Mapping quantitative trait loci conferring resistance to rice black-streaked virus in maize (Zea mays L.)

Maize rough dwarf disease (MRDD) is one of the most serious virus diseases of maize worldwide, and it causes great reduction of maize production. In China, the pathogen was shown to be rice black-streaked virus (RBSDV). Currently, MRDD has spread broadly and leads to significant loss in China. However, there has been little research devoted to this disease. Our aims were to identify the markers and loci underlying resistance to this virus disease. In this study, segregation populations were constructed from two maize elite lines '90110', which is highly resistant to MRDD and 'Ye478', which is highly susceptible to MRDD. The F(2) and BC(1) populations were used for bulk sergeant analysis (BSA) to identify resistance-related markers. One hundred and twenty F(7:9) RILs were used for quantitative trait loci (QTL) mapping through the experiment of multiple environments over 3 years. Natural occurrence and artificial inoculation were both used and combined to determine the phenotype of plants. Five QTL, qMRD2, qMRD6, qMRD7, qMRD8 and qMRD10 were measured in the experiments. The qMRD8 on chromosome 8 was proved to be one major QTL conferring resistance to RBSDV disease in almost all traits and environments, which explained 12.0-28.9 % of the phenotypic variance for disease severity in this present study.     

Mapping quantitative trait loci associated with southern leaf blight resistance in maize (Zea mays L.)

Southern leaf blight (SLB) caused by the fungus Cochliobolus heterostrophus (Drechs.) Drechs. is a major foliar disease of maize worldwide. Our objectives were to identify quantitative trait loci (QTL) for resistance to SLB and flowering traits in recombinant inbred line (RIL) population derived from the cross of inbred lines LM5 (resistant) and CM140 (susceptible). A set of 207 RILs were phenotyped for resistance to SLB at three time intervals for two consecutive years. Four putative QTL for SLB resistance were detected on chromosomes 3, 8 and 9 that accounted for 54% of the total phenotypic variation. Days to silking and anthesis–silking interval (ASI) QTL were located on chromosomes 6, 7 and 9. A comparison of the obtained results with the published SLB resistance QTL studies suggested that the detected bins 9.03/02 and 8.03/8.02 are the hot spots for SLB resistance whereas novel QTL were identified in bins 3.08 and 8.01/8.04. The linked markers are being utilized for marker‐assisted mobilization of QTL conferring resistance to SLB in elite maize backgrounds. Fine mapping of identified QTL will facilitate identification of candidate genes underlying SLB resistance.     

Mapping quantitative trait loci associated with stem-related traits in maize (Zea mays L.)

Plant Molecular Biology - Mapping QTL for stem-related traits using RIL population with ultra-high density bin map can better dissect pleiotropic QTL controlling stem architecture that can provide...     

Identification of quantitative trait loci for cold-tolerance of photosynthesis in maize (Zea mays L.)

The effects of low growth temperature (15 degrees C) on the photosynthetic apparatus of maize were investigated in a set of 233 recombinant inbred lines by means of chlorophyll fluorescence, gas exchange measurements and analysis of photosynthetic pigments. A quantitative trait loci (QTL) analysis of five traits related to the functioning of the photosynthetic apparatus revealed a total of eight genomic regions that were significantly involved in the expression of the target traits. Four of these QTLs, located on chromosomes 1 (around 146 cM), 2 (around 138 cM), 3 (around 70 cM), and 9 (around 62 cM), were identified across several traits and the phenotypic correlation observed among those traits confirmed at the genetic level. The two QTLs on chromosomes 1 and 9 were also expressed in leaves developed at near-optimal temperature (25 degrees C) whilst the two QTLs on chromosomes 2 and 3 were specific to leaves developed at sub-optimal temperature. A QTL analysis conducted on traits related to the pigment composition of the leaves developed at 15 degrees C detected the QTL on chromosome 3 around 70 cM in 7 of the 11 traits analysed. This QTL accounted for up to 28% of the phenotypic variance of the quantum yield of electron transport at PSII in the fourth leaf after about 3 weeks at a sub-optimal temperature. The results presented here suggest that key gene(s) involved in the development of functional chloroplasts of maize at low temperature should be located on chromosome 3, close to the centromere.     

