Freezing tolerance of selected perennial ryegrass (<Emphasis Type="Italic">Lolium perenne</Emphasis> L.) accessions and its association with field winterhardiness and turf traits

Reproductive output and fertility variation in teak were evaluated in five study sites in Western Ghats region of southern India. In four seed production areas (SPA1-4)) and a natural population (NAT) plots with 100 trees were investigated. The 40-year-old seed production areas are located in high rainfall (>2,500 mm) sites in Kerala state and the natural stand is at a drier location in Tamil Nadu. Fruit production per tree was rather high in the natural stand (1500) and quite variable in the seed production areas. SPA 4, located far south from the other sites, had the highest fruit production (almost twice that in the other study sites), high relative population size (N _r = 0.5) and predicted low genetic drift in two consecutive years. Fecundity was very low in SPAs 2 & 3 (200 fruits per tree). Reproductive output was similar in successive years except SPA 1, where the fruit production in the first year was almost five times that in the second year. Fertility variation (computed as sibling coefficient, Ψ) was in general higher in NAT and hence the relative population size was lower than in SPAs. The variation in female fertility in the natural stand was, somewhat surprisingly, similar to that in the seed production areas, while the male fertility variation was higher. In the seed production areas the male fertility variation was lower or similar to the female fertility variation. The fertility variation, Ψ was on average around 3 and correspondingly the relative effective population size, N _r = 0.36 and the variance effective number around 60. Selection for tree diameter would improve predicted diversity of the seed crop as it was positively correlated with reproductive output and negatively correlated with fertility variation among trees.     

Seed yield in perennial ryegrass (<Emphasis Type=Italic>Lolium perenne</Emphasis> L.): comparative importance of component traits and detection of seed-yield-related QTL

The aims of our study were to evaluate relationships amongst morphological traits associated with seed production in a perennial ryegrass biparental population and to identify genomic regions associated with phenotypic variation in those traits using QTL analysis. This was achieved using data from two field experiments at Palmerston North and Lincoln, New Zealand, in 2003, and days to heading (DTH), reassessed in 2004. Trait association was determined for the Palmerston North experiment where measured traits included seed yield per plant (SYPlant), seed yield per spike (SYSp), reproductive tiller number (RTiller), spikelets per spike (SpktSp), florets per spikelet (FSpkt), 1000 seed weight (TSW), spike length (SpLen), florets per spike (FSp), floret site utilization (FSUtil), spread of heading (SOH) and plant growth habit (PGHabit). Traits contributing to SYPlant in order of descending value were FSpkt, FSUtil, and RTiller. High TSW was only weakly linked to SYPlant. FSUtil, SOH and RTiller were identified as valuable breeding targets for improving seed yield potential in perennial ryegrass. QTL were identified for all traits except for RTiller. QTL for SYPlant occurred on linkage groups (LG) 2 and 6. Both were co-located with QTL for SYSp and sets of SYPlant components or related traits (FSpkt, FSp; FSUtil and TSW). Major QTL for DTH were identified on LG2 and LG4 and minor QTL on LG7 in consecutive years. There was a strong genotype-by-environment interaction for SYPlant that was reflected in a lack of consistent QTL across environments, while QTL for SYSp and DTH were stable across environments. Identification of component traits and QTL important for seed yield may accelerate genetic improvement in perennial ryegrass through conventional and marker-assisted breeding, respectively.     

Effects of introgressions from <Emphasis Type="Italic">Festuca pratensis</Emphasis> on winter hardiness of <Emphasis Type="Italic">Lolium perenne</Emphasis>

Previous studies reported that some genotypes with introgressed Festuca chromosome segment(s) in Lolium genome showed enhanced winter hardiness compared to Lolium. The aim of this study was to search comprehensively for the Festuca pratensis chromosome regions affecting winter hardiness-related traits when introgressed into the Lolium perenne genome. Association between F. pratensis introgression and winter hardiness-related traits (fall and winter hardiness indexes, early-spring dry matter yield, and freezing tolerance) were screened in the diploid introgression populations (n = 203) that had some F. pratensis chromosome segments introgressed. Eighty-four intron markers corresponding to unique rice genes randomly distributed across the genome were used for genotyping. Winter hardiness of almost all plants in the introgression populations was lower than that of the F. pratensis and triploid hybrid parents, but the average was higher than that of L. perenne. A significant positive effect of F. pratensis introgression on early-spring dry matter yield was detected on chromosome 7. This quantitative trait locus (QTL) was confirmed by linkage analysis using a backcross population with F. pratensis introgression in the target region of chromosome 7. However, the contribution of the newly identified QTL was rather small (6.7–9.6%), suggesting that superior winter hardiness of F. pratensis compared to L. perenne is conferred by multiple small-effect QTLs. We also detected a previously unreported negative effect of Festuca introgression on winter hardiness. Newly obtained QTL information in this study would contribute to the design of Festuca/Lolium hybrid breeding.     

