Mapping QTLs in breeding for drought tolerance in maize (Zea mays L.)

Summary Grain yield in the maize (Zea mays L) plant is sensitive to drought in the period three weeks either side of flowering. Maize is well-adapted to the use of restriction fragment length polymorphisms (RFLPs) to identify a tight linkage between gene(s) controlling the quantitative trait and a molecular marker. We have determined the chromosomal locations of quantitative trait loci (QTLs) affecting grain yield under drought, anthesis-silking interval, and number of ears per plant. The F₃ families derived from the cross SD34(tolerant) × SD35 (intolerant) were evaluated for these traits in a two replicated experiment. RFLP analysis of the maize genome included non-radioactive DNA-DNA hybridization detection using chemiluminescence. To identify QTLs underlying tolerance to drought, the mean phenotypic performances of F₃ families were compared based on genotypic classification at each of 70 RFLP marker loci. The genetic linkage map assembled from these markers was in good agreement with previously published maps. The phenotypic correlations between yield and other traits were highly significant. In the combined analyses, genomic regions significantly affecting tolerance to drought were found on chromosomes 1,3,5,6, and 8. For yield, a total of 50% of the phenotypic variance could be explained by five putative QTLs. Different types of gene action were found for the putative QTLs for the three traits.     

基于RIL群体鉴定棉花抗黄萎病相关QTLs

【目的】鉴定出能够稳定表达的棉花抗黄萎病相关数量性状位点(Quantitative trait loci,QTLs)。【方法】以抗落叶型黄萎病棉花品种常抗棉和感黄萎病品种TM-1为亲本配制的111个重组自交系家系为作图群体,筛选出多态性简单序列重复(Simple sequence repeat,SSR)标记,并用于构建遗传图谱。用完备复合区间作图法对该群体在安阳大田、新疆重病地及病圃等多个环境下的黄萎病病情指数进行QTLs检测。【结果】构建了1张含有12个连锁群、40个标记、总长212.5 cM(厘摩)的遗传图谱。获得了6个与抗黄萎病基因相关的QTLs,对数优势比(Logarithm of the odd score,LOD)分布在2.51～5.55,贡献率最大为20.34%,最小为6.93%。其中,qVR-D05-1能够在安阳大田2015年7月15日和新疆南疆重病地2016年7月9日2个环境中检测到,贡献率分别为12.96%和20.34%。【结论】本研究得到的qVR-D05-1能够为定位出稳定的棉花抗黄萎病相关QTLs提供参考。     

Mapping QTLs for Witches' Broom (Crinipellis Perniciosa) Resistance in Cacao (Theobroma Cacao L.)

Molecular markers (RAPD, AFLP and microsatellites) were used to generate a linkage map and to identify QTLs associated to witches' broom (Crinipellis perniciosa) resistance in cacao (Theobroma cacao), using 82 individuals of an F₂ population derived from the clones ICS-1 (susceptible) and Scavina-6 (resistant). Fifteen evaluations of the number of brooms have been carried out in six years (1997–2002). In order to increase the precision and accuracy in the measures of resistance, each F₂ plant was cloned in three replications in a randomized block design with single-tree plots and evaluated over 2 years. Three hundred and forty-two markers were obtained, being 33 microsatellites, 77 AFLPs and 232 RAPDs. The distribution of the number of brooms in the F₂ population was skewed to resistance, suggesting the involvement of major genes controlling resistance and the repeatability estimated for resistance was 44%. A strong putative QTL was detected as being related to witches' broom resistance. Associated to this QTL, the microsatellite mTcCIR35 explained 35.5% of the phenotypic variation in resistance. This marker is being used for marker-assisted selection in Scavina-6 progenies, including those selected in private plantations, as an auxiliary tool to the phenotypic selection.     