Mapping quantitative trait loci using naturally occurring genetic variance among commercial inbred lines of maize (Zea mays L.)

Many commercial inbred lines are available in crops. A large amount of genetic variation is preserved among these lines. The genealogical history of the inbred lines is usually well documented. However, quantitative trait loci (QTL) responsible for the genetic variances among the lines are largely unexplored due to lack of statistical methods. In this study, we show that the pedigree information of the lines along with the trait values and marker information can be used to map QTL without the need of further crossing experiments. We develop a Monte Carlo method to estimate locus-specific identity-by-descent (IBD) matrices. These IBD matrices are further incorporated into a mixed-model equation for variance component analysis. QTL variance is estimated and tested at every putative position of the genome. The actual QTL are detected by scanning the entire genome. Applying this new method to a well-documented pedigree of maize (Zea mays L.) that consists of 404 inbred lines, we mapped eight QTL for the maize male flowering trait, growing degree day heat units to pollen shedding (GDUSHD). These detected QTL contributed >80% of the variance observed among the inbred lines. The QTL were then used to evaluate all the inbred lines using the best linear unbiased prediction (BLUP) technique. Superior lines were selected according to the estimated QTL allelic values, a technique called marker-assisted selection (MAS). The MAS procedure implemented via BLUP may be routinely used by breeders to select superior lines and line combinations for development of new cultivars.     

Mapping of quantitative trait loci associated with chilling tolerance in maize (Zea mays L.) seedlings grown under field conditions

The effect of low growth temperature on morpho-physiological traits of maize was investigated by the means of a QTL analysis in a segregating F(2:3) population grown under field conditions in Switzerland. Chlorophyll fluorescence parameters, leaf greenness, leaf area, shoot dry weight, and shoot nitrogen content were investigated at the seedling stage for two years. Maize was sown on two dates in each year; thus, plants sown early were exposed to low temperature, whereas those sown later developed under more favourable conditions. The main QTLs involved in the functioning of the photosynthetic apparatus at low temperature were stable across the cold environments and were also identified under controlled conditions with suboptimal temperature in a previous study. Based on the QTL analysis, relationships between chlorophyll fluorescence parameters and leaf greenness were moderate. This indicates that the extent and functioning of the photosynthetic machinery may be under different genetic control. The functioning of the photosynthetic apparatus in plants developed at low temperature in the field did not noticeably affect biomass accumulation; since there were no co-locations between QTLs for leaf area and shoot dry weight, biomass accumulation did not seem to be carbon-limited at the seedling stage under cool conditions in the field.     

Quantitative trait loci for callus initiation and totipotency in maize (Zea mays L.)

Induction of embryogenic callus in culture is an important step in plant transformation procedures, but response is genotype specific and the genetics of the trait are not well understood. Quantitative trait loci (QTL) were mapped in a set of 126 recombinant inbred lines (RILs) of inbred H99 (high Type I callus response) by inbred Mo17 (low Type I callus response) that were evaluated over two years for Type I callus response. QTL were observed in a total of eleven bins on eight chromosomes, including eight QTL with main effects and three epistatic interactions. Many of the QTL were mapped to the same or bordering chromosomal bins as candidate genes for abscisic acid metabolism, indicating a possible role for the hormone in the induction of embryogenic callus, as has previously been indicated in microspore embryo induction. Further examinations of allelic variability for known candidate genes located near the observed QTL could be useful for expanding the understanding of the genetic basis of induction embryogenic callus. The QTL observed herein could also be used in a marker assisted selection (MAS) program to improve the response of agronomically useful inbreds, but only if the resources required for MAS are lower than those required for phenotypic selection.     

