Backcross Inbred Population Research Articles

Mapping quantitative trait loci for resistance to watermelon bud necrosis orthotospovirus in watermelon [Citrullus lanatus (Thunb.) Matsum & Nakai

Watermelon [Citrullus lanatus (Thunb.) Matsum & Nakai] is an important cucurbit crop cultivated worldwide. In an effort to map WBNV resistance, the current study consisted of two populations derived from a WBNV resistant accession, IIHR-82 belonging to Citrullus lanatus var. citroides (Syn. Citrullus amarus). The first population is a backcross inbred population (BC1F6) of 141 families (Pop I) that was developed by crossing IIHR-82 to an elite cultivar Arka Manik. A resistant family, BIL-53 belonging to Pop I was crossed to IIHR-140 to develop F3 population, consisting of 112 families (Pop II). Each of these populations was evaluated for WBNV incidence for two years under natural epiphytotic conditions. A significant correlation was observed for various resistance traits across years and populations. The frequency distribution graphs of Area Under Disease Progress Curve for WBNV incidence in both the populations exhibited a continuous distribution, indicating that trait is quantitative in nature. A total of 163 markers were mapped for the Pop I which spread onto 15 linkage groups (LGs) spanning a total map length of 3310.17 cM with a mean marker interval of 20.31 cM. The linkage map for the Pop II was constructed with 135 markers spread over 12 linkage groups spanning a total length of 1965.53 cM with an average interval between markers of 14.56 cM.The QTL analysis for WBNV resistance related traits revealed 14 major QTL's for Pop I and 19 for Pop II with a maximum PVE upto 21.20%. Multi-trait QTL regions were observed on LG 3b for Pop I and LG 2, LG 4, LG 7 and LG 8 for Pop II. Importantly, we observed common QTL regions for plant survival on LG 2 and PDI on LG 3 and LG 8 for both the populations. As this is the first attempt to map QTL's for WBNV resistance, the results obtained in the present study may provide a guide for fine mapping multi-trait QTL regions.

Registration of GA R01‐40‐08, a Gossypium hirsutum Upland Cotton Germplasm Line with qFL‐Chr.1 Introgressed from Gossypium barbadense Conferring Improved Fiber Length

GA R01‐40‐08 (Reg. no. GP‐1060, PI 690433), is a Gossypium hirsutum L. germplasm line developed by the Molecular Cotton Breeding Laboratory, Department of Crop and Soil Sciences, at the University of Georgia. GA R01‐40‐08 was selected from an interspecific backcross inbred population derived from the cross of ‘Tamcot 2111’ (G. hirsutum) with ‘Pima S‐6’ (G. barbadense L.). This G. hirsutum germplasm line harbors an introgressed quantitative trait locus (QTL), qFL‐Chr.1, conferring improved upper half mean fiber length (UHML) from Pima S‐6. Field trials conducted in Plains and Tifton, GA, in 2009, 2013, and 2014 indicate that GA R01‐40‐08 exhibits improved UHML of 1.5 mm longer than the Tamcot 2111 parent, representing a 5% improvement. GA R01‐40‐08 had fiber yields over 18% higher than the Pima S‐6 parent and equivalent to the higher‐yielding parent, Tamcot 2111. This germplasm line represents a milestone in upland cotton germplasm improvement as the first publicly released germplasm line carrying a fiber length QTL with an effect that has been validated in multiple environments. It will provide upland cotton breeders with an adapted source of the qFL‐Chr.1 QTL for improved UHML from G. barbadense, and the tightly linked markers published previously will allow breeders to use marker‐assisted selection for rapid incorporation.

A Comparative Genome-Wide Analysis of the R2R3-MYB Gene Family Among Four Gossypium Species and Their Sequence Variation and Association With Fiber Quality Traits in an Interspecific G. hirsutum × G. barbadense Population.