Mapping and validation of QTLs for resistance to an Indian isolate of Ascochyta blight pathogen in chickpea

Ascochyta blight (AB) caused by Ascochyta rabiei, is globally the most important foliar disease that limits the productivity of chickpea (Cicer arietinum L.). An intraspecific linkage map of cultivated chickpea was constructed using an F₂ population derived from a cross between an AB susceptible parent ICC 4991 (Pb 7) and an AB resistant parent ICCV 04516. The resultant map consisted of 82 simple sequence repeat (SSR) markers and 2 expressed sequence tag (EST) markers covering 10 linkage groups, spanning a distance of 724.4 cM with an average marker density of 1 marker per 8.6 cM. Three quantitative trait loci (QTLs) were identified that contributed to resistance to an Indian isolate of AB, based on the seedling and adult plant reaction. QTL1 was mapped to LG3 linked to marker TR58 and explained 18.6% of the phenotypic variance (R ²) for AB resistance at the adult plant stage. QTL2 and QTL3 were both mapped to LG4 close to four SSR markers and accounted for 7.7% and 9.3%, respectively, of the total phenotypic variance for AB resistance at seedling stage. The SSR markers which flanked the AB QTLs were validated in a half-sib population derived from the same resistant parent ICCV 04516. Markers TA146 and TR20, linked to QTL2 were shown to be significantly associated with AB resistance at the seedling stage in this half-sib population. The markers linked to these QTLs can be utilized in marker-assisted breeding for AB resistance in chickpea.     

Genetic control of seedling tolerance to aluminum toxicity in rice

An uncomplete diallel analysis was conducted for 56 F1 progenies derived from 8 male × 7 female parents with differential Al tolerance based on root tolerance index (RTI) in a solution culture with Al concentration of 1 mM Al. Remarkable variation in RTI among the parents was observed after 6 weeks in culture. Significant (P < 0.001) general combine ability (GCA) variance for both male and female parents and specific combine ability (SCA) variance were observed. The variance of GCA was much higher than that of SCA, indicating greater additive expression of the tolerant trait. Higher narrow-sense heritability (48%) was detected, indicating the possibility of a genetic gain in selection for Al tolerance based on RTI. The tolerant performance of F1 progenies appeared to be influenced by the susceptible genotype. suggesting the inconsistent dominance effect. The possible mechanisms of the apparent inconsistent dominance was discussed in terms of the genetic background in wheat. Two restore lines, Pedel and 02428, and one sterile variety, XieqinzaoA, were found to be high in the GCA effect and SCA variance in this case. These genotypes may be useful in development of hybrid rice production on acid soils. This revised version was published online in July 2006 with corrections to the Cover Date.     

Identification of QTLs for BYDV tolerance in bread wheat

We searched for QTLs involved in tolerance to barley yellow dwarf (BYD), a serious viral disease of small grain cereals in two wheat populations, Opata × Synthetic (ITMI)and Frontana × INIA66 (F × I), for which marker data had previously been generated. The populations were evaluated in replicated field trials under artificial inoculation with a BYDV-PAV-Mex isolate and under disease-free conditions. Disease symptoms (yellowing, dwarfism and biomass reduction) were visually recorded and agronomic traits (number of tillers,height, biomass, yield and thousand-kernel weight) were measured on five plants per plot. Phenotypic data on all evaluated traits showed normal distribution with high correlation between visual estimates and measured values. Heritabilities were mostly moderate to high in the 114 lines of the ITMI population, and from low to moderate in the 117 lines of the F × I population. QTL analyses were based on genetic maps containing 443 loci for the ITMI population and 317 loci for the F × I population. Using composite interval mapping, 22 QTLs in the ITMI population and seven in the F × I population were detected, explaining9.8–43.3% of total phenotypic variation (σ² _P)per agronomic trait in the first population, and 4.1–13.7% in the second. Individual QTLs explained less than 15.8%of σ² _P. In the F × I population a minor QTL explaining 7% of σ² _P for yellowing was detected on the short arm of 7D, linked to leaf tip necrosis, a morphological marker for linked genes Bdv1, Yr18 andLr34. A QTL consistently detected for several traits on 2D in the ITMI population and on the short arm of group 6 chromosome(6S) in F × I explained 10–15% of σ² _P. The large number of QTLs having mostly small effects and the continuous distribution of all evaluated traits confirmed the polygenic nature and complexity of BYD tolerance in wheat. This revised version was published online in August 2006 with corrections to the Cover Date.     

