Interval mapping of quantitative trait loci affecting NESTUR, a stem growth efficiency index of radiata pine seedlings

 NESTUR (needle-to-stem unit rate) is a stem growth index of conifer seedlings that measures the efficiency of stemwood production per unit of needle growth, and is related to other seedling traits such as height, stem diameter, stem volume and needle volume. Quantitative trait loci (QTLs) affecting the expression of stem growth efficiency in radiata pine seedlings were investigated using a RAPD linkage map constructed from markers scored on haploid, megagametophytic DNA. Four putative QTLs were detected which accounted for 8.5–36.4% of the population variance. A search for evidence of epistasis, using both complete pairwise and conditional interactions, did not yield any statistically significant result. Over a 3-year period, seedlings with high-NESTUR marker alleles showed a superior growth performance of 17–40% for height, diameter and volume over those with low-NESTUR marker alleles. Received: 10 July 1997 / Accepted: 31 March 1998     

Genome-wide association analyses of common wheat (Triticum aestivum L.) germplasm identifies multiple loci for aluminium resistance

Aluminium (Al3+) toxicity restricts productivity and profitability of wheat (Triticum aestivum L.) crops grown on acid soils worldwide. Continued gains will be obtained by identifying superior alleles and novel Al3+ resistance loci that can be incorporated into breeding programs. We used association mapping to identify genomic regions associated with Al3+ resistance using 1055 accessions of common wheat from different geographic regions of the world and 178 polymorphic diversity arrays technology (DArT) markers. Bayesian analyses based on genetic distance matrices classified these accessions into 12 subgroups. Genome-wide association analyses detected markers that were significantly associated with Al3+ resistance on chromosomes 1A, 1B, 2A, 2B, 2D, 3A, 3B, 4A, 4B, 4D, 5B, 6A, 6B, 7A, and 7B. Some of these genomic regions correspond to previously identified loci for Al3+ resistance, whereas others appear to be novel. Among the markers targeting TaALMT1 (the major Al3+-resistance gene located on chromosome 4D), those that detected alleles in the promoter explained most of the phenotypic variance for Al3+ resistance, which is consistent with this region controlling the level of TaALMT1 expression. These results demonstrate that genome-wide association mapping cannot only confirm known Al3+-resistance loci, such as those on chromosomes 4D and 4B, but they also highlight the utility of this technique in identifying novel resistance loci.     

GENSTAT programs for performing Muir's alternative partitioning of genotype-by-environment interaction

Genotype-by-environment (GE) interaction exists when different cultivars or strains have different phenotypic responses to environmental variation (Merila and Fry 1998). The phenomenon is of major concern in plant breeding, as it can limit gains in selecting superior cultivars. In animal breeding, the problem is also an important issue because breeding stocks are developed by a few companies but are used worldwide (Lin and Togashi 2002).     

Association mapping for soilborne pathogen resistance in synthetic hexaploid wheat

Soilborne pathogens such as cereal cyst nematode (CCN; Heterodera avenae) and root lesion nematode (Pratylenchus neglectus; PN) cause substantial yield losses in the major cereal-growing regions of the world. Incorporating resistance into wheat cultivars and breeding lines is considered the most cost-effective control measure for reducing nematode populations. To identify loci with molecular markers linked to genes conferring resistance to these pathogens, we employed a genome-wide association approach in which 332 synthetic hexaploid wheat lines previously screened for resistance to CCN and PN were genotyped with 660 Diversity Arrays Technology (DArT) markers. Two sequence-tagged site markers reportedly linked to genes known to confer resistance to CCN were also included in the analysis. Using the mixed linear model corrected for population structure and familial relatedness (Q+K matrices), we were able to confirm previously reported quantitative trait loci (QTL) for resistance to CCN and PN in bi-parental crosses. In addition, we identified other significant markers located in chromosome regions where no CCN and PN resistance genes have been reported. Seventeen DArT marker loci were found to be significantly associated with CCN and twelve to PN resistance. The novel QTL on chromosomes 1D, 4D, 5B, 5D and 7D for resistance to CCN and 4A, 5B and 7B for resistance to PN are suggested to represent new sources of genes which could be deployed in further wheat improvement against these two important root diseases of wheat.     