Cotton (Gossypium spp.) is the most important natural fiber crop in the world. The R2R3-MYB gene family is a large gene family involved in many plant functions including cotton fiber development. Although previous studies have reported its phylogenetic relationships, gene structures, and expression patterns in tetraploid G. hirsutum and diploid G. raimondii, little is known about the sequence variation of the members between G. hirsutum and G. barbadense and their involvement in the natural quantitative variation in fiber quality and yield. In this study, a comprehensive genome-wide comparative analysis was performed among the four Gossypium species using whole genome sequences, i.e., tetraploid G. hirsutum (AD1) and G. barbadense (AD2) as well as their likely ancestral diploid extants G. raimondii (D5) and G. arboreum (A2), leading to the identification of 406, 393, 216, and 213 R2R3-MYB genes, respectively. To elucidate whether the R2R3-MYB genes are genetically associated with fiber quality traits, 86 R2R3-MYB genes were co-localized with quantitative trait loci (QTL) hotspots for fiber quality and yield, including 42 genes localized within the fiber length QTL hotspots, in interspecific G. hirsutum × G. barbadense populations. There were 20 interspecific nonsynonymous single-nucleotide polymorphism (SNP) sites between the two tetraploid cultivated species, of which 16 developed from 11 R2R3-MYB genes were significantly correlated with fiber quality and yield in a backcross inbred population (BIL) of G. hirsutum × G. barbadense in at least one of the four field tests. Taken together, these results indicate that the sequence variation in these 11 R2R3-MYB genes is associated with the natural variation (i.e., QTL) in fiber quality and yield. Moreover, the functional SNPs of five R2R3-MYB allele pairs from the AD1 and AD2 genomes were significantly correlated with the gene expression related to fiber quality in fiber development. The results will be useful in further elucidating the role of the R2R3-MYB genes during fiber development.

Grain yield responses to varied level of moisture stress at reproductive stage in an interspecific population derived from Swarna/O. glaberrima introgression line

Understanding response of plants to drought stress is critical for developing drought tolerant genotypes with stable performance under water limiting conditions. A backcross inbred population derived in the background of a popular variety Swarna, was evaluated for yield and yield attributing traits under reproductive stage and shoot morphological traits at seedling stage under drought stress over a period of two years during 2011–2013. Selection intensity varied across seasons and years with varied level of moisture stress. Traits such as flowering (DTF), plant height (PH), spikelet fertility (SF), biomass (BM), harvest index (HI) and grain yield (GY) are drastically affected by drought across seasons. Yield reduction varied from 48.5% to 92.4% over control trials. Chlorophyll content (CC) and canopy temperature (CT) recorded higher under drought rather than control. Yield was highly associated with DTF (−0.29* to −0.76**), SF (0.32** to 0.77**), HI (0.82** to 0.97**) and CT (−0.38**). Heritability is found to be similar for grain yield under both conditions. Genotypes displaying higher SF and HI, lower CT, reduction in flowering delay and low DSI are able to produce better grain yield under drought. High yielding genotypes at reproductive stage stress also showed superior performance under stress at seedling stage. Hence, selection intensity for high yield potential under favorable conditions, drought tolerance to varied level of stress (across seasons) and screening under target population environment had the advantage of identifying stable high yielding genotypes with wider adaption suitable for drought-prone regions, which can significantly benefits the poor farmers relying on rainfed lowland rice.

Resistance to Crown and Root Rot Caused by Phytophthora capsici in a Tomato Advanced Backcross of Solanum habrochaites and Solanum lycopersicum.

Phytophthora capsici causes devastating disease on many vegetable crops, including tomato and other solanaceous species. Solanum habrochaites accession LA407, a wild relative of cultivated tomato, has shown complete resistance to four P. capsici isolates from Michigan cucurbitaceous and solanaceous crops in a previous study. Greenhouse experiments were conducted to evaluate 62 lines of a tomato inbred backcross population between LA407 and the cultivated tomato 'Hunt 100' and 'Peto 95-43' for resistance to two highly virulent P. capsici isolates. Roots of 6-week-old seedlings were inoculated with each of two P. capsici isolates and maintained in the greenhouse. Plants were evaluated for wilting and plant death three times per week for 5 weeks. Significant differences were observed in disease response among the inbred tomato lines. Most lines evaluated were susceptible to P. capsici isolate 12889 but resistant to isolate OP97; 24 tomato lines were resistant to both isolates. Heritability of Phytophthora root rot resistance was high in this population. Polymorphic molecular markers located in genes related to resistance and defense responses were identified and added to a genetic map previously generated for the population. Resistant lines and polymorphic markers identified in this study are a valuable resource for development of tomato varieties resistant to P. capsici.

