional cloning of the underlying genes as well as to improve the root parameters of cultivated varieties.

Crop to wild introgression in lettuce: following the fate of crop genome segments in backcross populations.

BackgroundAfter crop-wild hybridization, some of the crop genomic segments may become established in wild populations through selfing of the hybrids or through backcrosses to the wild parent. This constitutes a possible route through which crop (trans)genes could become established in natural populations. The likelihood of introgression of transgenes will not only be determined by fitness effects from the transgene itself but also by the crop genes linked to it. Although lettuce is generally regarded as self-pollinating, outbreeding does occur at a low frequency. Backcrossing to wild lettuce is a likely pathway to introgression along with selfing, due to the high frequency of wild individuals relative to the rarely occurring crop-wild hybrids. To test the effect of backcrossing on the vigour of inter-specific hybrids, Lactuca serriola, the closest wild relative of cultivated lettuce, was crossed with L. sativa and the F1 hybrid was backcrossed to L. serriola to generate BC1 and BC2 populations. Experiments were conducted on progeny from selfed plants of the backcrossing families (BC1S1 and BC2S1). Plant vigour of these two backcrossing populations was determined in the greenhouse under non-stress and abiotic stress conditions (salinity, drought, and nutrient deficiency).ResultsDespite the decreasing contribution of crop genomic blocks in the backcross populations, the BC1S1 and BC2S1 hybrids were characterized by a substantial genetic variation under both non-stress and stress conditions. Hybrids were identified that performed equally or better than the wild genotypes, indicating that two backcrossing events did not eliminate the effect of the crop genomic segments that contributed to the vigour of the BC1 and BC2 hybrids. QTLs for plant vigour under non-stress and the various stress conditions were detected in the two populations with positive as well as negative effects from the crop.ConclusionAs it was shown that the crop contributed QTLs with either a positive or a negative effect on plant vigour, we hypothesize that genomic regions exist where transgenes could preferentially be located in order to mitigate their persistence in natural populations through genetic hitchhiking.

Genome Characterization of a Breeding Line Derived from a Cross Between Oryza sativa and Oryza rufipogon

A preliminary screening was conducted on BC3F1 and BC4F1 backcross families developed from crossing Oryza sativa (MR219) and O. rufipogon (IRGC105491). Despite earlier results showing that O. rufipogon alleles (wild introgression) contributed to both number of panicles (qPPL-2) and tillers (qTPL-2) at loci RM250, RM208, and RM48 in line A20 of the BC2F2 population, we observed that wild introgression was lost at loci RM250 and RM208 but retained at locus RM48 in BC3F1 and BC4F1. Progeny tests conducted utilizing genotype and phenotype data on both BC4F1 and a reference population, BC2F7 (A20 line), did not show significant differences between groups having the MR219 allele and wild introgression at locus RM48. This suggests that there is no additive and transgressive effect of wild introgression in the BC3F1 and BC4F1 generated. The presence of wild introgression was largely due to gene contamination by cross-pollination during field breeding practices.

Mapping of QTLs involved in resistence to rice blast (Magnaporthe grisea) using Oryza minuta introgression lines

  Introgression lines derived from Oryza minuta and O. sativa subsp. japonica var. Junambyeo were crossed for a mapping of the population composed of 112 recombinant lines to identify putative QTLs against rice blast disease using the percentage of diseased leaf area. By using 148 Sequence Tagged Site (STS) and Single Sequence Repeat (SSR) markers, five QTLs on chromosomes 6, 7, 9 and 11 and seven epistatic QTLs were identified against two blast isolates (KI307 and KI209). Of them two QTLs (qKI307-2 and qKI209-3) shared a similar position on chromosome 11. O. minuta introgression contributed the resistance allele for all of these QTLs. Combined phenotypic variations by QTL and (E-QTL) accounted for 56.9% against KI307, and 53.4% against KI209. Each QTL could account for the resistance variation between 11 and 24.6%. The resistance from wild introgressions was attributable to a combination of QTLs and epistatic effects between different loci, capable of inducing hypersensitive reactions. Our findings are in support of the strategy of pyramiding major QTLs to develop improved rice varieties with durable broad spectrum resistance against the blast fungus.