Mapping quantitative trait loci (QTLs) for resistance to Cercospora leaf spot disease (Cercospora beticola Sacc.) in sugar beet (Beta vulgaris L.)

The breeding of sugar beet varieties that combine resistance to Cercospora and high yield under non-diseased conditions is a major challenge to the breeder. The understanding of the quantitative trait loci (QTLs) contributing to Cercospora resistance offers one route to solving this problem. A QTL analysis of Cercospora resistance in sugar beet was carried out using a linkage map based on AFLP and RFLP markers. Two different screening methods for Cercospora resistance (a field test at Copparo, Italy, under natural infection, and a newly-developed leaf disc test) were used to estimate the level of Cercospora resistance; the correlation between scores from the field (at 162 days after sowing) and the leaf disc test was significant. QTL analysis was based on F₂ and F₃ (half-sib family) generations derived from crosses between diploid single plants of 93164P (resistant to Cercospora leaf spot disease) and 95098P (susceptible). Four QTLs associated with Cercospora resistance (based on Lsmean data of the leaf disc test) on chromosomes III, IV, VII and IX were revealed using Composite interval mapping. To produce populations segregating for leaf spot resistance as a single Mendelian factor, we selected for plants heterozygous for only one of the QTLs (on chromosome IV or IX) but homozygous for the others. Received: 1 September 1999 / Accepted 7 October 1999     

Mapping quantitative trait loci (QTLs) for resistance to Gibberella zeae infection in maize

The basic prerequisite for an efficient breeding program to improve levels of resistance to pathogens in plants is the identification of genes controlling the resistance character. If the response to pathogens is under the control of a multilocus system, the utilization of molecular markers becomes essential. Stalk and ear rot caused by Gibberella zeae is a widespread disease of corn: resistance to G. zeae is quantitatively inherited. Our experimental approach to understanding the genetic basis of resistance to Gibberella is to estimate the genetic linkage between available molecular markers and the character, measured as the amount of diseased tissue 40 days after inoculation of a suspension of Fusarium graminearum, the conidial form of G. zeae, into the first stalk internode. Sensitive and resistant parental inbreds were crossed to obtain F₁ and F₂ populations: the analysis of the segregation of 95 RFLP (restriction fragment length polymorphism) clones and 10 RAPD (random amplified polymorphic DNA) markers was performed on a population of 150 F₂ individuals. Analysis of resistance was performed on the F₃ families obtained by selfing the F₂ plants. Quantitative trait loci (QTL) detection was based either on analysis of regression coefficients between family mean value and allele values in the F₂ population, or by means of interval mapping, using MAPMAKER-QTL. A linkage map of maize was obtained, in which four to five genomic regions are shown to carry factors involved in the resistance to G. zeae.     

Quantitative and qualitative trait loci affecting host-plant response to Exserohilum turcicum in maize (Zea mays L.)

Molecular markers at 103 loci were used to identify the location of quantitative sources of resistance to Exserohilum turcicum in 150 F₂₃ lines of a B52/Mo17 maize population. Host-plant response was measured in terms of the average number of lesions per leaf, the average percent leaf tissue diseased (severity), and the average size of lesions. The location of quantitative trait loci were compared with three loci having known qualitative effects, namely Ht1, Ht2 and bx1. Chromosomal regions containing the Ht1 and Ht2 loci showed a small contribution in determining lesion size, even though alleles with dominant, qualitative effects at these loci have never been reported in either inbred parent. Similar effects were not observed for the number of lesions or for disease severity. Likewise, some contribution was observed for chromosomal regions encompassing the bx1 locus in determining lesion size but not the number of lesions or disease severity. Overall the contribution of loci in the vicinity of Ht1, Ht2 and bx1 was small relative to variation attributable to loci with quantitative effects identified in this study. Molecular-marker-facilitated mapping concurred with previous reciprocal translocation mapping studies on the importance of chromosomes 3, 5 and 7, despite the fact that these studies utilized diverse sources of resistant germplasm.Journal Paper No. J-15177 of the Iowa Agriculture and Home Economics Experiment Station, Ames, Iowa. Project No. 3134     

RFLP mapping of quantitative trait loci controlling abscisic acid concentration in leaves of drought-stressed maize (Zea mays L.)