QTL mapping of agronomically important traits in sorghum (<Emphasis Type="Italic">Sorghum bicolor</Emphasis> L.)

Sorghum is one of the most important cereal crops; it is used to produce feed, sugar, and biofuel. To investigate genetic tradeoffs between grain and stem sugar production, we evaluated plant height, Brix (the percentage of soluble solids in stalk juice), 100-grain weight and flowering time over 3 years in a recombinant inbred line (RIL) population consisting of 189 individuals derived from a cross between the sweet sorghum cultivar ‘Rio’ and grain sorghum ‘BTx623’. We constructed a genetic linkage map (total length, 1418.71 cM; average distance between markers, 11.26 cM), which consisted of 118 simple sequence repeat (SSR) and 8 insertion-deletion (INDEL) markers. A total of 14 QTLs were detected on chromosomes 1, 3, 6, 7, and 9, which included 6 QTLs for plant height; 4 for Brix; and 2 QTLs for each 100-grain weight and flowering time. Eight QTLs were detected at least in 2 years. These results will be useful for future QTL fine mapping and gene mining for these traits, and useful for the improvement of sorghum through molecular marker-assisted selection.     

Genetic effects of introgression genomic components from Sea Island cotton (<Emphasis Type="Italic">Gossypium barbadense</Emphasis> L.) on fiber related traits in upland cotton (<Emphasis Type="Italic">G</Emphasis>. <Emphasis Type="Italic">hirsutum</Emphasis> L.)

The germplasm with exotic genomic components especially from Sea Island cotton (Gossypium barbadense L. Gb) is the dominant genetic resources to enhance fiber quality of upland cotton (G. hirsutum L., Gh). Due to low efficiency of phenotypic evaluation and selection on fiber quality, genetic dissection of favorable alleles using molecular markers is essential. Genetic dissection on putative Gb introgressions related to fiber traits were conducted by SSR markers with mapping populations derived from a cross between Luyuan343 (LY343), a superior fiber quality introgression line (IL) with genomic components from Gb, and an elite Upland cotton cv. Lumianyan#22 (LMY22). Among 82 polymorphic loci screened out from 4050 SSRs, 42 were identified as putative introgression alleles. A total of 29 fiber-related QTLs (23 for fiber quality and six for lint percentage) were detected and most of which clustered on the putative Gb introgression chromosomal segments of Chr.2, Chr.16, Chr.23 and Chr.25. As expected, a majority of favorable alleles of fiber quality QTLs (12/17, not considering the QTLs for fiber fineness) came from the IL parent and most of which (11/12) were conferred by the introgression genomic components while three of the six (3/6) favorable alleles for lint percentage came from the Gh parent. Validation of these QTLs using an F₈ breeding population from the same cross made previously indicated that 13 out of 29 QTLs showed considerable stability. The results suggest that fiber quality improvement using the introgression components could be facilitated by marker-assisted selection in cotton breeding program.     

QTL analysis for thousand-grain weight under terminal drought stress in bread wheat (<Emphasis Type="Italic">Triticum</Emphasis><Emphasis Type="Italic">aestivum</Emphasis> L.)

Grain yield under post-anthesis drought stress is one of the most complex traits, which is inherited quantitatively. The present study was conducted to identify genes determining post-anthesis drought stress tolerance in bread wheat through Quantitative Trait Loci (QTLs) analysis. Two cultivated bread wheat accessions were selected as parental lines. Population phenotyping was carried out on 133 F_2:3 families. Two field experiments and two experiments in the greenhouse were conducted at IPK-Gatersleben, Germany with control and post-anthesis stress conditions in each experiment. Thousand-grain weight was recorded as the main wheat yield component, which is reduced by post-anthesis drought stress. Chemical desiccation was applied in three experiments as simulator of post-anthesis drought stress whereas water stress was applied in one greenhouse experiment. Analysis of variance showed significant differences among the F_2:3 families. The molecular genetic linkage map including 293 marker loci associated to 19 wheat chromosomes was applied for QTL analysis. The present study revealed four and six QTLs for thousand-grain weight under control and stress conditions, respectively. Only one QTL on chromosome 4BL was common for both conditions. Five QTLs on chromosomes 1AL, 4AL, 7AS, and 7DS were found to be specific to the stress condition. Both parents contributed alleles for drought tolerance. Taking the known reciprocal translocation of chromosomes 4AL/7BS into account, the importance of the short arms of homoeologous group 7 is confirmed for drought stress.     