Molecular mapping of an aluminum tolerance locus on chromosome 4D of Chinese Spring wheat

Summary The tolerance of aluminum (Al) of disomic substitution lines having the chromosomes of the D genome of Triticum aestivum L. cv. Chinese Spring individually substituted for their homoeologues in T. turgidum L. cv. Langdon was investigated by the hematoxylin method. The disomic substitution lines involving chromosome 4D were more Al tolerant than Langdon. The tolerance was found to be controlled by a single dominant gene, designated Alt2, that is in the proximal region of the long arm of chromosome 4D. The locus was mapped relative to molecular markers utilizing a population of recombinant chromosomes from homoeologous recombination between Chinese Spring chromosome 4D and T. turgidum chromosome 4B. Comparison of the location of Alt2 in this map with a consensus map of chromosomes 4B and 4D based on homologous recombination indicated that Alt2 is in a vicinity of a 4 cM interval delineated by markers Xpsr914 and Xpsr1051. The Alt2 locus is distal to marker Xpsr39 and proximal to XksuC2. The Altw locus is also proximal to the Knal locus on chromosome 4D that controls K⁺/Na⁺ selectivity and salt tolerance. In two lines, Alt 2 and Knal were transferred on a single 4D segment into the long arm of T. turgidum chromosome 4B.     

Evaluation of maize plant introductions for cold tolerance

Summary We evaluated cold-tolerance responses of 144 plant introductions (PI) of maize (Zea mays L.), attempting to include in our sample at least one PI adapted to each of the countries or ecological zones respresented in the maize germplasm collection at the North Central Regional Plant Introduction Station at Ames, Iowa, USA. Plant introductions were grown for 42 days in plastic boxes (26 cm long × 19 cm wide × 10 cm deep) in a growth chamber maintained at 10±1 °C. Cold-tolerance responses of each PI were evaluated by three traits: 1) percentage emergence (recorded 30 days after planting), 2) emergence index, an estimate of rate of emergence, and 3) seedling dry weight (sampled 42 days after planting). Estimates of variances and heritabilities for these three traits were large, suggesting that genotypic variation for cold tolerance in the maize germplasm collection would be sufficient to permit selection advance. Furthermore, genotypic correlations among the three traits were high: therefore, improvement by index selection should be possible. Correlations between the cold-tolerance traits and days from planting to 50% silk emergence (an estimate of maturity obtained at Ames. Iowa, USA) were low. Days from planting to 50% silking emergence for the 25 most cold-tolerant PI's ranged from 46 for PI 214279 from Canada to 106 for PI 331440 from Ethiopia. It should be possible, therefore, to develop cold-tolerant genotypes adapted to all latitudes.Contribution from the Iowa Agriculture and Home Economics Experiment Station, Ames, Iowa 50011, and the Agricultural Research Service, U.S. Department of Agriculture, cooperating. Journal Paper No. J-8780 of the Iowa Agriculture and Home Economics Experiment Station, Ames, Iowa. Projects No. 1018 and 2152     

Mass selection for improved cold and density tolerance of two maize populations

Summary Data of planting and plant density are two cultural practices influencing grain yield of maize (Zea mays L.). Our study was designed to evaluate the usefulness of a mass selection scheme to improve cold and density tolerance of the BS2 and BS3 maize populations. Populations were planted at an early planting date and a high plant density, and three cycles of mass selection for well-filled ears on erect plants were conducted at earch of three Corn Belt locations (i.e., Waseca, MN; Ames, IA; Portageville, MO).Results showed that selection improved cold tolerance traits of BS3, but not of BS2. Mass selection did not increase density tolerance of either population at any location. Selection did not improve response to planting dates, although the early planting date did improve agronomic performance and grain yield of all entries. We concluded that mass selection at high plant densities and early planting dates at diverse geographical locations did not produce cycles adapted to specific environmental conditions.     

