DNA markers have enormous potential to improve the efficiency and precision of conventional plant breeding via marker-assisted selection (MAS). The large number of quantitative trait loci (QTLs) mapping studies for diverse crops species have provided an abundance of DNA marker–trait associations. In this review, we present an overview of the advantages of MAS and its most widely used applications in plant breeding, providing examples from cereal crops. We also consider reasons why MAS has had only a small impact on plant breeding so far and suggest ways in which the potential of MAS can be realized. Finally, we discuss reasons why the greater adoption of MAS in the future is inevitable, although the extent of its use will depend on available resources, especially for orphan crops, and may be delayed in less-developed countries. Achieving a substantial impact on crop improvement by MAS represents the great challenge for agricultural scientists in the next few decades.

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Marker-assisted selection: an approach for precision plant breeding in the twenty-first century

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

Wheat (Triticum aestivum L.), with a large genome (16000 Mb) and high proportion
( 80%) of repetitive sequences, has been a difficult crop for genomics research. However, the availability of extensive cytogenetics stocks has been an asset, which facilitated
significant progress in wheat genomic research in recent years. For instance, fairly dense
molecular maps (both genetic and physical maps) and a large set of ESTs allowed
genome-wide identification of gene-rich and gene-poor regions as well as QTL including
eQTL. The availability of markers associated with major economic traits also allowed
development of major programs on marker-assisted selection (MAS) in some countries,
and facilitated map-based cloning of a number of genes/QTL. Resources for functional
genomics including TILLING and RNA interference (RNAi) along with some new
approaches like epigenetics and association mapping are also being successfully used for
wheat genomics research. BAC/BIBAC libraries for the subgenome D and some
individual chromosomes have also been prepared to facilitate sequencing of gene space.
In this brief review, we discuss all these advances in some detail, and also describe
briefly the available resources, which can be used for future genomics research in this
important crop.

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Wheat Genomics: Present Status and Future Prospects

https://execdeanagriculture.rutgers.edu/pdfs/goodman-091.pdf

Biotechnology in the developing world: a case for increased investments in orphan crops

Grain yield forms one of the key economic drivers behind a successful wheat (Triticum aestivum L) cropping enterprise and is consequently a major target for wheat breeding programmes However, due to its complex nature, little is known regarding the genetic control of grain yield A doubled-haploid population, comprising 182 individuals, produced from a cross between two cultivars ‘Trident’ and ‘Molineux’, was used to construct a linkage map based largely on microsatellite molecular makers ‘Trident’ represents a lineage of wheat varieties from southern Australia that has achieved consistently high relative grain yield across a range of environments In comparison, ‘Molineux’ would be rated as a variety with low to moderate grain yield The doubled-haploid population was grown from 2002 to 2005 in replicated field experiments at a range of environments across the southern Australian wheat belt In total, grain yield data were recorded for the population at 18 site-year combinations Grain yield components were also measured at three of these environments Many loci previously found to be involved in the control of plant height, rust resistance and ear-emergence were found to influence grain yield and grain yield components in this population An additional nine QTL, apparently unrelated to these traits, were also associated with grain yield A QTL associated with grain yield on chromosome 1B, with no significant relationship with plant height, ear-emergence or rust resistance, was detected (LOD ≥2) at eight of the 18 environments The mean yield, across 18 environments, of individuals carrying the ‘Molineux’ allele at the 1B locus was 48% higher than the mean grain yield of those lines carrying the ‘Trident’ allele at this locus Another QTL identified on chromosome 4D was also associated with overall gain yield at six of the 18 environments Of the nine grain yield QTL not shown to be associated with plant height, phenology or rust resistance, two were located near QTL associated with grain yield components A third QTL, associated with grain yield components at each of the environments used for testing, was located on chromosome 7D However, this QTL was not associated with grain yield at any of the environments The implications of these findings on marker-assisted selection for grain yield are discussed