Metabolic fingerprinting reveals differences between shoots of wild and cultivated carrot (Daucus carota L.) and suggests maternal inheritance or wild trait dominance in hybrids

Differences between the metabolic content of cultivars and their related wild species not only have implications for breeding and food quality, but also for the increasingly studied area of crop to wild introgression. Wild and cultivated western carrots belong to the same outcrossing species and hybridize under natural conditions. The metabolic fingerprinting of Dutch wild carrot and of western orange carrot cultivar shoots using 1H NMR showed only quantitative differences in chemical content, indicating relatively low divergence after domestication. Main differences reside in the primary metabolite content and in the concentrations of chlorogenic acid and feruloyl quinic acid in the shoots of the different carrot types. Wild×cultivar hybrids cannot be distinguished from wild plants based on the metabolome, suggesting maternal, maternal environment, or dominance effects, and indicating high hybrid fitness in wild conditions. Considering these similarities, introgression is a real possibility in carrots, but understanding its consequences would require further studies using backcrosses in a multiple environments.

Genetic mapping of wild introgressions into cultivated peanut: a way toward enlarging the genetic basis of a recent allotetraploid.

BackgroundPeanut (Arachis hypogaea L.) is widely used as a food and cash crop around the world. It is considered to be an allotetraploid (2n = 4x = 40) originated from a single hybridization event between two wild diploids. The most probable hypothesis gave A. duranensis as the wild donor of the A genome and A. ipaënsis as the wild donor of the B genome. A low level of molecular polymorphism is found in cultivated germplasm and up to date few genetic linkage maps have been published. The utilization of wild germplasm in breeding programs has received little attention due to the reproductive barriers between wild and cultivated species and to the technical difficulties encountered in making large number of crosses. We report here the development of a SSR based genetic map and the analysis of genome-wide segment introgressions into the background of a cultivated variety through the utilization of a synthetic amphidiploid between A. duranensis and A. ipaënsis.ResultsTwo hundred ninety eight (298) loci were mapped in 21 linkage groups (LGs), spanning a total map distance of 1843.7 cM with an average distance of 6.1 cM between adjacent markers. The level of polymorphism observed between the parent of the amphidiploid and the cultivated variety is consistent with A. duranensis and A. ipaënsis being the most probable donor of the A and B genomes respectively. The synteny analysis between the A and B genomes revealed an overall good collinearity of the homeologous LGs. The comparison with the diploid and tetraploid maps shed new light on the evolutionary forces that contributed to the divergence of the A and B genome species and raised the question of the classification of the B genome species. Structural modifications such as chromosomal segment inversions and a major translocation event prior to the tetraploidisation of the cultivated species were revealed. Marker assisted selection of BC1F1 and then BC2F1 lines carrying the desirable donor segment with the best possible return to the background of the cultivated variety provided a set of lines offering an optimal distribution of the wild introgressions.ConclusionThe genetic map developed, allowed the synteny analysis of the A and B genomes, the comparison with diploid and tetraploid maps and the analysis of the introgression segments from the wild synthetic into the background of a cultivated variety. The material we have produced in this study should facilitate the development of advanced backcross and CSSL breeding populations for the improvement of cultivated peanut.