Genetic control of aluminum tolerance in mutant lines of the wheat cultivar Anahuac

The behavior of 17 gamma irradiation mutant lines derived from the aluminum sensitive wheat cultivar `Anahuac' was compared with two sensitive and three tolerant cultivars in nutritent solutions containing seven Al<sup>3+</sup> concentrations (0; 0.5; 1; 2; 4; 6 and10 mg/liter), at a temperature of 25 <sup>°</sup>C and 4.0 pH. Tolerance was measured by the continued growth of the primary roots in a solution without aluminum after 48 hours in a solution containing a known concentration of aluminum. 14 mutant lines were as tolerant to the presence of 10 mg/liter of Al<sup>3+</sup> in the treatment solutions as were the tolerant `BH-1146', `IAC-60' and `IAC-24' cultivars. Two mutant lines were tolerant and one was sensitive to the presence of 1 mg/liter of Al³⁺, while the cultivars `Siete Cerros' and `Anahuac' were sensitive to 1 and 0.5 mg/liter Al³⁺ in the solutions, respectively. F₂ seedlings, obtained from cross among one sensitive and twelve tolerant mutant lines to the sensitive cultivars (`Siete Cerros' or `Anahuac') and the tolerant cultivars (`BH-1146' or `IAC-24') were assessed for tolerance to 2 mg/liter Al³⁺ in nutritient solutions. The twelve tolerant mutant lines and the tolerant `IAC-60' and `IAC-24' cultivars differed from the sensitive `Siete Cerros' or `Anahuac' cultivars by one pair of dominant alleles. The results indicated that tolerance in the induced mutants was due to a single pair of dominant alleles and that these alleles expressed the same tolerance as `BH-1146' and `IAC-24' cultivars. This revised version was published online in July 2006 with corrections to the Cover Date.     

The effect of single D-genome chromosomes on aluminum tolerance of triticale

Aluminum tolerance of two sets of hexaploidtriticale (×Triticosecale Wittmack)lines with disomic substitutions of theD-genome chromosomes from Triticumaestivum L. was analyzed by themodified-pulse method. Of the 20substitution lines in winter triticalePresto, and 18 lines of spring triticaleRhino, six and nine lines, respectively,showed improved tolerance relative to thatobserved in the control lines. The D-genomechromosomes in substitutions 1D(1B),3D(3A), 3D(3B), 4D(4A), 4D(4B) and 6D(6B)significantly (p<0.01) improved Altolerance in both sets of lines. Highpercentages of tolerant plants were alsoobserved in 2D(2B) and 5D(5A) substitutionsin Presto and in 2D(2A), 2D(2B), 5D(5B),6D(6A) and 7D(7A) substitution lines ofRhino. In no instance, the removal ofindividual rye chromosomes, bysubstitutions, improved Al tolerance of therecipient line. Moreover, the presence of acomplete rye genome, and especially ofchromosome 3R, was necessary for triticale'stolerance to aluminum. The results alsoindicated some effects of allelic variationpresent on both rye and wheat chromosomes,and a possibility of interactions ofvarious factors.     

Mapping genes for deep-seeding tolerance in barley

Deep-seeding tolerance, the emergence of seedlings from deep seeded conditions, is involved in stand establishment in semi-arid regions, where the soil surface is too dry for seed germination. Genes determining deep-seeding tolerance in barley were mapped using two doubled haploid populations derived from the following crosses: Harrington × TR306 (H/T)and Step toe × Morex (S/M). Significant quantitative trait loci (QTLs) for deep-seeding tolerance were found in each population. Two QTL sex plained 40% of the phenotypic variation in the H/T population and one QTL (S/M) 8% of the total phenotypic variance. Multiple QTLs accounting for coleoptile length and first internode length were detected in both populations. In the H/T population, there were coincident QTLs for deep-seeding tolerance, coleoptile length and first internode length on the long arm of chromosome 5H. These QTLs correspond with previously reported QTLs for abscisic acid and gibberellic acid response. QTL coincidence may be due to the pleiotropic effects of alleles at a single locus. This information may be useful for breeding programs manipulating morphological and physiological traits in order to develop varieties for semi-arid regions. This revised version was published online in August 2006 with corrections to the Cover Date.     

