Advanced backcross QTL analysis of tomato. II. Evaluation of near-isogenic lines carrying single-donor introgressions for desirable wild QTL-alleles derived from Lycopersicon hirsutum and L. pimpinellifolium

 Improved-processing tomato lines were produced by the molecular breeding strategy of advanced backcross QTL (AB-QTL) analysis. These near-isogenic lines (NILs) contained unique introgressions of wild alleles originating from two donor wild species, Lycopersicon hirsutum (LA1777) and L. pimpinellifolium (LA1589). Wild alleles targeted for trait improvement were selected on the basis of previously published replicated QTL data obtained from advanced backcross populations for a battery of important agronomic traits. Twenty three NILs were developed for 15 genomic regions which were predicted to contain 25 quantitative trait factors for the improvement of seven agronomic traits: total yield, red yield, soluble solids, brix×red yield, viscosity, fruit color, and fruit firmness. An evaluation of the agronomic performance of the NILs in five locations worldwide revealed that 22 out of the 25 (88%) quantitative factors showed the phenotypic improvement predicted by QTL analysis of the BC₃ populations, as NILs in at least one location. Per-location gains over the elite control ranged from 9% to 59% for brix×red yield; 14% to 33% for fruit color; 17% to 34% for fruit firmness; 6% to 22% for soluble-solids content; 7% to 22% for viscosity; 15% to 48% for red yield, and 20% to 28% for total yield. The inheritance of QTLs, the implementation of the AB-QTL methodology for characterizing unadapted germplasm and the applicability of this method to other crops are discussed. Received: 27 October 1997 / Accepted: 25 November 1997     

Advanced backcross QTL analysis in tomato. I. Identification of QTLs for traits of agronomic importance from Lycopersicon hirsutum

 Advanced backcross QTL (AB-QTL) analysis is a new strategy for studying the effect of unadapted alleles on the agronomic performance of elite cultivated lines. In this paper we report results from the application of the AB-QTL strategy to cultivated tomato using the wild species Lycopersicon hirsutum LA1777 as the donor parent. RFLP genomic fingerprints were determined for 315 BC₂ plants and phenotypic data were collected for 19 agronomic traits from approximately 200 derived BC₃ lines which were grown in replicated field trials in three locations worldwide. Between 1 and 12 significant QTLs were identified for each of the 19 traits evaluated, with a total of 121 QTLs identified for all traits. For 25 of the QTLs (20%) corresponding to 12 traits (60%), the L. hirsutum allele was associated with an improvement of the trait from a horticultural perspective, despite the fact that L. hirsutum is overall phenotypically inferior to the elite parent. For example, L. hirsutum has fruit that remains green when ripe (lack of red pigment) yet alleles were found in this species that significantly increase red color when transferred into cultivated tomatoes. Wild alleles were also associated with increases in total yield and soluble solids (up to 15%) and brix×red yield (up to 41%). These results support the idea that one cannot predict the genetic potential of exotic germplasm based on phenotype alone and that marker-based methods, such as the AB-QTL strategy, should be applied to fully exploit exotic germplasm. Received: 27 October 1997 / Accepted: 25 November 1997     

Advanced backcross QTL analysis for the identification of quantitative trait loci alleles from wild relatives of wheat (<Emphasis Type="Italic">Triticum aestivum</Emphasis> L.)

Advanced backcross QTL (AB-QTL) analysis was used to identify quantitative trait loci (QTLs) for yield and yield components in a BC(2)F(2) population derived from a cross between the German winter wheat variety 'Prinz' and the synthetic wheat line W-7984 developed by CIMMYT. Two hundred and ten microsatellite markers were employed to genotype 72 pre-selected BC(2)F(2) plants and phenotypic data were collected for five agronomic traits from corresponding BC(2)F(3) families that were grown at four locations in Germany. Using single-marker regression and interval mapping, a total of 40 putative QTLs derived from W-7984 were detected, of which 11 were for yield, 16 for yield components, eight for ear emergence time and five for plant height. For 24 (60.0%) of them, alleles from the synthetic wheat W-7984 were associated with a positive effect on agronomic traits, despite the fact that synthetic wheat was overall inferior with respect to agronomic appearance and performance. The present study indicated that favorable QTL alleles could be transferred from wild relatives of wheat into an elite wheat variety for improvement of quantitative trait loci like yield by the advanced backcross QTL strategy and molecular breeding. To our knowledge, the results presented here were the first report on AB-QTL analysis in wheat.     