Phenotypic diversity in cold-tolerant peanut (<Emphasis Type="Italic">Arachis hypogaea</Emphasis> L.) germplasm

Tolerance to low temperature is an important prerequisite for optimal performance of peanut (Arachis hypogaea L.) in a number of temperate peanut-growing environments. One hundred fifty-eight peanut accessions belonging to five botanical types, known to be tolerant to low temperature (12°C) at germination, were evaluated for phenotypic diversity for 15 morphological traits in the 2001 rainy season and for 15 agronomic and two seed quality traits in the 2001 rainy and 2001/2002 post-rainy seasons. Analysis of data, using the residual maximum-likelihood approach indicated that variance components due to genotypes were significant for all traits in the rainy and for all but two traits in the post-rainy season. Clustering based on scores of nine principle components delineated four clusters. The cold-tolerant genotypes and the standard control cultivars in the four clusters differed in mean, variance, and range both during rainy and post-rainy seasons for a range of agronomic traits, indicating the diversity among the clusters. The cold-tolerant accessions were superior to control cultivars for several agronomic traits compared with their respective controls in both the rainy and post-rainy seasons, so their use in breeding should result in genetically diverse cold-tolerant high-yielding peanut cultivars.     

Genetic control of agronomic traits in alfalfa (<Emphasis Type="Italic">M. sativa</Emphasis> ssp. <Emphasis Type="Italic">sativa</Emphasis> L.)

The objective of this study was to develop diallel population hybrids by crossing selected germplasm and to determine the gene effects and genetic control of yield and yield components using diallel analysis. A complete diallel including reciprocals was made during 2003 and 2004 between five alfalfa cultivars of different geographic origin. For each pairwise cross, five plants were chosen at random from each of the two cultivars (~100 florets per plant) to obtain the F₁ generation. A spaced plant field was established in 2006 which included the five alfalfa cultivars (parents) and their 20 diallel hybrids (F₁). The results of the diallel analysis suggest that the genetic control of major agronomic traits is determined by both additive gene action (accumulation of frequency of desirable alleles represented by significant GCA effects) and nonadditive gene action (complementary gene interactions represented by significant SCA effects). This type of gene action expression in alfalfa also determines the way in which breeding is carried out and brings about changes in the methods used and has given rise to the idea of the semi-hybrid breeding of this crop. The concept involves: breeding alfalfas within the population, identification of heterotic germplasm, and the production of seed of the population hybrid (PH).     

Identification of coincident QTL for days to heading,spike length and spikelets per spike in <Emphasis Type="Italic">Lolium perenne</Emphasis> L.

Flowering time is a trait which has a major influence on the quality of forage. In addition, flowering and subsequent seed yields are important traits for seed production by grass breeders. In this study, we have identified quantitative trait loci (QTL) for flowering time and morphological traits of the flowering head in an F₁ mapping population in Lolium perenne L (perennial ryegrass), a number of which have not previously been identified in L. perenne mapping studies. QTL for days to heading (DTH) were mapped in both outdoor and glasshouse experiments, revealing three and five QTL for DTH which explained 53% and 42% of the total phenotypic variation observed, respectively. Two QTL for DTH were detected in both environments, although they had contrasting relative magnitudes in each environment. One QTL for spike length and three QTL for spikelets per spike were also identified explaining, a total of 32 and 33% of the phenotypic variance, respectively. Furthermore, the QTL for spike length and spikelets per spike generally coincided with QTL for days to heading, implying co-ordinate regulation by underlying genes. Of particular interest was a region harbouring overlapping QTL for days to heading, spike length and spikelets per spike on the top of linkage group 4, containing the major QTL for spike length identified in this population.     

Successful induction of trigenomic hexaploid <Emphasis Type="Italic">Brassica</Emphasis> from a triploid hybrid of <Emphasis Type="Italic">B.</Emphasis><Emphasis Type="Italic">napus</Emphasis> L. and <Emphasis Type="Italic">B. nigra</Emphasis> (L.) Koch