Participatory maize breeding for low nitrogen tolerance

The local maize variety Sol da Manhã has a broad genetic background. It was identified in 1985 in a participatory evaluation trial as being suitable for cultivation under low soil fertility conditions in Sol da Manhã, situated in Seropédica, State of Rio de Janeiro, Brazil. The variety was then improved for 6 selection cycles by the formal breeding sector at the experimental station of Embrapa Agrobiologia. There were three cycles of mass selection, one selection cycle between and within half-sib families, one selection cycle within full-sib families, and one selection cycle between and within S₁ families. Thereafter, the variety was improved in collaboration with the informal sector, viz. a group of farmers of the agricultural community of Sol da Manhã for 6 cycles of mass selection. The variety was evaluated in 1994 in field trials for grain yield and nitrogen use efficiency. Sol da Manhã can be characterised as efficient in nitrogen use, under both favourable and unfavourable growing conditions.     

Inheritance of root regrowth as an indicator of apparent aluminum tolerance in triticale

Aluminum (Al) toxicity is a predominant growth-limiting factor in acid soils. Better understanding of the genetic mechanisms by which plants tolerate toxic Al expedites the development of tolerant plant genotypes. The genetic behavior of apparent Al tolerance in two triticale crosses as measured by root regrowth of seedlings at a level of 10 μg · ^g−1 Al stress in nutrient solutions was analyzed by following a bi-parental (BIP) mating design. The validity of the additive-dominance genetic model was tested with relevant gene effects estimated. The continuous variation of regrown root length showed that apparent Al tolerance was a metrical character in nature. Both the additive and dominance effects were responsible while the additive effects played a major role in the expression of Al tolerance. Non-allelic interaction (or epistasis) was indicated from the inadequacy of the model and different types of epistatic gene effects were detected in the two crosses. These results suggest that Al tolerance was of polygenic system rather than simply inherited. One to three pairs of genes were involved in apparent Al tolerance for the parental difference. The moderately high value of estimates of heritability together with the estimates of genetic advance (GA) could be used in planning a selective breeding program aimed at greater Al tolerance. This revised version was published online in July 2006 with corrections to the Cover Date.     

Variation among Andean races of maize for cold tolerance during heterotrophic and early autotrophic growth

Cold in the initial growth stages is an important stressfactor for maize grown in regions with a temperate climate,particularly in case of early sowing. Sources of tolerancehave been identified in adapted genotypes, but promisinggenes for cold tolerance should also be found in materialdeveloped under the lower-temperature margins of the cropdistribution. This research was conducted in order to testAndean maize accessions for cold tolerance expressed duringboth the heterotrophic and early autotrophic growth stages.Experiments were conducted in controlled environments tostudy cold tolerance traits (germination %, germinationindex and plant growth rate) at continuous 10^°C (heterotrophic growth) and at varying 10–16^°C (autotrophic growth). An experiment was also performed inthe field with early sowing (both heterotrophic and autotrophic growth). In each experiment, a control trialwas conducted in more favourable conditions (i.e. continuous25^°C in a controlled environment or late planting inthe field) so that cold tolerance traits could also beexamined as the ratio between the stress and the controltrial. None of the accessions was superior for all coldtolerance traits. However, several Andean maize accessionsoutperformed the US Corn-belt hybrid checks for one or moretraits, both in heterotrophic and autotrophic growth. Overall, BOZM 855, PMS 636, Poblacion D, Poblacion E andBOZM 696 were the best accessions, suggesting that they canbe a promising source of genes for improving cold toleranceof adapted maize genotypes.     