Advanced backcross QTL analysis in progenies derived from a cross between a German elite winter wheat variety and a synthetic wheat (<Emphasis Type="Italic">Triticum aestivum</Emphasis>L.)

We report here the second advanced backcross quantitative trait locus (AB-QTL) analysis carried out in winter wheat. Seven agronomic traits were studied in a BC₂F₁population derived from a cross between the German winter wheat variety Flair and the synthetic wheat line XX86 developed in Japan. We selected 111 BC₂F₁ lines and genotyped these with 197 microsatellite markers. Field data for seven agronomic traits were collected from corresponding BC₂F₃ families that were grown at up to six locations in Germany. QTL analyses for yield and yield components were performed using single-marker regression and interval mapping. A total of 57 putative QTLs derived from XX86 were detected, of which 24 (42.1%) were found to have a positive effect from the synthetic wheat XX86. These favourable QTLs were mainly associated with thousand-grain weight and grain weight per ear. Many QTLs for correlated traits were mapped in similar chromosomal regions. The AB-QTL data obtained in the present study are discussed and compared with results from previous QTL analyses.     

Comparison of a set of allelic QTL-NILs for chromosome 4 of tomato: Deductions about natural variation and implications for germplasm utilization

Quantitative Trait Locus (QTL) allelic variation was studied by analyzing near-isogenic lines (NILs) carrying homologous introgressions on chromosome 4 from three green-fruited wild tomato species. The NILs affect agronomic (yield, brix, fruit weight) and fruit (fruit shape, color, epidermal reticulation) traits in a similar manner. However, significant differences were detected in the magnitudes of the effects, the dominance deviations and epistatic interactions, indicating that those species carry different alleles for the QTL. As the QTL did not show any interaction across environments, gene-tic backgrounds or other QTLs, it can be used to introduce novel genetic variation into a broad range of cultivars. Analysis of new recombinant NILs showed that fruit traits are controlled by several linked genetic loci, whereas multiple genetic loci control the agronomic traits within the original introgression. The hypothesis that QTLs may be composed of multiple linked genes can not be rejected prior to implement projects for QTL isolation and cloning. Loci involved in color enhancement could not be related to any known gene involved in the carotenoid biosynthesis pathway, therefore it is hypothesized that the function of those loci must be related to the genetic regulation of the carotenoid biosynthetic pathway. Received: 14 April 2000 / Accepted: 12 May 2000     

Comparative AB-QTL analysis in barley using a single exotic donor of Hordeum vulgare ssp. spontaneum.

This paper reports on the first comparative advanced backcross quantitative trait locus (AB-QTL) study in barley. The BC₂F₂ population H×101 was generated from crossing var. Harry [H; Hordeum vulgare ssp. vulgare (Hv)] with ISR101-23 [101; H. v. ssp. spontaneum (Hsp)]. The results of the AB-QTL analysis for 13 quantitative traits are presented and, subsequently, compared with the AB-QTL study of the barley cross Apex × ISR101-23 (A×101; Pillen et al., Theor Appl Genet 107:340–352). Both AB populations share the exotic Hsp donor accession ISR101-23. In H×101, 108 putative QTLs (17%) were identified among the 650 marker×trait combinations tested. Altogether 52 (48 %) favorable effects were identified from the exotic parent. At these marker loci, the homozygous Hsp genotype was associated with an improvement in the trait compared to the homozygous Hv genotype. The percentage of QTLs detected in H×101 was comparable to that in A×101 (17% vs. 15%), however more favorable exotic QTL alleles were located in H×101 than in A×101 (48% vs. 34%). In H×101, the Hsp QTL allele at EBmac0679_[4H] was associated with a yield increase of 5.9% averaged across the six environments tested. A comparison of putative QTLs between H×101 and A×101 was based on 26 shared SSR markers. In total, 26% of the putative QTLs could be detected simultaneously in both AB populations. This finding indicates that only a portion of the QTL effects of the donor allele can be transferred from one elite recipient to the next.Communicated by G. WenzelThis work is dedicated to the 65th birthday of Prof. Dr. H.H. Geiger, Department of Plant Breeding, Seed Science and Population Genetics, University of Hohenheim, Germany.     