A triploid hybrid with an ABC genome constitution, produced from an interspecific cross between Brassica napus (AACC genome) and B. nigra (BB genome), was used as source material for chromosome doubling. Two approaches were undertaken for the production of hexaploids: firstly, by self-pollination and open-pollination of the triploid hybrid; and secondly, by application of colchicine to axillary meristems of triploid plants. Sixteen seeds were harvested from triploid plants and two seedlings were confirmed to be hexaploids with 54 chromosomes. Pollen viability increased from 13% in triploids to a maximum of 49% in hexaploids. Petal length increased from 1.3 cm (triploid) to 1.9 cm and 1.8 cm in the two hexaploids and longest stamen length increased from 0.9 cm (triploid) to 1.1 cm in the hexaploids. Pollen grains were longer in hexaploids (43.7 and 46.3 μm) compared to the triploid (25.4 μm). A few aneuploid offsprings were also observed, with chromosome number ranging from 34 to 48. This study shows that trigenomic hexaploids can be produced in Brassica through interspecific hybridisation of B. napus and B. nigra followed by colchicine treatment.     

Fine mapping of a <Emphasis Type="Italic">Xantha</Emphasis> mutation in rice (<Emphasis Type="Italic">Oryza sativa</Emphasis> L.)

The recessive mutation of the XANTHA gene (XNT) transforms seedlings and plants into a yellow color, visually distinguishable from normal (green) rice. Thus, it has been introduced into male sterile lines as a distinct marker for rapidly testing and efficiently increasing varietal purity in seed and paddy production of hybrid rice. To identify closely linked markers and eventually isolate the XNT gene, two mapping populations were developed by crossing the xantha mutant line Huangyu B (indica) with two wild type japonica varieties; a total of 1,720 mutant type F₂ individuals were analyzed for fine mapping using polymorphic InDel markers and high dense microsatellite markers. The XNT gene was mapped on chromosome 11, within in a fragment of ~100 kb, where 13 genes are annotated. The NP_001067671.1 gene within the delimited region is likely to be a candidate XNT gene, since it encodes ATP-dependent chloroplast protease ATP-binding subunit clp A. However, no sequence differences were observed between the mutant and its parent. Bioinformatics analysis demonstrated that four chlorophyll deficient mutations that were previously mapped on the same chromosome are located outside the XNT region, indicating XNT is a new gene. The results provide useful DNA markers not only for marker assisted selection of the xantha trait but also its eventual cloning.     

A simple,rapid and reliable bioassay for evaluating seedling vigor under submergence in <Emphasis Type="Italic">indica</Emphasis> and <Emphasis Type="Italic">japonica</Emphasis> rice (<Emphasis Type="Italic">Oryza sativa</Emphasis> L.)

Submergence is a major stress causing yield losses particularly in the direct-seeded rice cultivation system and necessitates the development of a simple, rapid and reliable bioassay for a large scale screening of rice germplasms with tolerance against submergence stress. We developed two new bioassay methods that were based primarily on the seedling vigor evaluated by the ability of fast shoot elongation under submerged conditions, and compared their effectiveness with two other available methods. All four bioassay methods using cultivars of 7 indica and 6 japonica types revealed significant and consistent cultivar differences in seedling vigor under submergence and/or submergence tolerance. Japonica cultivars were more vigorous than indica cultivars, with Nipponbare being the most vigorous. The simplest test tube method showed the highest correlations to all other methods. Our results suggest that seedling vigor serves as a submergence avoidance mechanism and confers tolerance on rice seedlings to flooding during early crop establishment. A possible relationship is discussed between seedling vigor based on fast shoot elongation and submergence tolerance defined by recovery from submergence stress.     

Identification of common QTL for resistance to <Emphasis Type="Italic">Sclerotinia sclerotiorum</Emphasis> in three doubled haploid populations of <Emphasis Type="Italic">Brassica napus</Emphasis> (L.)

Sclerotinia stem rot (SR) is one of the most devastating diseases of canola/rapeseed. Quantitative trait loci (QTL) analyses were carried out to identify loci responsible for resistance to SR in three doubled haploid DH populations (H1, H2 and H3). Petiole inoculation technique PIT was used to evaluate the all populations for resistance to SR. Genetic maps were developed using sequence related amplified polymorphism SRAP and simple sequence repeat SSR markers. Genetic maps of the H1 and H2 populations were developed using 508 and 478 markers, respectively. Previously published genetic map of the H3 population was also used in this study. The QTL analysis was carried out for each replicate separately as well as on the average of all the replicates. The numbers of identified QTL in each analysis varied from four to six in the H1 population, three to six in the H2 population and two to six in the H3 population. A number of common QTL were identified between the replicates of each population. Two common QTL were identified on linkage group A7 and C6 between the H1 and H3 populations and one QTL on A9 between the H2 and H3 populations. We are the first to report, identification of common QTL between different populations of Brassica napus.     