Heritability, Correlation and Path Analysis among Yield and Yield Attributing Traits for Drought Tolerance in an Interspecific Cross Derived from <i>Oryza sativa x O. glaberrima </i>Introgression Line under Contrasting Moisture Regimes

Drought is a major constraint for rainfed lowland and upland rice productivity throughout world. A backcross inbred population derived from ‘Swarna’ and ‘WAB450-I-B-P-157-2-1’ (Oryza sativa L. x O. glaberrima) was evaluated under both irrigated and lowland drought stresses for yield and yield related traits across three different seasons. Significant differences were found among all the analyzed traits. Coefficients of variation were recorded relatively high for filled grains per panicle, spikelet fertility, test weight, harvest index and grain yield and low for panicle length under both conditions during the study interval. Broad sense heritability varied from 0.28 (panicle number) to 0.83 (plant height) under stress and 0.31 (test weight) to 0.86 (plant height) under control. However, heritability estimates for grain yield and harvest index were found to be similar under both conditions. Traits such as filled grains per panicle, spikelet fertility, harvest index and grain yield recorded higher values of both heritability, as well as genetic advance under both conditions, indicating the suitability of these traits as selection criteria to derive high yielding genotypes for drought prone regions. Harvest index exhibited maximum positive direct effect on grain yield under both the conditions; in addition, filled grains per panicle, spikelet fertility and biomass had positive direct effect on grain yield under both irrigated and lowland drought stresses state. Hence, for improving the rice yield under lowland drought ecology, a genotype should posses a large number of panicles per plant, filled grains per panicle, high spikelet fertility and maintains higher biomass and harvest index.

Genetic and physiological analysis of tolerance to acute iron toxicity in rice.

BackgroundFe toxicity occurs in lowland rice production due to excess ferrous iron (Fe2+) formation in reduced soils. To contribute to the breeding for tolerance to Fe toxicity in rice, we determined quantitative trait loci (QTL) by screening two different bi-parental mapping populations under iron pulse stresses (1,000 mg L−1 = 17.9 mM Fe2+ for 5 days) in hydroponic solution, followed by experiments with selected lines to determine whether QTLs were associated with iron exclusion (i.e. root based mechanisms), or iron inclusion (i.e. shoot-based mechanisms).ResultsIn an IR29/Pokkali F8 recombinant inbred population, 7 QTLs were detected for leaf bronzing score on chromosome 1, 2, 4, 7 and 12, respectively, individually explaining 9.2-18.7% of the phenotypic variation. Two tolerant recombinant inbred lines carrying putative QTLs were selected for further experiments. Based on Fe uptake into the shoot, the dominant tolerance mechanism of the tolerant line FL510 was determined to be exclusion with its root architecture being conducive to air transport and thus the ability to oxidize Fe2+ in rhizosphere. In line FL483, the iron tolerance was related mainly to shoot-based mechanisms (tolerant inclusion mechanism). In a Nipponbare/Kasalath/Nipponbare backcross inbred population, 3 QTLs were mapped on chromosomes 1, 3 and 8, respectively. These QTLs explained 11.6-18.6% of the total phenotypic variation. The effect of QTLs on chromosome 1 and 3 were confirmed by using chromosome segment substitution lines (SL), carrying Kasalath introgressions in the genetic background on Nipponbare. The Fe uptake in shoots of substitution lines suggests that the effect of the QTL on chromosome 1 was associated with shoot tolerance while the QTL on chromosome 3 was associated with iron exclusion.ConclusionTolerance of certain genotypes were classified into shoot- and root- based mechanisms. Comparing our findings with previously reported QTLs for iron toxicity tolerance, we identified co-localization for some QTLs in both pluse and chronic stresses, especially on chromosome 1.