Identification of Hordeum spontaneum QTL alleles improving field performance of barley grown under rainfed conditions

Advanced backcross QTL (AB-QTL) analysis was deployed to identify allelic variation in wild barley (Hordeum vulgare ssp. spontaneum) of value in the improvement of grain yield and other agronomically important traits in barley (Hordeum vulgare ssp. vulgare) grown under conditions of water deficit in Mediterranean countries. A population of 123 double haploid (DH) lines obtained from BC₁F₂ plants derived from a cross between Barke (European two-row cultivar) and HOR11508 (wild barley accession) were tested in replicated field trials, under varying conditions of water availability in Italy, Morocco and Tunisia, for seven quantitative traits. Significant QTL effects at one (P 0.001) or more trial sites (P 0.01) were identified for all traits. At 42 (52%) of the 80 putative QTLs identified, the allele increasing a “traits' value” was contributed by H. spontaneum. For example, though the majority (67%) of QTL alleles increasing grain yield were contributed by H. vulgare, H. spontaneum contributed the alleles increasing grain yield at six regions on chromosomes 2H, 3H, 5H and 7H. Among them, two QTLs (associated to Bmac0093 on chromosome 2H and to Bmac0684 on chromosome 5H) were identified in all three locations and had the highest additive effects. The present study shows the validity of deploying AB-QTL analysis for identifying favourable QTL alleles from wild germplasm and indicates its potential as an enhancement strategy for the genetic improvement of cultivars better adapted to drought-prone environments.     

Identification of agronomically favorable quantitative trait loci alleles from a dent corn inbred Dan232 using advanced backcross QTL analysis and comparison with the F<Subscript>2:3</Subscript> population in popcorn

Specific traits are an important consideration in plant breeding. In popcorn, inferior agronomic traits could be improved using dent or flint corn backcrossed with popcorn. In this study, we used advanced backcross quantitative trait locus (AB-QTL) analysis to identify trait-improving QTL alleles from a dent maize inbred Dan232, and compared the detection of QTL in the BC₂S₁ population with QTL results using F_2:3 families of the same population. Two hundred and twenty BC₂S₁ families developed from a cross between Dan232 and an elite popcorn inbred N04 were evaluated for nine plant traits in replicated field trials under two environments. Using composite interval mapping (CIM), a total of 28 significant QTL were detected, and of these, 23 (82.14%) had favorable alleles contributed by the dent corn parent Dan232. Nine QTL (32.14%) detected in the BC₂S₁ population were also located in or near the same chromosome intervals in the F_2:3 population. All of the favorable QTL alleles from Dan232 could be used in marker-assisted selection (MAS) to improve the respective plant traits in popcorn breeding. In addition, their near isogenic lines (QTL-NILs) could be obtained through selfing or another 1–2 backcross with N04. Also, N04 improved for the studied plant traits could be developed from the BC₂S₁ families used in this study. This study demonstrated that the AB-QTL method can be applied to identify favorable QTL from dent corn inbred in popcorn breeding and, once identified, the alleles could be used in marker-assisted selection to improve the respective plant traits.     

Identification of trait-improving quantitative trait loci for grain yield components from a dent corn inbred line in an advanced backcross BC<Subscript>2</Subscript>F<Subscript>2</Subscript> population and comparison with its F<Subscript>2:3</Subscript> population in popcorn

Normal maize germplasm could be used to improve the grain yield of popcorn inbreds. Our first objective was to locate genetic factors associated with trait variation and make first assessment on the efficiency of advanced backcross quantitative trait locus (AB-QTL) analysis for the identification and transfer of favorable QTL alleles for grain yield components from the dent corn inbred. A second objective was to compare the detection of QTL in the BC₂F₂ population with results using F_2:3 lines of the same parents. Two hundred and twenty selected BC₂F₂ families developed from a cross between Dan232 and an elite popcorn inbred N04 were evaluated for six grain yield components under two environments, and genotyped by means of 170 SSR markers. Using composite interval mapping (CIM), a total of 19 significant QTL were detected. Eighteen QTL had favorable alleles contributed by the dent corn parent Dan232. Sixteen of these favorable QTL alleles were not in the same or near marker intervals with QTL for popping characteristics. Six QTL were also detected in the F_2:3 population. Improved N04 could be developed from 210 and 208 families with higher grain weight per plant and/or 100-grain weight, respectively, and 35 families with the same or higher popping expansion volume than N04. In addition, near isogenic lines containing detected QTL (QTL-NILs) for grain weight per plant and/or 100-grain weight could be obtained from 12 families. Our study demonstrated that the AB-QTL method can be applied to identify and manipulate favorable QTL alleles from normal corn inbreds and combine QTL detection and popcorn breeding efficiently.     