Comparative linkage mapping of Oryza glumaepatula and Oryza sativa interspecific crosses based on microsatellite and expressed sequence tag markers

Molecular linkage maps representing the rice genome have been an important tool for breeding programs because they allow the elucidation of polygenic traits and are an efficient tool for monitoring wild introgressions in interspecific crosses. Common markers among rice genetic maps are important in defining the homology of chromosomes and the synteny between genomic target regions. We used 148 markers (expressed sequence tags, microsatellites and single nucleotide polymorphisms) to construct a molecular linkage map based on co-dominant markers for an interspecific backcross population using a wild rice (Oryza glumaepatula) from Brazil and performed a comparative analysis with other interspecific maps. The comparative analysis revealed a Spearman correlation index of 0.86 for marker order conservation to a previous map constructed for an interspecific cross using the same wild parent. Approximately 90% of markers common to other interspecific maps kept the same order. These results indicate that it will be possible to generate a unique genetic map using the wild donor and that it may be a helpful tool for breeding programs because plants derived from different interspecific populations can be rapidly scanned using markers associated with useful wild traits.

Phenotypic and Molecular Evaluation of Interspecific Peanut (Arachis) Lines

Abstract Peanut breeders are constantly in search of new sources of genes that confer tolerance or resistance to biotic and abiotic stresses to improve the production and quality. The objective of this study was to evaluate peanut lines generated from interspecific crosses for amounts of wild species introgression, including genes for resistance to peanut root-knot nematodes, tomato spotted wilt virus and leaf spot diseases. Nine diploid Arachis species were crossed with peanut breeding lines and 130 different interspecific hybrid lines were developed. These lines were evaluated for the amount of introgression using RFLP analyses, plant morphology, and disease resistant phenotypes. Based on RFLPs, 41 lines showed measurable introgression and 12 hexaploid-derived lines were polymorphic for at least four probes. Greenhouse and field evaluations indicated that resistance was not present in the lines tested for tomato spotted wilt virus, early leaf spot, or Cylindrocladium black rot. However, resistance approaching that of the wild species was found for the peanut root-knot nematode (Meloidogyne arenaria) among lines derived from crosses with Arachis diogoi, A. correntina, A. batizocoi, and A. cardenasii. Introgression lines were resistant (disease ratings of 1.5 to 4.5 and lesion numbers 8 to 63) compared to Southern Runner (ratings of 5.5 to 6 and lesion numbers of nearly 500) for late leaf spot (Cercosporidium personation) in field evaluations performed in Gainesville, FL over 2 yr. The greatest resistance was found among lines from crosses with A. batizocoi, A. duranensis, A. stenosperma, A. magma, and A. diogoi. Results indicate that it should be possible to identify molecular markers to tag resistance genes for use in conventional breeding programs and stack these genes in highly productive peanut cultivars.

Interspecific Crossability of Nine Diploid Fragaria Species

As part of a wild species introgression program, Fragaria vesca, F. viridis, F. nubicola, F. nipponica, F. nilgerrensis, F. pentaphylla, F. gracilis, F. daltoniana, and F. iinumae were crossed in most combinations possible, the exceptions being F. daltoniana and F. iinumae, which produced only a few flowers each. Crosses with F. vesca as a female and either F. gracilis, F. nipponica, or F. iinumae as males produced good seed set, but seedlings died in the cotyledon stage in every case. No seed set occurred when F. iinumae was crossed with F. viridis or F. nubicola. F. pentaphylla, F. gracilis, and F. iinumae were observed to be self-incompatible while F. daltoniana was self-compatible. Three overlapping groups based on crossing data have emerged. Within the following groups, hybrid plants were obtained in all species combinations, although not necessarily for reciprocal combinations: Group A: F. vesca, F. viridis, F. nubicola, and F. pentaphylla. Group B: F. vesca, F. nilgerrensis, F. daltoniana, and F. pentaphylla. Group C: F. pentaphylla, F. gracilis, and F. nipponica. Fertile or semifertile diploid hybrids were obtained for all species combinations within group A indicating genomic similarity or that breeding at the diploid level could occur with these species. Fertility has not been determined for hybrids in groups B and C. It is interesting to note the presence of F. pentaphylla in all three groups, perhaps this species plays an important role in Fragaria evolution.