Indirect Selection Tool Research Articles

Progress and prospects of marker assisted backcrossing as a tool in crop breeding programs

Marker assisted backcrossing (MAB) is one of the most anticipated and frequently cited benefits of molecular markers as indirect selection tools in breeding programs. However, routine implementations of MAB in ongoing plant breeding programs are still scarce. Currently MAB of single gene is perhaps the most powerful approach that uses DNA markers effectively. Improvement of quantitative traits loci (QTLs) through MAB resulted to variable results ranging from limited success and/or even a failure to a few highly successful stories. A major constraint to the implementation of MAB in pragmatic breeding programs has been the high relative cost compared to conventional phenotypic selection. It is a popular misconception that a ‘DNA fingerprint’ is always to be preferred. To be useful to plant breeders, gains made from MAB must be more cost-effective than gains through traditional breeding or MAB must generate significant time savings, which justifies the additional cost involved. Currently, most national agricultural research systems (NARS) in Africa have either no or very limited facilities, skilled manpower, and financing for integrating molecular markers as part of their breeding programs. Therefore, conventional breeding methods remain the main option for NARS for many years to come, but targeted use of MAB may become a supplement if well-validated markers are developed or available through collaboration with the international agricultural research centers. This paper provides detail review of the current literature on MAB, including requirements and selected experimental results.

The Potential of Using Spectral Reflectance Indices to Estimate Yield in Wheat Grown Under Reduced Irrigation

The objectives of this research were to study the association in bread wheat between spectral reflectance indices (SRIs) and grain yield, estimate their heritability, and correlated response to selection (CR) for grain yield estimated from SRIs under reduced irrigation conditions. Reflectance was measured at three different growth stages (booting, heading and grainfilling) and five SRIs were calculated, namely normalized difference vegetation index (NDVI), simple ratio (SR), water index (WI), normalized water index-1 (NWI-1), and normalized water index-2 (NWI-2). Three field experiments were conducted (each with 30 advanced lines) in three different years. Two reduced irrigation environments were created: (1) one-irrigation level (pre-planting), and (2) two-irrigation level (pre-planting and at booting stage), both representing levels of reduced moisture. Maximum yield levels in the experimental zone were generally obtained with 4–6 irrigations. Genotypic variations for all SRIs were significant. Three NIR (near infrared radiation) based indices (WI, NWI-1, and NWI-2) gave the highest level of association (both phenotypic and genotypic) with grain yield under both reduced irrigation environments. Use of the mean SRI values averaged over growth stages and the progressive integration of SRIs from booting to grainfilling increased the capacity to explain variation among genotypes for yield under these reduced irrigation conditions. A higher level of broad-sense heritability was found with the two-irrigation environment (0.80) than with the one-irrigation environment (0.63). Overall, 50% to 75% of the 12.5% highest yielding genotypes, and 50% to 87% of the 25% highest yielding genotypes were selected when the NWI-2 index was applied as an indirect selection tool. Strong genetic correlations, moderate to high heritability, a correlated response for grain yield close to direct selection for grain yield, and a very high efficiency of selecting superior genotypes indicate the potential of using these three SRIs in breeding programs for selecting increased genetic gains in grain yield under reduced irrigation conditions.

Spectral Reflectance Indices as a Potential Indirect Selection Criteria for Wheat Yield under Irrigation

The objectives of this study were to assess the potential of using spectral reflectance indices (SRI) as an indirect selection tool to differentiate spring wheat (Triticum aestivum L.) genotypes for grain yield under irrigated conditions. This paper demonstrates only the first step in using the SRI as indirect selection criteria by reporting genetic variation for SRI among genotypes, the effect of phenology and year on SRI and their interaction with genotypes, and the correlations between SRI and grain yield and yield components of wheat. Three field experiments—15 CIMMYT globally adapted genotypes (GHIST), 25 random F3–derived lines (RLs1), and 36 random F3–derived lines (RLs2)—were conducted under irrigated conditions at the CIMMYT research station in northwest Mexico in three different years. Five previously developed SRI (photochemical reflectance index [PRI], water index [WI], red normalized difference vegetation index [RNDVI], green normalized difference vegetation index [GNDVI], simple ratio [SR]) and two newly calculated SRI (normalized water index‐1 [NWI‐1] and normalized water index‐2 [NWI‐2]) were evaluated in the experiments. In general, genotypic variation for all the indices was significant. Near infrared radiation (NIR)–based indices (WI, NWI‐1, NWI‐2) gave the highest levels of association with grain yield during the 3 yr of the study. A clear trend for higher association between grain yield and the NIR‐based indices was observed at heading and grainfilling than at booting. Overall, NIR‐based indices were more consistent and differentiated grain yield more effectively compared to the other indices. The results demonstrated the potential of using SRI as a tool in breeding programs for selecting for increased genetic gains for yield.