利用水稻回交群体定位氯酸钾抗性基因

氯酸钾抗性是区分籼粳分化的指标之一。本研究以珍汕97（ZS97）和日本晴（Nipponbare）所构建的回交群体BC4F2为材料，用2‰浓度的氯酸钾溶液对芽长约5mm的幼芽持续处理24h后，根据其发芽数和具次生根苗数筛选获得6份对氯酸钾抗性的导入系，用BC5F1进一步验证发现其中3份株系存在抗性分离。这3份株系平均含有两个外源导入片段，背景回复率平均为95．4％。结果表明，在水稻第1、6、11、12染色体上存在4个氯酸钾抗性基因。     

Detection of linkage between RFLP markers and genes affecting anthocyanin pigmentation in maize (Zea mays L.)

Summary Linkages between molecular markers and genes involved in the expression of agronomical traits have already been described in all of the major crops. In most cases, the genetic model underlying the Quantitative Traits Loci (QTL) is discussed. Here, Restriction Fragment Length Polymorphisms (RFLPs) and Mapmaker-QTL have been used to pinpoint seven regions of the genome significantly correlated with four pigmentation qualitative traits of maize (Zea mays L.). Two of these, located on chromosomes 2 and 10, explain most of the variation of these traits. The R and B gene loci known to be involved in the regulation of the anthocyanin pathway map to the same regions and we suggest that these loci could be the candidate genes involved in the correlations detected with RFLPs. This type of result is in accordance with the hypothesis of the candidate gene which supposes that, if we have a very high density map of randomly-selected cDNA clones, it should theoretically be possible to associate a cloned genic sequence with a phenotypic trait where correlations are found.     

Detection of QTLs for salt tolerance in Asian barley (Hordeum vulgare L.) by association analysis with SNP markers

Two hundred ninety-six Asian barley (Hordeum vulgare L.) accessions were assessed to detect QTLs underlying salt tolerance by association analysis using a 384 single nucleotide polymorphism (SNP) marker system. The experiment was laid out at the seedling stage in a hydroponic solution under control and 250 mM NaCl solution with three replications of four plants each. Salt tolerance was assessed by leaf injury score (LIS) and salt tolerance indices (STIs) of the number of leaves (NL), shoot length (SL), root length (RL), shoot dry weight (SDW) and root dry weight (RDW). LIS was scored from 1 to 5 according to the severity of necrosis and chlorosis observed on leaves. There was a wide variation in salt tolerance among Asian barley accessions. LIS and STI (SDW) were the most suitable traits for screening salt tolerance. Association was estimated between markers and traits to detect QTLs for LIS and STI (SDW). Seven significant QTLs were located on chromosomes 1H (2 QTLs), 2H (2 QTLs), 3H (1 QTL), 4H (1 QTL) and 5H (1 QTL). Five QTLs were associated with LIS and 2 QTLs with STI (SDW). Two QTLs associated with LIS were newly identified on chromosomes 3H and 4H.     

Molecular mapping of quantitative trait loci (QTLs) controlling aluminium tolerance in bread wheat

Aluminium (Al) toxicity is a major constraint to crop productivity in acidic soils. A quantitative trait locus (QTL) analysis was performed to identify the genetic basis of Al tolerance in the wheat cultivar ‘Chinese Spring’. A nutrient solution culture approach was undertaken with the root tolerance index (RTI) and hematoxylin staining method as parameters to assess the Al tolerance. Using a set of D genome introgression lines, a major Al tolerance QTL was located on chromosome arm 4DL, explaining 31% of the phenotypic variance present in the population. A doubled haploid population was used to map a second major Al tolerance QTL to chromosome arm 3BL. This major QTL (Qalt _CS .ipk-3B) in ‘Chinese Spring’ accounted for 49% of the phenotypic variation. Linkage of this latter QTL to SSR markers opens the possibility to apply marker-assisted selection (MAS) and pyramiding of this new QTL to improve the Al tolerance of wheat cultivars in breeding programmes.