QTL dissection of the loss of green colour during post-anthesis grain maturation in two-rowed barley

Ability to genetically manipulate the loss of green colour during grain maturation has potentials for increasing productivity, disease resistance, and drought and heat tolerance in crop plants. Two doubled haploid, two-rowed barley populations (Vlamingh × Buloke and VB9524 × ND11231*12) were monitored over 2 years for loss of green colour during grain filling using a portable active sensor. The aims were to determine the genomic regions that control trait heritability by quantitative trait locus (QTL) analysis, and to examine patterns of QTL-environment interactions under different conditions of water stress. In the Vlamingh × Buloke cross, broad-sense heritability estimate for loss of green colour (measured as the difference in sensor readings taken at anthesis and maturity, ?SRI) was 0.68, and 0.78 for the VB9524 × ND11231*12 population. In the VB9524 × ND11231*12 population, rapid loss of green colour was positively associated with grain yield and percent plump grains, but in the Vlamingh × Buloke population, a slower loss of green colour (low ?SRI) was associated with increased grain plumpness. With the aid of a dense array of single nucleotide polymorphisms (SNPs) and EST-derived SSR markers, a total of nine QTLs were detected across the two populations. Of these, a single major locus on the short arm of barley chromosome 5H was consistently linked with trait variation across the populations and multiple environments. The QTL was independent of flowering time and explained between 5.4 and 15.4 % of the variation observed in both populations, depending on the environment, and although a QTL × E interaction was detected, it was largely due to a change in the magnitude of the effect, rather than a change in direction. The results suggest that loss of green colour during grain maturation may be under the control of a simple genetic architecture, but a careful study of target populations and environments would be required for breeding purposes.     

Age-related changes in the expression of QTLs for growth in radiata pine seedlings

 Haploid megagametophytes from a full-sib cross of Pinus radiata were used to construct a genetic linkage map for radiata pine based on random amplified polymorphic DNA (RAPD) markers. The map, which was made from 222 markers, was used to carry out a QTL analysis of growth using measurements made on seedlings from which these megagametophytes were collected at an early germination stage. Trends in the expression of QTLs for stem diameter, volume and height were compared using measurements made at 5 months of age, and at 1, 2 and 3 years of age. None of the observed trends showed complete stability, i.e. none of the putative QTL positions detected at any one age was strongly expressed at all of the four stages of measurement. However, 45% of the trends showed partial stability, i.e. putative QTLs significant at one age were also detected at a subsequent age. Trends in QTL expression with age followed one of three patterns: (1) putative QTLs at some locations showed a gradual linear increase in influence from 5 months of age and were highest at 3 years of age; (2) QTLs detected at 5 months of age gradually became less significant with age; and (3) some putative QTLs showed a curvilinear increase in effect from 5 months of age, reaching their peak expression at 1 to 2 years, and sometimes were still detected at 3 years of age. Received: 10 July 1997 / Accepted: 31 March 1998     

Linkage of RAPD markers to NESTUR, a stem growth index in radiata pine seedlings

 Needle-to-stem unit rate (NESTUR) is a stem growth index of conifer seedlings that measures the efficiency of stemwood production per unit of foliage growth. The random amplified polymorphic DNA (RAPD) technique was applied to haploid DNA from the megagametophytes of a full-sib radiata pine cross to find markers linked to factors controlling the NESTUR trait. Using the bulked segregant analysis approach, 23 of 933 primers displayed putative linkage to factors controlling NESTUR. Based on the genotypic analysis of 174 individuals, two quantitative trait loci (QTLs) controlling NESTUR were identified at ANOVA P-levels of 0.01–0.001. The QTLs were identified by RAPD markers OPE-06₄₅₀ and OPA-10₁₂₀₀, which were linked to each other (r=7%), and UBC-333₅₅₀, which was not linked to the other two. Linkage to components of NESTUR (increments in stem diameter and stem volume) was demonstrated for UBC-333₅₅₀, while the others were not linked to NESTUR components. Received: 18 December 1996/Accepted: 24 January 1997     

Quantitative trait locus (QTL) analysis of growth and vegetative propagation traits in <Emphasis Type="Italic">Eucalyptus nitens</Emphasis> full-sib families

