Recognizing the enormous potential of DNA markers in plant breeding, many agricultural research centers and plant breeding institutes have adopted the capacity for marker development and marker-assisted selection (MAS). However, due to rapid developments in marker technology, statistical methodology for identifying quantitative trait loci (QTLs) and the jargon used by molecular biologists, the utility of DNA markers in plant breeding may not be clearly understood by non-molecular biologists. This review provides an introduction to DNA markers and the concept of polymorphism, linkage analysis and map construction, the principles of QTL analysis and how markers may be applied in breeding programs using MAS. This review has been specifically written for readers who have only a basic knowledge of molecular biology and/or plant genetics. Its format is therefore ideal for conventional plant breeders, physiologists, pathologists, other plant scientists and students.

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An introduction to markers, quantitative trait loci (QTL) mapping and marker-assisted selection for crop improvement: The basic concepts

Asian rice, Oryza sativa is a cultivated, inbreeding species that feeds over half of the world ’ s population. Understanding the genetic basis of diverse physiological, developmental, and morphological traits provides the basis for improving yield, quality and sustainability of rice. Here we show the results of a genome-wide association study based on genotyping 44,100 SNP variants across 413 diverse accessions of O. sativa collected from 82 countries that were systematically phenotyped for 34 traits. Using cross-population-based mapping strategies, we identifi ed dozens of common variants infl uencing numerous complex traits. Signifi cant heterogeneity was observed in the genetic architecture associated with subpopulation structure and response to environment. This work establishes an open-source translational research platform for genome-wide association studies in rice that directly links molecular variation in genes and metabolic pathways with the germplasm resources needed to accelerate varietal development and crop improvement.

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Genome-wide association mapping reveals a rich genetic architecture of complex traits in Oryza sativa

There has been limited success over the past 30 yr in the development of superior soybean cultivars [Glycine max (L.) Merr] with insect resistance. Success may be hampered by the quantitative nature of resistance and by linkage drag from resistant plant introduction (Pl) donor parents. Soybean insect resistance quantitative trait loci (SIR QTLs) have been identified from PI 229358 and PI 171451 by restriction fragment length polymorphism (RFLP) analysis. The objective of this study was to tag the SIR QTLs from PI 229358 with simple sequence repeat (SSR) markers and to determine the extent to which the SIR QTLs have been introgressed in registered cultivars, germplasm releases, or breeding lines that have resistance derived from this PI or from PI 171451. Marker analysis defined intervals by 5 centimorgans (cM) or less for a SIR QTL on linkage group D1b (SIR-D1b), and for SIR-G, SIR-H, and SIR-M. SIR QTLs were tracked through pedigrees by evaluating the inheritance of PI alleles at marker loci tightly linked to the QTLs during the phenotypic selection for insect resistance. It was inferred that at least 13 of the 15 SIR genotypes studied had introgressed SIR-M. PI genome introgression around SIR-M was measured to assess linkage drag. Some genotypes exhibited a dramatic reduction in the amount of linked PI genome, which likely occurred in response to phenotypic selection for agronomic performance as a means of reducing linkage drag. Only a few genotypes were inferred to possess SIR-G or SIR-H, and no genotypes possessed SIR-D1b. The results of this study indicate that marker-assisted selection for SIR QTLs is needed to introgress these loci into elite genetic backgrounds.

http://parrottlab.uga.edu/parrottlab/Publications/Narveletal2001.pdf

A retrospective DNA marker assessment of the development of insect resistant soybean

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

The improvement of crop yield has been possible through the indirect manipulation of quantitative trait loci (QTLs) that control heritable variability of the traits and physiological mechanisms that determine biomass production and its partitioning. This article surveys how QTL-based approaches

Quantitative Trait Loci and Crop Performance under Abiotic Stress: Where Do We Stand?

Three physiological traits that may affect performance of soybean [Glycine max (L.) Merr.] when soil water availability is limiting are (i) water use efficiency (WUE), (ii) regulation of whole plant water use in response to soil water content, and (iii) leaf epidermal conductance (ge) when stomata are closed. Six soybean plant introductions (PIs), eight breeding lines derived from them, and nine cultivars were compared for variability in these three traits during vegetative growth in two greenhouse studies. In the first experiment, whole plant water use, normalized both to plant size and evaporative demand (the normalized transpiration ratio, NTR), was monitored during a 10-d cycle of gradually increasing drought stress and then for an additional 2 d following rewatering. The critical soil water content at which each plant began to reduce its water use (FTSWC), was determined. The WUE was estimated as the ratio of total plant dry weight to total water used. In the second experiment, ge was determined for these same 23 genotypes by measuring leaf water vapor exchange after a 36-h dark adaptation. Substantial variation was found among genotypes for WUE, FTSWC, ge, and also the extent to which NTR recovered on rewatering. Generally, adapted cultivars had greater WUE and lower ge than did PIs. However, PI 471938 and its progeny N98-7264 were clear exceptions to this trend. An unexpected finding was that WUE was significantly negatively correlated with ge across genotypes.