Association and Heritability Studies for Drought Resistance under Varied Moisture Stress Regimes in Backcross Inbred Population of Rice

Drought stress is one of the major constraints affecting rice production and yield stability in the rainfed regions. To understand the physiological basis of drought resistance related component traits, we used a backcross inbred population of rice under three kinds of moisture regimes viz., non-stress, moderate (24.48%) and severe stress (73.97%) conditions which reflect the differential responses of the genotypes to varying stress intensities. The plot yield, 1000-grain weight, panicle exsertion and canopy air temperature difference exhibited high heritability under the control conditions, whereas spikelet sterility and single plant yield exhibited high heritability under the moderate stress conditions. Traits such as days to 50% flowering, plant height and osmotic potential showed high heritability under the severe stress conditions. Plot yield under stress was significantly and positively correlated with harvest index and 1000-grain weight, but negatively associated with leaf rolling score and days to 50% flowering. The drought susceptibility index and drought response index were negatively correlated between each other both under the moderate and severe stress conditions. The derived traits viz., difference in panicle length between the control and the severe stress was associated with osmotic adjustment measured under field conditions. Difference in plant height and panicle length was negatively associated with plot yield under stress.

Mapping quantitative trait loci for lint yield and fiber quality across environments in a Gossypium hirsutum × Gossypium barbadense backcross inbred line population

Identification of stable quantitative trait loci (QTLs) across different environments and mapping populations is a prerequisite for marker-assisted selection (MAS) for cotton yield and fiber quality. To construct a genetic linkage map and to identify QTLs for fiber quality and yield traits, a backcross inbred line (BIL) population of 146 lines was developed from a cross between Upland cotton (Gossypium hirsutum) and Egyptian cotton (Gossypium barbadense) through two generations of backcrossing using Upland cotton as the recurrent parent followed by four generations of self pollination. The BIL population together with its two parents was tested in five environments representing three major cotton production regions in China. The genetic map spanned a total genetic distance of 2,895 cM and contained 392 polymorphic SSR loci with an average genetic distance of 7.4 cM per marker. A total of 67 QTLs including 28 for fiber quality and 39 for yield and its components were detected on 23 chromosomes, each of which explained 6.65-25.27% of the phenotypic variation. Twenty-nine QTLs were located on the At subgenome originated from a cultivated diploid cotton, while 38 were on the Dt subgenome from an ancestor that does not produce spinnable fibers. Of the eight common QTLs (12%) detected in more than two environments, two were for fiber quality traits including one for fiber strength and one for uniformity, and six for yield and its components including three for lint yield, one for seedcotton yield, one for lint percentage and one for boll weight. QTL clusters for the same traits or different traits were also identified. This research represents one of the first reports using a permanent advanced backcross inbred population of an interspecific hybrid population to identify QTLs for fiber quality and yield traits in cotton across diverse environments. It provides useful information for transferring desirable genes from G. barbadense to G. hirsutum using MAS.

Genetic relationship between grain chalkiness, protein content, and paste viscosity properties in a backcross inbred population of rice

A backcross inbred line population derived from a cross between Koshihikari and Kasalath was used to dissect the genetic relationship among chalkiness, protein content, and paste viscosity properties in rice in three environments. A total of 11 traits (or parameters) were analyzed, including percentage of grains with chalkiness (PGWC), protein content (PC) and protein index (PI), and eight parameters from the viscosity profile. PGWC, PC and PI were significantly correlated with the paste viscosity parameters. We identified 39 QTLs in three environments; ten QTL clusters emerged. Eight QTLs were consistently detected across the three environments and further confirmed using a set of chromosome segment substitution lines (CSSLs) where Kasalath was used as the donor parent and Koshihikari as the recurrent parent. One and two major clusters on chromosome 6 corresponded to the Wx and Alk loci, respectively. The former was responsible for PGWC and most of the viscosity parameters, and the latter for PI and some viscosity parameters. Particularly, QTL qPI-6.1 was linked with both the Wx and Alk loci. The co-locations of QTLs for PGWC and viscosity parameters and the linkage of qPI-6.1 and qBDV-6 at the Wx locus could be largely responsible for the phenotypic correlations between these traits.