Tree growth and vegetative propagation are complex but important traits under selection in many tree improvement programmes. To understand the genetic control of these traits, we conducted a quantitative trait locus (QTL) study in three full-sib families of Eucalyptus nitens growing at two different sites. One family growing at Ridgley, Tasmania had 300 progeny and two clonally replicated families growing at Mt. Gambier, South Australia had 327 and 210 progeny. Tree growth was measured over several years at both sites and percentages of roots produced by either stem cuttings or tissue culture were assessed in the two Mt. Gambier families. Linkage analysis of growth traits revealed several QTLs for later year traits but few for early year traits, reflecting temporal differences in the heritabilities of these traits. Two growth QTL positions, one on LG8 and another on LG11 were common between the Ridgley and Mt. Gambier families. Four QTLs were observed for each of the two vegetative propagation methods. Two QTLs for vegetative propagation on LG7 and LG11 were validated in the second family at Mt. Gambier. These results suggest that growth and vegetative propagation traits are controlled by several small effect loci. The QTLs identified in this study are useful starting points for identifying candidate genes using the Eucalyptus grandis genome sequence.     

Genetic control of grain yield and grain physical characteristics in a bread wheat population grown under a range of environmental conditions

Key message

Genetic analysis of the yield and physical quality of wheat revealed complex genetic control, including strong effects of photoperiod-sensitivity loci.

Abstract

Environmental conditions such as moisture deficit and high temperatures during the growing period affect the grain yield and grain characteristics of bread wheat (Triticum aestivum L.). The aim of this study was to map quantitative trait loci (QTL) for grain yield and grain quality traits using a Drysdale/Gladius bread wheat mapping population grown under a range of environmental conditions in Australia and Mexico. In general, yield and grain quality were reduced in environments exposed to drought and/or heat stress. Despite large effects of known photoperiod-sensitivity loci (Ppd-B1 and Ppd-D1) on crop development, grain yield and grain quality traits, it was possible to detect QTL elsewhere in the genome. Some of these QTL were detected consistently across environments. A locus on chromosome 6A (TaGW2) that is known to be associated with grain development was associated with grain width, thickness and roundness. The grain hardness (Ha) locus on chromosome 5D was associated with particle size index and flour extraction and a region on chromosome 3B was associated with grain width, thickness, thousand grain weight and yield. The genetic control of grain length appeared to be largely independent of the genetic control of the other grain dimensions. As expected, effects on grain yield were detected at loci that also affected yield components. Some QTL displayed QTL-by-environment interactions, with some having effects only in environments subject to water limitation and/or heat stress.     

QTL mapping identifies a major locus for resistance in wheat to Sunn pest (<Emphasis Type="Italic">Eurygaster</Emphasis><Emphasis Type="Italic">integriceps</Emphasis>) feeding at the vegetative growth stage

Key message

This research provides the first report of a major locus controlling wheat resistance to Sunn pest. It developed and validated SNP markers that will be useful for marker-assisted selection.

Abstract

Sunn pest (Eurygaster integriceps Puton) is the most destructive insect pest of bread wheat and durum wheat in West and Central Asia and East Europe. Breeding for resistance at the vegetative stage of growth is vital in reducing the damage caused by overwintered adult populations that feed on shoot and leaves of seedlings, and in reducing the next generation of pest populations (nymphs and adults), which can cause damage to grain quality by feeding on spikes. In the present study, two doubled haploid (DH) populations involving resistant landraces from Afghanistan were genotyped with the 90k SNP iSelect assay and candidate gene-based KASP markers. The DH lines and parents were phenotyped for resistance to Sunn pest feeding, using artificial infestation cages at Terbol station, in Lebanon, over three years. Quantitative trait locus (QTL) analysis identified a single major locus on chromosome 4BS in the two populations, with the resistance allele derived from the landrace accessions, IG139431 and IG139883. The QTL explained a maximum of 42 % of the phenotypic variation in the Cham6 × IG139431 and 56 % in the Cham6 × IG139883 populations. SNP markers closest to the QTL showed high similarity to rice genes that putatively encode proteins for defense response to herbivory and wounding. The markers were validated in a large, unrelated population of parental wheat genotypes. All wheat lines carrying the ‘C–G’ haplotype at the identified SNPs were resistant, suggesting that selection based on a haplotype of favourable alleles would be effective in predicting resistance status of unknown genotypes.