Mapping quantitative trait loci and marker assisted selection for the improvement of drought tolerance in rice

Drought stress is a major constraint to rice production especially in rainfed ecosystems. The development of drought tolerant rice cultivars through conventional breeding has met with little success. The complexity of drought tolerance mechanism(s) and the difficulty in incorporation of physiological selection criteria in breeding programmes are important reasons for this lack of progress. Deep and thick roots enable rice plants to access deep soil moisture and help to avoid drought. Capacity for osmotic adjustment (OA) helps to maintain turgor under water stress and sustains growth under declining soil moisture. Both root traits and OA are difficult to phenotype in large segregating progenies. Quantitative trait loci (QTL) mapping combined with marker-assisted selection (MAS) approach offers a tool for indirect selection of complex traits such as drought tolerance. Molecular markers linked to various root traits and OA have been mapped in rice. Consistent QTL linked to root traits and OA have been identified thus enabling MAS of these traits. However, the value of these QTL have to be tested under field conditions in the target ecosystems using near isogenic lines. QTL linked to field drought tolerance in terms of grain yield under stress have been mapped recently. QTL for root traits overlapped with QTL for drought tolerance in the field. Identification and introgression of such QTL into high yielding elite cultivars will lead to increase in rice production in drought- prone rainfed ecosystems. Drought stress is a major constraint to rice production especially in rainfed ecosystems. The development of drought tolerant rice cultivars through conventional breeding has met with little success. The complexity of drought tolerance mechanism(s) and the difficulty in incorporation of physiological selection criteria in breeding programmes are important reasons for this lack of progress. Deep and thick roots enable rice plants to access deep soil moisture and help to avoid drought. Capacity for osmotic adjustment (OA) helps to maintain turgor under water stress and sustains growth under declining soil moisture. Both root traits and OA are difficult to phenotype in large segregating progenies. Quantitative trait loci (QTL) mapping combined with marker-assisted selection (MAS) approach offers a tool for indirect selection of complex traits such as drought tolerance. Molecular markers linked to various root traits and OA have been mapped in rice. Consistent QTL linked to root traits and OA have been identified thus enabling MAS of these traits. However, the value of these QTL have to be tested under field conditions in the target ecosystems using near isogenic lines. QTL linked to field drought tolerance in terms of grain yield under stress have been mapped recently. QTL for root traits overlapped with QTL for drought tolerance in the field. Identification and introgression of such QTL into high yielding elite cultivars will lead to increase in rice production in drought- prone rainfed ecosystems.

Genotypic variation of gas exchange parameters and carbon isotope discrimination in winter wheat

Summary Carbon isotope discrimination (Δ) has been suggested as an indirect selection tool for plant water use efficiency and yield potential in wheat ( Triticum aestivum L.). Plant available soil water content (PASW) and vapor pressure deficit (VPD) are among some important factors affecting gas exchange and Δ. A two-year field experiment was conducted to (1) investigate the differences in gas exchange parameters: net CO 2 assimilation rate (An), stomatal conductance (Gs), intercellular CO 2 concentration (Ci), An/Ci, transpiration rate (E), water use efficiency (WUE), and Δ between older and newer cultivars in winter wheat; and (2) determine the relationships between Δ and gas exchange parameters, WUE and grain yield as influenced by PASW and VPD. Differences in An and An/Ci between the two years was influenced more by PASW conditions than by cultivar. In general, WUE decreased in all cultivars when PASW

Aspergillus Colonization and Aflatoxin Contamination in Peanut Genotypes with Resistance to Other Fungal Pathogens.

Indirect selection tools would be valuable in the development of peanut (Arachis hypogaea) cultivars with resistance to aflatoxin contamination. The objective of this study was to determine whether resistance to other fungi could be used as an indirect selection tool for resistance to colonization of peanut by Aspergillus flavus group fungi or aflatoxin contamination. Nine peanut genotypes with resistance to late leaf spot (Cercosporidium personatum) or white mold (Sclerotium rolfsii) were evaluated for 2 years at Tifton, GA, and Yuma, AZ. Plots were subjected to late-season heat and drought stress. None of the genotypes exhibited less colonization of shells or kernels by A. flavus group fungi than cv. Florunner when tested in Georgia or Arizona. None of the genotypes showed a reduced level of aflatoxin contamination in comparison to Florunner at either location. These results indicate that the mechanisms of resistance to other fungi operating in these genotypes are not effective in providing resistance to colonization by A. flavus group fungi or reducing aflatoxin contamination. Therefore, resistance to these fungi cannot be used as an indirect selection tool for resistance to aflatoxin contamination.

Low aromatic amino acid concentrations in leaf proteins determine resistance to Frankliniella occidentalis in four vegetable crops

AbstractAnalysis of total aromatic amino acid (free and bound) in some cucumber accessions selected previously for resistance to western flower thrips, Frankliniella occidentalis (Pergande) [Thysanoptera: Thripidae], indicated that low concentrations of these essential nutrients, relative to total leaf protein, were correlated with a reduction in damage by the insect. Further analysis of samples of four important horticultural crops (lettuce, tomato, pepper and cucumber) with unknown levels of resistance to thrips showed a significant genotypic variation in the concentrations of total aromatic amino acids relative to the total leaf protein. Accessions from each crop with low or high concentrations of aromatic amino acids in proteins were exposed to thrips larvae. Regression analysis showed a highly significant positive correlation between aromatic amino acid concentration in leaf protein and thrips damage, regardless of crop species. It is concluded that higher concentrations of aromatic amino acids in plant proteins are important for successful thrips development. These results provide plant breeders with a promising tool for indirect selection without using undesirable insect bioassays.