Mapping quantitative trait loci for cottonseed oil, protein and gossypol content in a Gossypium hirsutum × Gossypium barbadense backcross inbred line population

Cotton is one of the most important oil-producing crops and the cottonseed meal provides important protein nutrients as animal feed. However, information on the genetic basis of cottonseed oil and protein contents is lacking. A backcross inbred line (BIL) population from a cross between Gossypium hirsutum as the recurrent parent and G. barbadense was used to identify quantitative trait loci (QTLs) for cottonseed oil, protein, and gossypol contents. The BIL population of 146 lines together with the two parental lines was tested in the same location for three years in China. Based on a genetic map of 392 SSR markers and a total genetic distance of 2,895.2 cM, 17 QTLs on 12 chromosomes for oil content, 22 QTLs on 12 chromosomes for protein content and three QTLs on two chromosomes for gossypol content were detected. Seed oil content was significantly and negatively correlated with seed protein content, which can be explained by eight QTLs for both oil and protein contents co-localized in the same regions but with opposite additive effects. This research represents the first report using a permanent advanced backcross inbred population of an interspecific hybrid population to identify QTLs for seed quality traits in cotton in three environments.

Identification of QTL associated with resistance to bacterial spot race T4 in tomato

Bacterial spot of tomato (Solanum lycopersicum L.), caused by several Xanthomonas sp., is a serious but difficult disease to control by chemical means. Development of resistance has been hindered by emergence of races virulent to tomato, by the quantitative inheritance of resistance, and by a low correlation between seedling assays and resistance in the field. Resistance to multiple races, including race T4, has been described in the S. lycopersicum var. cerasiformae accession PI 114490. We used molecular markers to identify associations with quantitative trait loci (QTL) in an elite inbred backcross (IBC) population derived from OH 9242, PI 114490 and Fla. 7600, a breeding line with tomato accession Hawaii 7998 (H7998) in its pedigree. Race T4 resistance has also been described in the advanced breeding lines Fla. 8233, Fla. 8517, and Fla. 8326, and a selective genotyping approach was used to identify introgressions associated with resistance in segregating progeny derived from crosses with these lines. In the IBC population, loci on chromosomes 11 and 3, respectively, explained as much as 29.4 and 4.8% of resistance variation. Both these loci were also confirmed by selective genotyping: PI 114490 and H7998 alleles on chromosome 11 each provided resistance. The PI 114490 allele on chromosome 3 was confirmed in the Fla. 8517 population, and an allele of undetermined descent was confirmed at this locus in the Fla. 8326 population. A chromosome 12 allele was associated with susceptibility in the Fla. 8517 population. Additional loci contributing minor effects were also implicated in the IBC population or by selective genotyping. Selection for the major QTL in a marker-directed phenotyping approach should significantly improve the efficiency of breeding for resistance to bacterial spot race T4, although as yet undetected QTL would be necessary to carry out strict marker assisted selection.

Characterization of Hypersensitive Resistance to Bacterial Spot Race T3 (Xanthomonas perforans) from Tomato Accession PI 128216