AB-QTL analysis in winter wheat: I. Synthetic hexaploid wheat (<Emphasis Type="Italic">T. turgidum</Emphasis> ssp. <Emphasis Type="Italic">dicoccoides </Emphasis> × <Emphasis Type="Italic">T. tauschii</Emphasis>) as a source of favourable alleles for milling and baking quality traits

The advanced backcross QTL (AB-QTL) strategy was utilised to locate quantitative trait loci (QTLs) for baking quality traits in two BC₂F₃ populations of winter wheat. The backcrosses are derived from two German winter wheat cultivars, Batis and Zentos, and two synthetic, hexaploid wheat accessions, Syn022 and Syn086. The synthetics originate from hybridisations of wild emmer (T. turgidum spp. dicoccoides) and T. tauschii, rather than from durum wheat and T. tauschii and thus allowed for the first time to test for exotic QTL effects on wheat genomes A and B in addition to genome D. The investigated quality traits comprised hectolitre weight, grain hardness, flour yield Type 550, falling number, grain protein content, sedimentation volume and baking volume. One hundred and forty-nine SSR markers were applied to genotype a total of 400 BC₂F₃ lines. For QTL detection, a mixed-model ANOVA was conducted, including the effects DNA marker, BC₂F₃ line, environment and marker × environment interaction. Overall 38 QTLs significant for a marker main effect were detected. The exotic allele improved trait performance at 14 QTLs (36.8%), while the elite genotype contributed the favourable effect at 24 QTLs (63.2%). The favourable exotic alleles were mainly associated with grain protein content, though the greatest improvement of trait performance due to the exotic alleles was achieved for the traits falling number and sedimentation volume. At the QTL on chromosome 4B the exotic allele increased the falling number by 19.6% and at the QTL on chromosome 6D the exotic allele led to an increase of the sedimentation volume by 21.7%. The results indicate that synthetic wheat derived from wild emmer × T. tauschii carries favourable QTL alleles for baking quality traits, which might be useful for breeding improved wheat varieties by marker-assisted selection.     

Advanced backcross QTL analysis of a<Emphasis Type="Italic"> Lycopersicon esculentum</Emphasis> ×<Emphasis Type="Italic"> L</Emphasis>.<Emphasis Type="Italic"> pennellii</Emphasis> cross and identification of possible orthologs in the Solanaceae

In this study, the advanced backcross QTL (AB-QTL) mapping strategy was used to identify loci for yield, processing and fruit quality traits in a population derived from the interspecific cross Lycopersicon esculentum E6203 × Lycopersicon pennellii accession LA1657. A total of 175 BC₂ plants were genotyped with 150 molecular markers and BC₂F₁ plots were grown and phenotyped for 25 traits in three locations in Israel and California, U.S.A. A total of 84 different QTLs were identified, 45% of which have been possibly identified in other wild-species-derived populations of tomato. Moreover, three fruit-weight/size and shape QTLs (fsz2b.1, fw3.1/fsz3.1 and fs8.1) appear to have putative orthologs in the related solanaceous species, pepper and eggplant. For the 23 traits for which allelic effects could be deemed as favorable or unfavorable, 26% of the identified loci had L. pennellii alleles that enhanced the performance of the elite parent. Alleles that could be targeted for further introgression into cultivated tomato were also identified.Communicated by G. Wenzel     

AB-QTL analysis in spring barley: III. Identification of exotic alleles for the improvement of malting quality in spring barley (<Emphasis Type="Italic">H. vulgare</Emphasis> ssp. <Emphasis Type="Italic">spontaneum</Emphasis>)