Genome-wide SNP-based association mapping of resistance to <Emphasis Type="Italic">Phytophthora sojae</Emphasis> in soybean (<Emphasis Type="Italic">Glycine max</Emphasis> (L.) Merr.)

Phytophthora root rot (PRR) is among the most important soybean (Glycine max (L.) Merr.) diseases worldwide, and the host displays complex genetic resistance. A genome-wide association study was performed on 337 accessions from the Yangtze-Huai soybean breeding germplasm to identify resistance regions associated with PRR resistance using 60,862 high-quality single nucleotide polymorphisms markers. Twenty-six significant SNP-trait associations were detected on chromosomes 01 using a mixed linear model with the Q matrix and K matrix as covariates. In addition, twenty-six SNPs belonged to three adjacent haplotype blocks according to a linkage disequilibrium blocks analysis, and no previous studies have reported resistance loci in this 441 kb region. The real-time RT-PCR analysis of the possible candidate genes showed that two genes (Glyma01g32800 and Glyma01g32855) are likely involved in PRR resistance. Markers associated with resistance can contribute to marker-assisted selection in breeding programs. Analyses of candidate genes can lay a foundation for exploring the mechanism of P. sojae resistance.     

Identification of quantitative trait loci involved in resistance to <Emphasis Type="Italic">Pseudomonas syringae</Emphasis> pv. <Emphasis Type="Italic">syringae</Emphasis> in pea (<Emphasis Type="Italic">Pisum sativum</Emphasis> L.)

Pseudomonas syringae is the main pathogen responsible for bacterial blight disease in pea and can cause yield losses of 70%. P. syringae pv. pisi is prevalent in most countries but the importance of P. syringae pv. syringae (Psy) is increasing. Several sources of resistance to Psy have been identified but genetics of the resistance is unknown. In this study the inheritance of resistance to Psy was studied in the pea recombinant inbred line population P665 × ‘Messire’. Results suggest a polygenic control of the resistance and two quantitative trait loci (QTL) associated with resistance, Psy1 and Psy2, were identified. The QTL explained individually 22.2 and 8.6% of the phenotypic variation, respectively. In addition 21 SSR markers were included in the P665 × ‘Messire’ map, of which six had not been mapped on the pea genome in previous studies.     

Epistasis and heritability of resistance to <Emphasis Type="Italic">Phytophthora nicotianae</Emphasis> in pepper (<Emphasis Type="Italic">Capsicum annuum</Emphasis> L.)

Gene effects of resistance to two isolates of Phytophthora nicotianae in two crosses of pepper were investigated using separate generation means analysis. Additive-dominance models were inadequate in all cases. Digenic parameter models were adequate in three cases and the probability of goodness of fit of models was negatively correlated with the aggressiveness of the pathogen. None of these models explained variation among generation means in the combined cross Beldi × CM334 with P. nicotianae isolate Pn_2. Additive × additive, dominance × dominance and dominance × additive effects were significant in most cases. Additive and dominance effects (of negative sign) contribute more to resistance than to susceptibility. Additive variance was greater than environmental and dominance variance and ranged from 0.038 to 0.224. Narrow-sense heritabilities were dependent upon the cross and inoculate and ranged from 86 to 92%. The results of this study indicate that selection with more aggressive isolates of the pathogen will be useful for enhancing resistance in pepper.     

QTL mapping and analysis of epistatic interactions for grain yield and yield-related traits in <Emphasis Type="Italic">Triticum turgidum</Emphasis> L. var. <Emphasis Type="Italic">durum</Emphasis>

A quantitative trait loci (QTL) analysis of grain yield and yield-related traits was performed on 93 durum wheat recombinant inbred lines derived from the cross UC1113 × Kofa. The mapping population and parental lines were analyzed considering 19 traits assessed in different Argentine environments, namely grain yield, heading date, flowering time, plant height, biomass per plant, and spikelet number per ear, among others. A total of 224 QTL with logarithm of odds ratio (LOD) ≥ 3 and 47 additional QTL with LOD > 2.0 were detected. These QTL were clustered in 35 regions with overlapping QTL, and 12 genomic regions were associated with only one phenotypic trait. The regions with the highest number of multi-trait and stable QTL were 3BS.1, 3BS.2, 2BS.1, 1BL.1, 3AL.1, 1AS, and 4AL.3. The effects of epistatic QTL and QTL × environment interactions were also analyzed. QTL putatively located at major gene loci (Rht, Vrn, Eps, and Ppd) as well as additional major/minor QTL involved in the complex genetic basis of yield-related traits expressed in Argentine environments were identified. Interestingly, the 3AL.1 region was found to increase yield without altering grain quality or crop phenology.