Bacterial spot of tomato is caused by four species of Xanthomonas. The accession PI 128216 (Solanum pimpinellifolium) displays a hypersensitive reaction (HR) to race T3 strains (predominantely Xanthomonas perforans). We developed an inbred backcross (IBC) population (BC(2)S(5), 178 families) derived from PI 128216 and OH88119 (S. lycopersicum) as the susceptible recurrent parent for simultaneous introgression and genetic analysis of the HR response. These IBC families were evaluated in the greenhouse for HR to race T3 strain Xcv761. The IBC population was genotyped with molecular markers distributed throughout the genome in order to identify candidate loci conferring resistance. We treated the IBC population as a hypothesis forming generation to guide validation in subsequent crosses. Nonparametric analysis identified an association between HR and markers clustered on chromosome 11 (P < 0.05 to 0.0001) and chromosome 6 (0.04 > P > 0.002). Further analysis of the IBC population suggested that markers on chromosome 6 and 11 failed to assort independently, a phenomenon known as gametic phase disequilibrium. Therefore, to validate marker-trait linkages, resistant IBC plants were crossed with OH88119 and BC(3)F(2) progeny were evaluated for HR in the greenhouse. In these subsequent populations, the HR response was associated with the chromosome 11 markers (P < 0.0002) but not with the markers on chromosome 6 (P > 0.25). Independent F(2) families were developed by crossing resistant IBC lines to OH8245, OH88119, and OH7530. These populations were genotyped, organized into classes based on chromosome 11 markers, and evaluated for resistance in the field. The PI 128216 locus on chromosome 11 provided resistance that was dependent on gene dosage and genetic background. These results define a single locus, Rx-4, from PI 128216, which provides resistance to bacterial spot race T3, has additive gene action, and is located on chromosome 11.

Marker‐Facilitated Selection for a Major QTL Associated with Root Rot Resistance in Snap Bean (Phaseolus vulgaris L.)

The use of molecular markers associated with quantitative trait loci (QTL) can improve the efficiency of breeding programs. In previous research, randomly amplified polymorphic DNA marker alleles AD9.950+ derived from the root rot resistant snap bean (Phaseolus vulgaris L.) cultivar Puebla 152 and S18.1500− derived from the susceptible cultivar Eagle were linked in repulsion phase and mapped to the same locus. The alleles were associated with a major QTL that explained 25 and 49% of the variation for the root rot complex for plant vigor and plant biomass, respectively. The objective of the current study was to estimate the average effect of allelic substitution in BC1F3 families that were indirectly selected for root rot resistance or susceptibility based on the AD9.950 and S18.1500 marker phenotypes. Four BC1F3 inbred backcross populations were developed by crossing two susceptible snap bean cultivars (Hercules and Nicelo) with two root rot resistant donor inbred lines. When evaluated in a field with high levels of root rot inocula, families carrying the AD9.950+/S18.1500− marker alleles had a mean plant vigor of 3.95 ± 0.96 and mean plant biomass of 25.09 ± 0.89 g plant−1 compared with 7.01 ± 0.96 and 7.05 ± 0.90, respectively, in families that lacked these alleles. Realized gains in plant biomass and plant vigor validate the effectiveness of substituting the AD9.950+ and the S18.1500− marker alleles to introgress root rot resistance into susceptible genetic backgrounds.

Validation of RAPD Markers for White Mold Resistance in Two Snap Bean Populations Based on Field and Greenhouse Evaluations

White mold [Sclerotinia sclerotiorum (Lib.) de Bary] is a fungal disease that can reduce yield of beans (Phaseolus vulgaris L.). A recombinant inbred line population and an independent inbred backcross population were developed that share a common white mold resistant donor parent, G122. Both populations were evaluated for physiological resistance in the greenhouse using the oxalic acid test and a modified straw test (ST). The populations were also field evaluated for disease incidence (DI) and disease severity (DS). The heritabilities for physiological resistance based on greenhouse tests were higher than those based on field evaluations in both populations. Low rank correlations, ranging from r = 0.17 to r = 0.44, were observed between greenhouse and field‐based evaluations over years and populations. Of 10 quantitative trait loci previously identified in independent dry bean populations for field resistance based on either DI or DS and the ST, only three markers, OJ09.950, Phs, and OC07.850, were associated with both the field (DI or DS) and the ST in the G122 × Astrel population. The results suggest that direct selection in the greenhouse based on the modified ST for physiological resistance, though higher in heritability, will result in a negligible correlated response for improved field performance for white mold resistance in snap bean populations where architectural traits and avoidance mechanisms may be more important than physiological resistance.