Malting quality is genetically determined by the complex interaction of numerous traits which are expressed prior to and, in particular, during the malting process. Here, we applied the advanced backcross quantitative trait locus (AB-QTL) strategy (Tanksley and Nelson, Theor Appl Genet 92:191–203, 1996), to detect QTLs for malting quality traits and, in addition, to identify favourable exotic alleles for the improvement of malting quality. For this, the BC₂DH population S42 was generated from a cross between the spring barley cultivar Scarlett and the wild barley accession ISR42-8 (Hordeum vulgare ssp. spontaneum). A QTL analysis in S42 for seven malting parameters measured in two different environments yielded 48 QTLs. The exotic genotype improved the trait performance at 18 (37.5%) of 48 QTLs. These favourable exotic alleles were detected, in particular, on the chromosome arms 3HL, 4HS, 4HL and 6HL. The exotic allele on 4HL, for example, improved α-amylase activity by 16.3%, fermentability by 0.8% and reduced raw protein by 2.4%. On chromosome 6HL, the exotic allele increased α-amylase by 16.0%, fermentability by 1.3%, friability by 7.3% and reduced viscosity by 2.9%. Favourable transgressive segregation, i.e. S42 lines exhibiting significantly better performance than the recurrent parent Scarlett, was recorded for four traits. For α-amylase, fermentability, fine-grind extract and VZ45 20, 16, 2 and 26 S42 lines, respectively, surpassed the recurrent parent Scarlett. The present study hence demonstrates that wild barley does harbour valuable alleles, which can enrich the genetic basis of cultivated barley and improve malting quality traits.     

Identification of quantitative trait loci contributing to yield and seed quality parameters under terminal drought in barley advanced backcross lines

Drought is a major limiting factor for barley production, especially in the primary areas of its cultivation. Wild barley represents a major source of favourable alleles for increasing the genetic variation for multiple traits including resistance to both biotic and abiotic stresses. We used advanced backcross quantitative trait locus (AB-QTL) analysis of a BC3-doubled haploid population developed between the cultivated parent Brenda (Hordeum vulgare ssp. vulgare) and the wild accession HS584 (H. vulgare ssp. spontaneum) to study the contribution of wild barley in improving various agronomic and seed quality traits under post-anthesis drought. The experiment was carried out at two different locations (IPK, Gatersleben and Nordsaat, Böhnshausen) and terminal drought was imposed by withholding water or spraying with potassium iodide at 10 days after flowering under greenhouse or field conditions, respectively. QTL analysis indicated that wild barley contributed favourably to most of the traits studied under both control and drought conditions. A total of seven hot-spot QTL regions with co-localizing QTL for various traits harboured more than 80 % of the stable QTL detected in the present study. For yield and thousand-grain weight and their respective drought tolerance indices, most of the QTL were derived from Brenda. On the other hand, for traits like seed length and seed nitrogen content, all the QTL were contributed by HS584, the parent having higher trait value. A significantly reduced carbon/nitrogen (C/N) ratio in the selected contrasting inferior lines compared to superior ones suggests that C/N ratio could be a potential parameter for screening not just seed quality parameters but also grain weight performance under terminal drought.     

QTL analysis of yield traits in an advanced backcross population derived from a cultivated Andean × wild common bean (Phaseolus vulgaris L.) cross

Advanced backcross QTL analysis was used to identify quantitative trait loci (QTL) for agronomic performance in a population of BC₂F_3:5 introgression lines created from the cross of a Colombian large red-seeded commercial cultivar, ICA Cerinza, and a wild common bean accession, G24404. A total of 157 lines were evaluated for phenological traits, plant architecture, seed weight, yield and yield components in replicated trials in three environments in Colombia and genotyped with microsatellite, SCAR, and phaseolin markers that were used to create a genetic map that covered all 11 linkage groups of the common bean genome with markers spaced at an average distance of every 10.4 cM. Segregation distortion was most significant in regions orthologous for a seed coat color locus (R-C) on linkage group b08 and two domestication syndrome genes, one on linkage group b01 at the determinacy (fin) locus and the other on linkage group b02 at the seed-shattering (st) locus. Composite interval mapping analysis identified a total of 41 significant QTL for the eight traits measured of which five for seed weight, two for days to flowering, and one for yield were consistent across two or more environments. QTL were located on every linkage group with b06 showing the greatest number of independent loci. A total of 13 QTL for plant height, yield and yield components along with a single QTL for seed size showed positive alleles from the wild parent while the remaining QTL showed positive alleles from the cultivated parent. Some QTL co-localized with regions that had previously been described to be important for these traits. Compensation was observed between greater pod and seed production and smaller seed size and may have resulted from QTL for these traits being linked or pleiotropic. Although wild beans have been used before to transfer biotic stress resistance traits, this study is the first to attempt to simultaneously obtain a higher yield potential from wild beans and to analyze this trait with single-copy markers. The wild accession was notable for being from a unique center of diversity and for contributing positive alleles for yield and other traits to the introgression lines showing the potential that advanced backcrossing has in common bean improvement.     

