In the mid-1980s, the development of abundant molecular markers, appropriate statistical pro- cedures, and user-friendly computer software that implemented these statistical procedures permitted the detection of molecular markers associated with quantitative trait loci (QTL) for complex traits. Marker-assisted selection was then proposed as a means of exploiting mark- ers linked to QTL to develop improved cultivars. But while thousands of marker-trait associations have been reported for many traits in different plant species, far fewer examples of success- fully exploiting mapped QTL have been reported in the literature. Key lessons learned from apply- ing markers in plant breeding include the follow- ing: (i) the purpose of detecting QTL should be clearly defi ned before embarking on QTL map- ping; (ii) procedures for marker-based selection depend on the number of QTL; (iii) estimates of QTL effects for complex traits are often incon- sistent; and (iv) gain per unit cost and time rather than gain per cycle should be considered. Future applications for complex traits will likely focus on predictive methodologies for marker-based selection before phenotyping and for marker- based selection without QTL mapping. These applications will take advantage of cheaper costs of genotyping than of phenotyping.

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Molecular Markers and Selection for Complex Traits in Plants: Learning from the Last 20 Years

Fusarium head blight (FHB) is a devastating disease of wheat and barley worldwide. Resistant cultivars could reduce damage from FHB. Chinese wheat cultivar Sumai 3 and its derivatives represent the greatest degree of resistance to FHB known. A major quantitative trait locus (QTL) on chromosome 3BS and other minor QTL for FHB resistance have been identified in these cultivars and used in wheat-breeding programs worldwide. Many breeding lines with the 3BS resistance QTL and improved agronomic traits have been developed. In barley, only limited sources of FHB resistance are available, especially in six-rowed barley, and none of them contains a DON level low enough to meet the safety requirement of the brewing industry. Several QTL have been identified for lower FHB severity, DON content, and kernel discoloration and used to enhance FHB resistance in barley. Marker-assisted selection for FHB resistance QTL on 3BS of wheat and on 2H of barley is in progress.

Management and resistance in wheat and barley to fusarium head blight.

During the past decade, numerous studies have been published on molecular mapping of Fusarium head blight (FHB) resistance in wheat. We summarize the relevant findings from 52 quantitative trait loci (QTL) mapping studies, nine research articles on marker-assisted selection and seven on marker-assisted germplasm evaluation. QTL for FHB resistance were found on all wheat chromosomes except chromosome 7D. Some QTL were found in several independent mapping studies indicating that such QTL are stable and therefore useful in breeding programmes. We summarize and update current knowledge on the genetics of FHB resistance in wheat resulting from QTL mapping investigations and review and suggest FHB breeding strategies based on the available information and DNA markers.

https://onlinelibrary.wiley.com/doi/pdf/10.1111/j.1439-0523.2008.01550.x

QTL mapping and marker-assisted selection for Fusarium head blight resistance in wheat: A review

Microsatellite DNA markers are consistently found to be more informative than other classes of markers in hexaploid wheat. The objectives of this research were to develop new primers flanking wheat microsatellites and to position the associated loci on the wheat genome map by genetic linkage mapping in the ITMI W7984 x Opata85 recombinant inbred line (RIL) population and/or by physical mapping with cytogenetic stocks. We observed that the efficiency of marker development could be increased in wheat by creating libraries from sheared rather than enzyme-digested DNA fragments for microsatellite screening, by focusing on microsatellites with the [ATT/TAA]n motif, and by adding an untemplated G-C clamp to the 5'-end of primers. A total of 540 microsatellite-flanking primer pairs were developed, tested, and annotated from random genomic libraries. Primer pairs and associated loci were assigned identifiers prefixed with BARC (the acronym for the USDA-ARS Beltsville Agricultural Research Center) or Xbarc, respectively. A subset of 315 primer sets was used to map 347 loci. One hundred and twenty-five loci were localized by physical mapping alone. Of the 222 loci mapped with the ITMI population, 126 were also physically mapped. Considering all mapped loci, 126, 125, and 96 mapped to the A, B, and D genomes, respectively. Twenty-three of the new loci were positioned in gaps larger than 10 cM in the map based on pre-existing markers, and 14 mapped to the ends of chromosomes. The length of the linkage map was extended by 80.7 cM. Map positions were consistent for 111 of the 126 loci positioned by both genetic and physical mapping. The majority of the 15 discrepancies between genetic and physical mapping involved chromosome group 5.