 Abscisic acid (ABA) concentration in leaves of drought-stressed plants is a quantitatively inherited trait. In order to identify quantitative trait loci (QTLs) controlling leaf ABA concentration (L-ABA) in maize, leaf samples were collected from 80 F_3:4 families of the cross Os420 (high L-ABA)×IABO78 (low L-ABA) tested under drought conditions in field trials conducted over 2 years. In each year, leaf samples were collected at stem elongation and near anthesis. The genetic map obtained with 106 restriction fragment length polymorphism (RFLP) loci covered 1370 cM, which represented approximately 85% of the UMC maize map. Sixteen different QTLs with a LOD>2.0 were revealed in at least one sampling. Across samplings, only four QTLs significantly influenced L-ABA, accounting for 66% of the phenotypic variation and 76% of the genetic variation among families. At these QTLs, the alleles which increased L-ABA were contributed by Os420. The two most important QTLs were mapped on chromosome 2 near csu133 and csu109a. The effects associated with the QTL near csu133 were more pronounced near anthesis. The support intervals of the four primary QTLs for L-ABA did not overlap the presumed map position of mutants impaired in ABA biosynthesis. Received: 27 January 1998 / Accepted: 22 April 1998     

Quantitative trait loci analysis of plant height and ear height in maize (Zea mays L.)

Genetic map containing 103 microsatellite loci obtained on 200 F₂ plants derived from the cross R15 × 478 was used for quantitative trait loci (QTL) mapping in maize. QTLs were characterized in a population of 200 F_2:4 lines, derived from selfing the F₂ plants, and were evaluated with two replications in two environments. QTL determinations were made from the mean of these two environments. Plant height (PH) and ear height (EH) were measured. Using composite interval mapping (CIM) method, a total of 14 distinct QTLs were identified: nine for PH and five for EH. Additive, partial dominance, dominance, and overdominance actions existed among all detected QTLs affecting plant height and ear height. The QTLs explained 78.27% of the phenotypic variance of PH and 41.50% of EH. The 14 QTLs displayed mostly dominance or partial dominance gene action and mapped to chromosomes 2, 3, 4, 8, and 9. The text was submitted by the authors in English.     

Detection of quantitative trait loci for seminal root traits in maize (Zea mays L.) seedlings grown under differential phosphorus levels

Suboptimal phosphorus availability is a primary constraint for terrestrial plant growth. Seminal roots play an important role in acquisition of nutrients by plant seedlings. The length and number of seminal roots may be particularly important in acquisition of immobile nutrients such as phosphorus by increasing soil exploration. The objective of this study was to identify quantitative trait loci (QTL) controlling seminal root growth in response to phosphorus stress in maize, and to characterize epistatic interactions among QTL. Seminal root length and number were evaluated in 162 recombinant inbred lines derived from a cross between B73 and Mo17 in seedlings grown in a controlled environment. B73 and Mo17 significantly differed for seminal root length under low phosphorus, but not under adequate phosphorus conditions. Seminal root length of the population grown under low phosphorus ranged from 0 to 79.2 cm with a mean of 32.3 cm; while seminal root length of plants grown under high phosphorus ranged from 0.67 to 59.0 cm with a mean of 23.4 cm. Under low phosphorus, one main-effect QTL was associated with seminal root length and three QTL with seminal root number; under high phosphorus, two QTL with seminal root length and three QTL for seminal root number. These accounted for 11, 25.4, 22.8, and 24.1% of the phenotypic variations for seminal root length and number at low phosphorus, and seminal root length and number at high phosphorus, respectively. Di-genic epistatic loci were detected for seminal root length at low phosphorus (two pairs) seminal root number at low phosphorus (eight pairs), seminal root length at high phosphorus (four pairs), and seminal root number at high phosphorus (two pairs), which accounted for 23.2, 50.6, 32.2, and 20.3% of the total variations, respectively. Seminal root traits observed here were positively yet weakly correlated with shoot biomass in the field under low phosphorus, although no coincident QTL were detected. These results suggest that epistatic interactions are important in controlling genotypic variation associated with seedling seminal root traits.     