Dissecting a wheat QTL for yield present in a range of environments: from the QTL to candidate genes

Previous studies with 95 bread wheat doubled haploid lines (DHLs) from the cross Chinese Spring (CS)xSQ1 trialled over 24 yearxtreatmentxlocations identified major yield quantitative trait loci (QTLs) in homoeologous locations on 7AL and 7BL, expressed mainly under stressed and non-stressed conditions, respectively. SQ1 and CS contributed alleles increasing yield on 7AL and 7BL, respectively. The yield component most strongly associated with these QTLs was grains per ear. Additional results which focus on the 7AL yield QTL are presented here. Trials monitoring agronomic, morphological, physiological, and anatomical traits revealed that the 7AL yield QTL was not associated with differences in flowering time or plant height, but with significant differences in biomass at maturity and anthesis, biomass per tiller, and biomass during tillering. In some trials, flag leaf chlorophyll content and leaf width at tillering were also associated with the QTL. Thus, it is likely that the yield gene(s) on 7AL affects plant productivity. Near-isogenic lines (NILs) for the 7AL yield QTL with CS or SQ1 alleles in an SQ1 background showed the SQ1 allele to be associated with >20% higher yield per ear, significantly higher flag leaf chlorophyll content, and wider flag leaves. Epidermal cell width and distance between leaf vascular bundles did not differ significantly between NILs, so the yield-associated gene may influence the number of cell files across the leaf through effects on cell division. Interestingly, comparative mapping with rice identified AINTEGUMENTA and G-protein subunit genes affecting lateral cell division at locations homologous to the wheat 7AL yield QTL.     

Identification of positive yield QTL alleles from exotic soybean germplasm in two backcross populations

Increasing seed yield is an important breeding goal of soybean [Glycine max (L.) Merr.] improvement efforts. Due to the small number of ancestors and subsequent breeding and selection, the genetic base of current soybean cultivars in North America is narrow. The objective of this study was to map quantitative trait loci (QTL) in two backcross populations developed using soybean plant introductions as donor parents. The first population included 116 BC(2)F(3)-derived lines developed using "Elgin" as the recurrent parent and PI 436684 as the donor parent (E population). The second population included 93 BC(3)F(3)-derived lines developed with "Williams 82" as the recurrent parent and PI 90566-1 as the donor parent (W population). The two populations were evaluated with 1,536 SNP markers and during 2?years for seed yield and other agronomic traits. Genotypic and phenotypic data were analyzed using the programs MapQTL and QTLNetwork to identify major QTL and epistatic QTL. In the E population, two yield QTL were identified by both MapQTL and QTLNetwork, and the PI 436684 alleles were associated with yield increases. In the W population, a QTL allele from PI 90566-1 accounted for 30?% of the yield variation; however, the PI region was also associated with later maturity and shorter plant height. No epistasis for seed yield was identified in either population. No yield QTL was previously reported at the regions where these QTL map indicating that exotic germplasm can be a source of new alleles that can improve soybean yield.     

QTL Analysis for Root Protein in a Backcross Family of Cassava Derived from Manihot esculenta ssp flabellifolia

Root protein content of elite cassava is very low, largely due to breeder’s selection for other agronomic traits mainly fresh weight yield and disease resistance. Increased protein content in the root of cassava will improve its usefulness as a more complete food source in the developing world. An inter-specific F₁ hybrid CW 198 - 11 was earlier developed at International Center for Tropical Agriculture (CIAT), Cali, Colombia by genetic crosses of OW 230 - 1 (FLA 441 - 5) and CW 30–65 (an inter-specific hybrid between an improved cassava variety SG 427 - 87 and an accession of Manihot esculenta ssp flabellifolia (MESCFLAX – 80)). The inter-specific cross was ‘backcrossed’, in the sense of another cross to cassava (MTAI – 8) to generate a B₁P₂ family with 225 progenies in which major quantitative trait loci (QTL) for root protein in the backcross population of cassava were identified. A linkage map from the female parent of the backcross population was used for QTL detection. A total of three QTL (protg.7, protg.13 and protg.23) controlling protein were identified in three different environments. One QTL was expressed across all three environments. These results demonstrated high broad sense heritability of 61.6% for protein over 2 years, in two different locations. The individual effects of alleles at these QTL explained from 15% to 25% of the phenotypic variance. The consistency of QTL controlling protein across environments reveals their potential for use in marker-assisted recurrent selection.     