Development and mapping of microsatellite (SSR) markers in wheat.

Fusarium head blight (FHB, scab) is a fungal disease of wheat and other small cereals that is found in both temperate and semi-tropical regions. FHB causes severe yield and quality losses, but the most-serious concern is the possible mycotoxin contamination of cereal food and feed. Breeding for FHB resistance by conventional selection is feasible, but tedious and expensive. This study was conducted to identify and map DNA markers associated with FHB resistance genes in wheat. A population of 364 F1-derived doubled-haploid (DH) lines from the cross ’CM-82036’ (resistant)/’Remus’ (susceptible) was evaluated for Type II resistance (spread within the spike) during 2 years under field conditions. Marker analysis was performed on 239 randomly chosen DH lines. Different marker types were applied, with an emphasis on AFLP and SSR markers. Analysis of variance, as well as simple and composite interval mapping, were applied. Three genomic regions were found significantly associated with FHB resistance. The most-prominent effect was detected on the short arm of chromosome 3B, explaining up to 60% of the phenotypic variance for Type II FHB resistance. A further QTL was located on chromosome 5A and a third one on 1B. The QTL regions on 3B and 5A were tagged with flanking SSR markers, the 1B QTL was found associated with the high-molecular-weight glutenin locus. These results indicate that FHB resistance is under control of a few major QTLs operating together with unknown numbers of minor genes. Marker-assisted selection for these major QTLs involved in FHB resistance appears feasible and should accelerate the development of resistant and agronomically improved wheat cultivars.

Molecular mapping of QTLs for Fusarium head blight resistance in spring wheat. I. Resistance to fungal spread (Type II resistance)

Genetic resistance to Fusarium head blight (FHB), caused by Fusarium graminearum, is necessary to reduce the wheat grain yield and quality losses caused by this disease. Development of resistant cultivars has been slowed by poorly adapted and incomplete resistance sources and confounding environmental effects that make screening of germplasm difficult. DNA markers for FHB resistance QTLs have been identified and may be used to speed the introgression of resistance genes into adapted germplasm. This study was conducted to identify and map additional DNA markers linked to genes controlling FHB resistance in two spring wheat recombinant inbred populations, both segregating for genes from the widely used resistance source ’Sumai 3’. The first population was from the cross of Sumai 3/Stoa in which we previously identified five resistance QTLs. The second population was from the cross of ND2603 (Sumai 3/Wheaton) (resistant)/ Butte 86 (moderately susceptible). Both populations were evaluated for reaction to inoculation with F. graminearum in two greenhouse experiments. A combination of 521 RFLP, AFLP, and SSR markers were mapped in the Sumai 3/Stoa population and all DNA markers associated with resistance were screened on the ND2603/Butte 86 population. Two new QTL on chromosomes 3AL and 6AS wer found in the ND2603/Butte 86 population, and AFLP and SSR markers were identified that explained a greater portion of the phenotypic variation compared to the previous RFLP markers. Both of the Sumai 3-derived QTL regions (on chromosomes 3BS, and 6BS) from the Sumai 3/Stoa population were associated with FHB resistance in the ND2603/Butte 86 population. Markers in the 3BS QTL region (Qfhs.ndsu-3BS) alone explain 41.6 and 24.8% of the resistance to FHB in the Sumai 3/Stoa and ND2603/Butte 86 populations, respectively. This region contains a major QTL for resistance to FHB and should be useful in marker-assisted selection.

A. D. Fjeld

Papers

DNA markers for Fusarium head blight resistance QTLs in two wheat populations