Identification and Confirmation of Quantitative Trait Loci for Root Rot Resistance in Snap Bean

Root rot, caused by several pathogens including Pythium ultimum Trow and Aphanomyces euteiches Drechs f. sp. phaseoli W.F. Pfender and D.J. Hagedorn, is an important disease complex of snap bean (Phaseolus vulgaris L.). The objectives of this study were to identify, map, and validate markers associated with root rot resistance in three snap bean populations. An ‘Eagle’ × ‘Puebla 152’ recombinant inbred line (RIL) population was evaluated for root rot by plant stand percentage, plant vigor, and plant biomass. Field data were combined with a random amplified polymorphic DNA (RAPD) map to identify quantitative trait loci (QTL) associated with resistance using composite interval mapping. In addition, two inbred backcross (IBC) populations (EEP and EPH) derived from a cross (Eagle × Puebla 152) to Eagle and ‘Hystyle’ respectively were evaluated. Five regions from linkage groups B6, B3, and B7 of the P. vulgaris core map were associated with QTL for root rot resistance. High levels of resistance were also observed in several lines of the IBC populations. A major QTL for root rot resistance was associated with the tightly linked AD9.950 and S18.1500 RAPD marker alleles from linkage group B6 in the RIL population and confirmed explaining 25 to 49% of the variability for plant vigor and biomass in the IBC populations. The exploitation of the linkage disequilibrium between the AD9.950 and S18.1500 RAPD markers derived from Puebla 152 and Eagle can facilitate the development of root rot resistant cultivars.

Quantitative trait loci controlling flowering time and related traits in a Solanum lycopersicum × S. pimpinellifolium cross

Flowering time is an important factor determining early yield in tomato. However, the quantitative trait loci (QTLs) controlling flowering time and their relation to other QTLs for morphological and physiological traits have not been well studied. The aim of this study was to map the chromosomal regions controlling days to flowering (DTF) concurrently with other traits, such as the number of leaves preceding the first inflorescence (LN), length of the largest leaf (LL), number of lateral shoots (LS), fresh weight (FRW) and plant height (PH). This was undertaken using an inbred backcross population derived from a cross between the commercial cultivar Solanum lycopersicum cv. ‘M570018’ and its close wild relative S. pimpinellifolium (PI124039). S. pimpinellifolium flowers earlier than the cultivated tomato. Plants were grown in spring and summer. Composite interval mapping detected 16 QTLs for the six traits evaluated. These QTLs explained 10–42% of the individual phenotypic variation. QTLs detected in spring generally did not differ from those detected in summer. In chromosome 1, the DTF QTL was co-located with the QTLs for LL, LS and FRW, while in chromosome 3 it was co-located with the QTLs for LN, FRW (summer) and PH. One DTF QTL that was detected in chromosome 3 and conferred by the S. pimpinellifolium allele hastens flowering. The co-location of the DTF QTL with the LN QTL suggested that the DTF QTL in chromosome 3 controls the period from the vegetative to reproductive phase. Co-locations of DTF QTLs with the other traits might be pleiotropic effects of a single gene or cluster of genes via physiological relationships among traits because they were found to be highly significantly correlated.

Identification of QTLs controlling rice drought tolerance at seedling stage in hydroponic culture

‘Drought avoidance’ and ‘drought tolerance’ are two mechanisms by which plants adapt under water stress. These mechanisms are difficult to evaluate separately in field experiments. Using hydroponic culture, we studied the genetic control of drought tolerance in rice (Oryza sativa L.) without the effect of drought avoidance. A backcross inbred population of ‘Akihikari’ (lowland cultivar) × ‘IRAT109’ (upland cultivar) with 106 lines was cultured with (stressed condition) and without (non-stressed condition) polyethylene glycol (PEG) at seedling stage. The relative growth rate (RGR), specific water use (SWU), and water use efficiency (WUE) showed significant genotype × environment interactions with or without PEG, indicating that each line responded differently to water stress. A quantitative trait locus (QTL) analysis revealed that these interactions were QTL specific. A total of three QTLs on chromosomes 2, 4, and 7 were detected for RGR. The QTL on chromosome 7 had a constant effect across environments, while the QTL on chromosome 4 had an effect only under non-stressed condition and that on chromosome 2 only under stressed condition. The stress-specific QTL on chromosome 2 was not co-located with any QTLs for root system depth previously reported from the same mapping population. However, this QTL was co-located with a stress-specific QTL for SWU, suggesting that the control of transpiration was relevant to dry matter production under drought. We concluded that PEG-treated hydroponic culture is very effective for use in genetic analyses of drought tolerance at seedling stage.