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Genotypic Variation for Three Physiological Traits Affecting Drought Tolerance in Soybean

Asian soybean rust (ASR), caused by Phakopsora pachyrhizi Syd., is a widespread disease of soybean [Glycine max (L.) Merr.] with the potential to cause serious economic losses. The objective of this study was to genetically map red-brown lesion type resistance from the cultivar Hyuuga. A population of 117 recombinant inbred lines (RILs) from the cross of Dillon (tan lesion) x Hyuuga (red-brown [RB] lesion) was rated for ASR lesion type in the field and inoculated with P. pachyrhizi in the greenhouse. The RB resistance gene mapped between Satt460 and Satt307 on linkage group (LG)-C2. When field severity and lesion density in the greenhouse were mapped, the Rpp?(Hyuuga) locus explained 22 and 15% of the variation, respectively (P < 0.0001). The RB lesion type was associated with lower severity, fewer lesions, and reduced sporulation when compared to the tan lesion type. A population from the cross of Benning x Hyuuga was screened with simple sequence repeat (SSR) markers in the region on LG-C2 flanked by Satt134 and Satt460. Genotype at these markers was used to predict lesion type when the plants were exposed to P. pachyrhizi. All the lines selected for the Hyuuga markers in this interval had the RB lesion type and they averaged approximately 50% fewer lesions compared to lines with tan lesions. Sporulation was only detected in 6% of the RB lines compared with 100% of the tan lines. Marker-assisted selection can be used to develop soybean cultivars with the Rpp?(Hyuuga) gene for resistance to ASR.

Mapping and Confirmation of the ‘Hyuuga’ Red-Brown Lesion Resistance Gene for Asian Soybean Rust

In soybean [Glycine max (L.) Merr.], there is limited and inconsistent information on the confirmation of previously reported QTL. The objectives of this study were to: (i) confirm previously reported QTL for seed protein, seed oil, and seed weight in an independent population of PI97100 × 'Coker 237' with the same RFLP markers and (ii) verify previously reported QTL in an independent population of 'Young' × PI416937 for the same seed traits using SSR markers mapped in the same region as the original RFLP markers. Each population consisted of 176 F 24 lines and was grown in randomized complete block trials in two or three different environments. Single-factor analysis of variance was used to verify the QTL that had significant (P ≤ 0.01) associations. In the PI97100 × Coker 237 population, two (cqProt-001 and cqProt-002) of four previously described QTL for seed protein, two (cqOil-001 and cqOil-002) of three QTL for oil content, and none of three QTL for seed weight were confirmed in the independent population. In the Young × PI416937 population, none of the three previously reported QTL for protein was confirmed. One (cqOil-003) of three QTL for oil content and two (cqSd wt-001 and cqSd wt-002) of three QTL for seed weight were verified. The unconfirmed QTL may have been false positive or they may have been specific for the sample of lines used in the original populations. These results confirm the necessity of validating QTL in parallel populations before utilizing them in a plant improvement program.

Validation and Designation of Quantitative Trait Loci for Seed Protein, Seed Oil, and Seed Weight from Two Soybean Populations

A transgenic line of the soybean ‘Jack’, Glycine max (L.) Merrill, expressing a synthetic cry1Ac gene from Bacillus thuringiensis variety kurstaki (Jack-Bt), was evaluated for resistance to four lepidopteran pests in the field. Jack-Bt and genotypes serving as susceptible and resistant controls were planted in field cages and artificially infested with larvae of corn earworm, Helicoverpa zea (Boddie), and velvetbean caterpillar, Anticarsia gemmatalis (Hubner), in 1996, 1997, and 1998, and also with soybean looper, Pseudoplusia includens (Walker), in 1996. Susceptible controls included Jack (1996–1998), ‘Cobb’ (1996), and Jack-HPH (1996). GatIR 81–296 was used as the resistant control in all 3 yr. Compared with untransformed Jack, Jack-Bt showed three to five times less defoliation from corn earworm and eight to nine times less damage from velvetbean caterpillar. Defoliation of GatIR 81–296 was intermediate between that of Jack and Jack-Bt for corn earworm, and similar to that of Jack for velveltbean caterpillar. Jack-Bt exhibited significant, but lower resistance to soybean looper. Jack-Bt also showed four times greater resistance than Jack to natural infestations of lesser cornstalk borer, Elasmopalpus lignosellus (Zeller), in conventional field plots at two locations in 1998. Data from these experiments suggest that expression of this cry1Ac construct in soybean should provide adequate levels of resistance to several lepidopteran pests under field conditions.

https://bioone.org/journals/Journal-of-Economic-Entomology/volume-93/issue-3/0022-0493-93.3.613/Field-Evaluation-of-Soybean-Engineered-with-a-Synthetic-cry1Ac-Transgene/10.1603/0022-0493-93.3.613.pdf

Field Evaluation of Soybean Engineered with a Synthetic cry1Ac Transgene for Resistance to Corn Earworm, Soybean Looper, Velvetbean Caterpillar (Lepidoptera: Noctuidae), and Lesser Cornstalk Borer (Lepidoptera: Pyralidae)

H. Roger Boerma

Papers

A retrospective DNA marker assessment of the development of insect resistant soybean

Genotypic Variation for Three Physiological Traits Affecting Drought Tolerance in Soybean

Mapping and Confirmation of the ‘Hyuuga’ Red-Brown Lesion Resistance Gene for Asian Soybean Rust

Validation and Designation of Quantitative Trait Loci for Seed Protein, Seed Oil, and Seed Weight from Two Soybean Populations

Field Evaluation of Soybean Engineered with a Synthetic cry1Ac Transgene for Resistance to Corn Earworm, Soybean Looper, Velvetbean Caterpillar (Lepidoptera: Noctuidae), and Lesser Cornstalk Borer (Lepidoptera: Pyralidae)