Quantitative trait analysis of seed yield and other complex traits in hybrid spring rapeseed (Brassica napus L.): 2. Identification of alleles from unadapted germplasm

Unadapted germplasm may contain alleles that could improve hybrid cultivars of spring oilseed Brassica napus. Quantitative trait loci (QTL) mapping was used to identify potentially useful alleles from two unadapted germplasm sources, a Chinese winter cultivar and a re-synthesized B. napus, that increase seed yield when introgressed into a B. napus spring hybrid combination. Two populations of 160 doubled haploid (DH) lines were created from crosses between the unadapted germplasm source and a genetically engineered male-fertility restorer line (P1804). A genetically engineered male-sterile tester line was used to create hybrids with each DH line (testcrosses). The two DH line populations were evaluated in two environments and the two testcross populations were evaluated in three or four environments for seed yield and other agronomic traits. Several genomic regions were found in the two testcross populations which contained QTL for seed yield. The map positions of QTL for days to flowering and resistance to a bacterial leaf blight disease coincided with QTL for seed yield and other agronomic traits, suggesting the occurrence of pleiotropic or linked effects. For two hybrid seed yield QTL, the favorable alleles increasing seed yield originated from the unadapted parents, and one of these QTL was detected in multiple environments and in both populations. In this QTL region, a chromosome rearrangement was identified in P1804, which may have affected seed yield.Electronic Supplementary Material Supplementary material is available to authorised users in the online version of this article at .     

Four rice QTL controlling number of spikelets per panicle expressed the characteristics of single Mendelian gene in near isogenic backgrounds

Development of quantitative trait loci (QTL) near isogenic lines is a crucial step to QTL isolation using the strategy of map-based cloning. In this study, a recombinant inbred line (RIL) population derived from two indica rice varieties, Zhenshan 97 and HR5, was employed to map QTL for spikelets per panicle (SPP). One major QTL (qSPP7) and three minor QTL (qSPP1, qSPP2 and qSPP3) were identified on chromosomes 7, 1, 2 and 3, respectively. Four sets of near isogenic lines (NILs) BC₄F₂ targeted for the four QTL were developed by following a standard procedure of consecutive backcross, respectively. These QTL were not only validated in corresponding NILs, but also explained amounts of phenotypic variation with much larger LOD scores compared with those identified in RILs. SPP in the four QTL-NILs expressed bimodal or discontinuous distributions and followed the expected segregation ratio of single Mendelian factor by progeny test. Finally, qSPP1, qSPP2, qSPP3 and qSPP7 were respectively mapped to a locus, 0.5 cM from MRG2746, 0.6 cM from MRG2762, 0.8 cM from RM49 and 0.7 cM from MRG4436, as co-dominant markers on the basis of progeny tests. These results indicate no matter how small effect minor QTL is, QTL may still express the characteristics of single Mendelian factor in NILs and isolation of minor QTL will be possible using high quality NILs. Pyramiding these QTL into a variety will largely enhance rice grain yield.     

Advanced backcross QTL analysis in a cross between an elite processing line of tomato and its wild relative L. pimpinellifolium

Approximately 170 BC2 plants from a cross between an elite processing inbred (recurrent parent) and the wild species Lycopersicon pimpinellifolium LA1589 (donor parent) were analyzed with segregating molecular markers covering the entire tomato genome. Marker data were used to identify QTLs controlling a battery of horticultural traits measured on BC2F1 and BC3 families derived from the BC2 individuals. Despite its overall inferior appearance, L. pimpinellifolium was shown to possess QTL alleles capable of enhancing most traits important in processing tomato production. QTL-NIL lines, containing specific QTLs modifying fruit size and shape, were subsequently constructed and shown to display the transgressive phenotypes predicted from the original BC2 QTL analysis. The potential of exploiting unadapted and wild germplasm via advanced backcross QTL analysis for the enhancement of elite crop varieties is discussed.