Genetic dissection of grain yield in bread wheat. I. QTL analysis

The objectives of this study were to validate the major quantitative trait locus (QTL) for scab resistance on the short arm of chromosome 3B in bread wheat and to isolate near-isogenic lines for this QTL using marker-assisted selection (MAS). Two resistant by susceptible populations, both using ‘Ning7840’ as the source of resistance, were developed to examine the effect of the 3BS QTL in different genetic backgrounds. Data for scab resistance and simple sequence repeat (SSR) markers linked to the resistance QTL were analyzed in the F2:3 lines of one population and in the F3:4 lines of the other. Markers linked to the major QTL on chromosome 3BS in the original mapping population (‘Ning7840’/‘Clark’) were closely associated with scab resistance in both validation populations. Marker-assisted selection for the QTL with the SSR markers combined with phenotypic selection was more effective than selection based solely on phenotypic evaluation in early generations. Marker-assisted selection of the major QTL during the seedling stage plus phenotypic selection after flowering effectively identified scab resistant lines in this experiment. Near-isogenic lines for this 3BS QTL were isolated from the F6 generation of the cross ‘Ning7840’/‘IL89-7978’ based on two flanking SSR markers, Xgwm389 and Xbarc147. Based on these results, MAS for the major scab resistance QTL can improve selection efficiency and may facilitate stacking of scab resistance genes from different sources.

Validation of a major QTL for scab resistance with SSR markers and use of marker-assisted selection in wheat

Six sets of spring oat (Avena sativa L.) germplasm lines (Reg. No GP-94 to GP-121, PI 641972 to PI 641999) with lines within a set differing for tolerance to barley yellow dwarf virus (BYDV) were developed and released by the Illinois Agricultural Experiment Station of the University of Illinois and the USDA-ARS. Barley yellow dwarf virus (BYDV) infects a wide range of host species and causes economic losses in small grain cereal crops around the world (D’Arcy, 1995; Lister and Ranieri, 1995). Symptoms of BYDV infection in oats include chlorosis, blasting of florets, stunting, and reduction in root growth (Jensen and D’Arcy, 1995; Kolb et al., 1991a). Host plant resistance or tolerance (as defined by Cooper and Jones, 1983) is an important control strategy for reduction of losses due to the BYDVs (Burnett et al., 1995). The near-isogenic lines differing in tolerance to BYDV were developed for use in research on BYDV, to study the inheritance of BYDV, and for use in the discovery of molecular markers associated with genes for tolerance to BYDV. The six sets of lines (28 lines total) listed in Table 1 and released in 2003 were developed using four different BYDV tolerant parents. The four BYDV tolerant parents involved are IL86–1156, IL86–5698, IL86–6404, and Ogle. Two of the BYDV tolerant parents (IL86–5698 and IL86–6404) were released as BYDV tolerant germplasm lines (Kolb et al., 1991b), and Ogle (Brown and Jedlinski, 1983) is a well-known spring oat cultivar with good BYDV tolerance. In all crosses, Clintland 64 was the BYDV susceptible recurrent parent. Each group of lines consists of either four or six lines. Within a group the lines differ only in BYDV tolerance. The range in BYDV tolerance varies among the groups. Within a group all of the lines trace to a single F2 plant in the original cross. In 1995 and 1996, 110 BC5 lines were evaluated in randomized, inoculated hills using three replications each year. The hills were inoculated at Feekes GS 1 using viruliferous aphids [Rhopalosiphum padi (Linnaeus)] carrying BYDV-PAV-IL. The lines (plus the parents and checks) were evaluated twice in the field using three replications of paired control and BYDVPAV inoculated hills in each evaluation. The BYDV tolerance of the hills was evaluated several times each year using a scale in which 05 no symptoms and 95 very severe symptoms. The 28 lines proposed for release were selected from the total of 110 lines. Each line originated from a single BC5F4 plant. It is not known if the BYDV tolerance genes in the four tolerant parents are the same or different. These lines will be useful primarily for research purposes, but will not be useful for cultivar development. The lines have already been used for research on the detection of molecular markers associated with genes for BYDV tolerance. Small quantities of seed (#3 g) of each germplasm line are available for research and parental purposes on request to the corresponding author. The source of the germplasm should be appropriately recognized if a germplasm line contributes to the development of germplasm, a cultivar or a publication. Seed will be maintained by the Department of Crop Sciences, University of Illinois for at least 5 yr, and seed has been deposited in the USDA-ARS National Plant Germplasm System.

N.J. Smith

Papers

Validation of a major QTL for scab resistance with SSR markers and use of marker-assisted selection in wheat

Registration of six sets of near-isogenic spring oat germplasm lines differing in tolerance to Barley yellow dwarf virus

Registration of ‘Reins’ Oat

Registration of ‘Saber’ Oat

Registration of seven Barley yellow dwarf virus tolerant oat germplasm lines