Mapping quantitative trait loci (QTLs) for resistance to Gibberella zeae infection in maize

The basic prerequisite for an efficient breeding program to improve levels of resistance to pathogens in plants is the identification of genes controlling the resistance character. If the response to pathogens is under the control of a multilocus system, the utilization of molecular markers becomes essential. Stalk and ear rot caused by Gibberella zeae is a widespread disease of corn: resistance to G. zeae is quantitatively inherited. Our experimental approach to understanding the genetic basis of resistance to Gibberella is to estimate the genetic linkage between available molecular markers and the character, measured as the amount of diseased tissue 40 days after inoculation of a suspension of Fusarium graminearum, the conidial form of G. zeae, into the first stalk internode. Sensitive and resistant parental inbreds were crossed to obtain F₁ and F₂ populations: the analysis of the segregation of 95 RFLP (restriction fragment length polymorphism) clones and 10 RAPD (random amplified polymorphic DNA) markers was performed on a population of 150 F₂ individuals. Analysis of resistance was performed on the F₃ families obtained by selfing the F₂ plants. Quantitative trait loci (QTL) detection was based either on analysis of regression coefficients between family mean value and allele values in the F₂ population, or by means of interval mapping, using MAPMAKER-QTL. A linkage map of maize was obtained, in which four to five genomic regions are shown to carry factors involved in the resistance to G. zeae.     

Quantitative trait loci mapping of leaf angle and leaf orientation value in maize (Zea mays L.)

A major limiting factor for high productivity of maize (Zea mays L.) in dense planting is light penetration through the canopy. Plant architecture with a narrower leaf angle (LA) and an optimum leaf orientation value (LOV) is desirable to increase light capture for photosynthesis and production per unit area. However, the genetic control of the plant architecture traits remains poorly understood in maize. In this study, QTL for LA, LOV, and related traits were mapped using a set of 229 F_2:3 families derived from the cross between compact and expanded inbred lines, evaluated in three environments. Twenty-five QTL were detected in total. Three of the QTL explained 37.4% and five of the QTL explained 53.9% of the phenotypic variance for LA and LOV, respectively. Two key genome regions controlling leaf angle and leaf orientation were identified. qLA1 and qLOV1 at nearest marker umc2226 on chromosome 1.02 accounted for 20.4 and 23.2% of the phenotypic variance, respectively; qLA5 and qLOV5 at nearest bnlg1287 on chromosome 5 accounted for 9.7 and 9.8% of the phenotypic variance, respectively. These QTL could provide useful information for marker-assisted selection in improving performance of plant architecture with regard to leaf angle and orientation.     

Cytoplasmic effects on quantitative characters in maize (Zea mays L.)

Summary The investigations were carried out with ten genetically diverse maize varieties and all possible crosses between them, including reciprocals, at two agro-climatically different locations in Punjab (India). The materials were studied in a split-split plot design with plant population level of 59200, 74000 and 98700 plants per hectare. The variances due to reciprocal cross effects were significant for plant height, ear height and ear girth in the pooled analysis and the effects were quite consistent over plant population levels and locations. The data on days to silk were recorded only at one location and highly significant reciprocal effects were observed. The cytoplasmic effects, however, did not depend on the cytoplasm alone but also on the interaction of genotype with cytoplasm. The reciprocal effects were more distinct in early × late combinations of varieties than in early × early or late × late combinations. Early parents when used as female tended to reduce plant and ear height and days to silk, indicating a common developmental pathway for these three traits. Since the cytoplasmic effects for these characters were not associated with significant effects on yield, the results can be of practical significance. The cytoplasmic effects for days to silk were maintained even in the F₂ and back-crosses. These findings encourage the use of particular cytoplasm in developing early maturing varieties.     

