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.

A set of 114 recombinant inbred lines of the 'International Triticeae Mapping Initiative' mapping population was grown during the seasons 1997, 1998, 1999 and 2000 under several environments. Twenty morphological (glume colour, awn colour, waxiness, leaf erectness, peduncle length), agronomical (ear emergence time, flowering time, grain filling time, ear length, plant height, lodging, grain number, thousand-grain-weight, grain weight per ear, grain protein content, winter hardiness) and disease resistance (powdery mildew, yellow rust, leaf rust, fusarium) traits were studied. Not all traits were scored in each experiment. In total 210 QTLs with a LOD threshold of >2.0 (minor QTLs) were detected of which 64 reached a LOD score of >3.0 (major QTLs). Often QTLs were detected in comparable positions in different experiments. Homologous and homoeologous relationships of the detected QTLs, and already described major genes or QTLs determining the same traits in wheat or other Triticeae members, are discussed.

Mapping of quantitative trait loci determining agronomic important characters in hexaploid wheat ( Triticum aestivum L.).

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.

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

Recent epidemics of fusarium head blight (FHB), caused by Fusarium graminearum Schwabe (telomorph: Gibberella zeae), in the USA and Canada have caused severe yield and quality losses in wheat (Triticum aestivum L.). Development of resistant cultivars has been difficult because of the complex inheritance of resistance and confounding environmental effects. This study was conducted to identify and map DNA markers linked to genes associated with FHB resistance. A population of 112 F 5 -derived recombinant inbred (RI) wheat lines from the cross 'Sumai 3' (resistant)/ 'Stoa' (moderately susceptible) was evaluated in two greenhouse experiments for Type II resistance (spread within the spike). On the basis of restriction fragment length polymorphis (RFLP) marker analyses, five genomic regions were significantly (P < 0.01) associated with FHB resistance, three derived from Sumai 3 and two from Stoa. Regions on Chromosomes 3BS (from Sumai 3) and 2AL (from Stoa) were identified by interval analysis using a LOD threshold of 3.0. These two quantitative trait loci (QTL) have been assigned the gene designations QFhs.ndsu-3B and QFhs. ndsu-2A, respectively. Recombinant inbred lines with these two QTL had a median severity of 20.9%, compared with 36.2% for all RI lines. The best RFLP marker in the 3BS region explained 15.4% of the variation and a multiple regression model consisting of three QTL explained 29.5% of the variation. These results indicate that resistance to FHB is inherited in a quantitative manner and that marker-assisted selection may aid the development of FHB-resistant cultivars.

B. Moreno-Sevilla

Papers

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

RFLP mapping of QTL for fusarium head blight resistance in wheat