Quantitative Trait Loci Associated with Bacterial Brown Spot in Phaseolus vulgaris L.

Bacterial brown spot (BBS) is caused by Pseudomonas syringae pv. syringae, an epiphytic, ice nucleation active bacterium and a pathogen of many crop species. In snap bean (Phaseolus vulgaris L.), BBS reduces crop value due to blemishes on the pods. A recombinant inbred line population (EP‐RIL) and an inbred backcross population (EEP‐IBC) developed from crosses between a BBS‐resistant landrace, Puebla 152, and a susceptible cultivar, Eagle, were tested for ice nucleation and number of BBS lesions. The rank correlation between leaf ice nucleation and number of BBS lesions was 0.65. Regions located on linkage groups B1, B3, B6, and B11 were associated with quantitative trait loci (QTL) for both resistance traits in the EP‐RIL by composite interval mapping. Random amplified polymorphic DNA (RAPD) marker P1.1500 located on linkage group B1, and AN6.1600 located linkage group B6, were confirmed in the EEP‐IBC population. These regions explained 13 and 19% of the variation for BBS in the EP‐RIL population. The region from linkage group B3 was not confirmed in the EEP‐IBC population, but was significantly associated with BBS resistance in an independent population in a previous study. The results indicate that indirect selection for RAPD markers associated with QTL can be effective in introgressing BBS resistance.

Tomato Bacterial Spot Resistance Derived from PI 114490; Inheritance of Resistance to Race T2 and Relationship across Three Pathogen Races

Crosses were made between tomato (Lycopersicon esculentum Mill.) inbreds susceptible to races T2 and T3 of bacterial spot (Xanthomonas vesicatoria and Xanthomonas campestris pv. vesicatoria, respectively) and accession PI 114490 with resistance to races T1, T2, and T3. Resistance to race T2 was analyzed using the parents, F1, and F2 generations from one of the crosses. The F1 was intermediate between the parents for disease severity suggesting additive gene action. The segregation of F2 progeny fit a two-locus model (χ2 = 0.96, P = 0.9-0.5) where four resistance alleles are required for a high resistance level, two or three resistance alleles provide intermediate resistance, and zero or one resistance allele results in susceptibility. The narrow sense heritability of resistance to T2 strains was estimated to be 0.37 ± 0.1 based on F2 to F3 parent-offspring regression. A second cross was developed into an inbred backcross (IBC) population to facilitate multilocation replicated testing with multiple races. Segregation for T2 resistance in the inbred backcross population also suggested control was by two loci, lending support to the two-locus model hypothesized based on the F2 segregation. To determine if the same loci conferred resistance to the other races, selections for race T2 resistance were made in the F2 and F3 generations and for race T3 resistance in the F2 through F4 generations. Six T3 selections (F5), 13 T2 selections (F4's that diverged from seven F2 selections), and control lines were then evaluated for disease severity to races T1, T2, and T3 over two seasons. Linear correlations were used to estimate the efficiency of selecting for resistance to multiple races based on a disease nursery inoculated with a single race. Race T1 and race T2 disease severities were correlated (r ≥ 0.80, P&lt; 0.001) within and between years while neither was correlated to race T3 either year. These results suggest that selecting for race T2 resistance in progeny derived from crosses to PI 114490 would be an effective strategy to obtain resistance to both race T1 and T2 in the populations tested. In contrast, selection for race T3 or T2 will be less likely to result in lines with resistance to the other race. PI 114490 had less resistance to T3 than to T2 or T1. Independent segregation of T2 and T3 resistance from the IBC population derived from PI 114490 suggests that T3 resistance is not controlled by the same genes as T2 resistance, supporting the linear correlation data.