Epistasis in maize (Zea mays L.)

Summary Three flint and three dent maize (Zea mays L.) inbred lines, their possible F₁ crosses, F₂ and backcross progenies, and all possible three-way crosses were evaluated in a three-year experiment for yield, ear moisture, and plant height. The purpose was to estimate genetic parameters in European breeding materials from (i) generation means analysis, (ii) diallel analysis of generation means, and (iii) analysis of F₁ and three-way cross hybrids. Method (i) was based on the F-metric model and methods (ii) and (iii) on the Eberhart-Gardner (1966) genetic model; both models extended for heterotic maternal effects.Differences among generation means for yield and plant height were mainly attributable to dominance effects. Epistatic effects were significantly different from zero in a few crosses and considerably reduced heterosis in both traits. Additive x additive and domiance x dominance effects for yield were consistently positive and negative, respectively. Significant maternal effects were established to the advantage of generations with a heterozygous seed parent. In the diallel analysis, mean squares for dominance effects were greater than for additive effects for yield and plant height but smaller for ear moisture. Though significant for yield and plant height, epistatic variation was small compared to additive and dominance variation. Estimates of additive x additive epistasis for yield were significantly negative in 11 of 15 crosses, suggesting that advantageous gene combinations in the lines had been disrupted by recombination in the segregating generations. The analysis of hybrids supported the above findings regarding the analysis of variance. However, the estimates of additive x additive epistasis for yield were considerably smaller and only minimally correlated with those from the diallel analysis. Use of noninbred materials as opposed to materials with different levels of inbreeding is considered the main reason for the discrepancies in the results.     

Inheritance of resistance to Helminthosporium maydis blight in maize (Zea mays L.)

Summary The nature and mode of inheritance of resistance to Helminthosporium maydis blight was investigated in two maize varieties, RbU-W and DIC. The study of F₁, F₂, and reciprocal backcross populations of crosses between these two varieties on the one hand and two susceptible varieties, UVE and ZPSc-58c on the other, revealed that resistance in the two varieties is monogenic recessive. The genes for resistance in the two varieties are allelic. Resistance was shown to be a lesion-type and measurements revealed that it operated through reduced lesion size and lesion number.     

Quantitative trait loci for grain moisture at harvest and field grain drying rate in maize (Zea mays, L.)

Hybrids with low grain moisture (GM) at harvest are specially required in mid- to short-season environments. One of the most important factors determining this trait is field grain drying rate (FDR). To produce hybrids with low GM at harvest, inbred lines can be obtained through selection for either GM or FDR. Thus, a single-cross population (181 F _2:3-generation plants) of two divergent inbred lines was evaluated to locate QTL affecting GM at harvest and FDR as a starting point for marker assisted selection (MAS). Moisture measurements were made with a hand-held moisture meter. Detection of QTL was facilitated with interval mapping in one and two dimensions including an interaction term, and a genetic linkage map of 122 SSR loci covering 1,557.8 cM. The markers were arranged in ten linkage groups. QTL mapping was made for the mean trait performance of the F _2:3 population across years. Ten QTL and an interaction were associated with GM. These QTL accounted for 54.8 and 65.2% of the phenotypic and genotypic variation, respectively. Eight QTL and two interactions were associated with FDR accounting for 35.7 and 45.2% of the phenotypic and genotypic variation, respectively. Two regions were in common between traits. The interaction between QTL for GM at harvest had practical implications for MAS. We conclude that MAS per se will not be an efficient method for reducing GM at harvest and/or increasing FDR. A selection index including both molecular marker information and phenotypic values, each appropriately weighted, would be the best selection strategy.