Many systems for field-based, high-throughput phenotyping (FB-HTP) quantify and characterize the reflected radiation from the crop canopy to derive phenotypes, as well as infer plant function and health status. However, given the technology's nascent status, it remains unknown how biophysical and physiological properties of the plant canopy impact downstream interpretation and application of canopy reflectance data. In that light, we assessed relationships between leaf thickness and several canopy-associated traits, including normalized difference vegetation index (NDVI), which was collected via active reflectance sensors carried on a mobile FB-HTP system, carbon isotope discrimination (CID), and chlorophyll content. To investigate the relationships among traits, two distinct cotton populations, an upland (Gossypium hirsutum L.) recombinant inbred line (RIL) population of 95 lines and a Pima (G, barbaderise L.) population composed of 25 diverse cultivars, were evaluated under contrasting irrigation regimes, water-limited (WL) and well-watered pm conditions, across 3 years. We detected four quantitative trait loci (QTL) and significant variation in both populations for leaf thickness among genotypes as well as high estimates of broad-sense heritability (on average, above 0.7 for both populations), indicating a strong genetic basis for leaf thickness. Strong phenotypic correlations (maximum r = -0.73) were observed between leaf thickness and NDVI in the Pima population, but not the RIL population. Additionally, estimated genotypic correlations within the RIL population for leaf thickness with CID, chlorophyll content, and nitrogen discrimination (r(gij) = -0.32, 0.48, and 0.40, respectively) were all significant under WW but not WL conditions. Economically important fiber quality traits did not exhibit significant phenotypic or genotypic correlations with canopy traits. Overall, our results support considering variation in leaf thickness as a potential contributing factor to variation in NDVI or other canopy traits measured via proximal sensing, and as a trait that impacts fundamental physiological responses of plants.

Sunflower is grown worldwide for oil production. In Australia, sunflower is under intense competition from canola as an oil crop. Confectionery sunflower aimed for the overseas snack food market is a potential opportunity for Australian farmers due to its ability to provide off-season supply to the major market located mainly in the northern hemisphere. To serve this aim, new confectionery sunflower hybrids adapted to Australian production system with drought tolerance, large achenes, high self-fertility and rust resistance are of paramount importance. The objectives of this project were to understand the genetic inheritance and genetic linkage relationships of the above traits and also to identify linked DNA markers with the potential for marker-assisted selection (MAS). The inheritance of achene-length was studied in a 12 x 12 diallel and a 14 x 12 North Carolina design II (NC II) mating design. Achene-length was evaluated under three environments for each mating design. Genetic correlation among all five achene-size related traits (achene-length, -width, - thickness and also kernel-length and -width) and 100-achene weight were moderate to high. Narrow-and broad-sense heritability for achene-length was moderate to high and similar for each design. The general combining ability (GCA) and maternal effects were found to be the main genetic factors controlling achene-length and each accounted for around 45% of the total genotypic variance. The inheritance of self-fertility (SF) was assessed with the same 12 x 12 diallel mating design evaluated in two environments. The 12 parents also displayed various levels of SF in addition to a wide range of achene-length. Negative genetic correlations between SF and all five achene-size related traits and 100-achene weight were observed. Modelling achene-length as a covariate revealed that certain pre-pollination floret characteristics represented by achene-length at maturity strongly affects SF in sunflower. When the effect of achene-length was removed statistically as a covariate, the specific combining ability (SCA) effect increased dramatically and became the major factor (other than pre-pollination floret characteristics) for SF determination and accounted for 65% of the total variance. Long achene genotypes tended to have low SF and a positive SCA effect was observed more frequently in F1 hybrids that involved small achene lines. The broad sense heritability was moderate (0.663 ± 0.017), while the estimate of narrow-sense heritability was nearly zero. A segregating F6:7 recombinant inbred line population with 239 progeny was developed from a cross between HaR4, a low delta (Δ), high transpiration efficiency (TE), sunflower line with rust resistance but relatively low SF, and SA52 with all the characteristics in the opposite direction. The population was evaluated in two environments for three TE-related traits including Δ, specific leaf weight (SLW) and chlorophyll content (CC) and four agronomic traits i.e. days to flowering (DTF), plant height (PlantH), SF and rust resistance (RustR). A linkage map 1074.6 cM in length with 138 SSR and 37 ISSR markers consisting of 19 linkage groups was constructed. Spatially adjusted BLUPs were used in QTL analysis for individual and combined environments. Altogether, 10 QTL were identified for Δ, SLW and CC at individual environments, and 7 were detected by a combined analysis. Sixteen QTL were identified for 4 agronomic traits and 14 of them were confirmed by a combined analysis. Significant linkage among all three TE related traits was discovered on linkage group 4 (LG4), where alleles from one parent had the same direction of influence on TE which suggested either coupling phase linkage or pleiotropy. QTL for SF and RustR were closely linked on LG13. An F2 population with 502 progeny developed from a cross between Jumbo, a large achene confectionery sunflower line, and RIL25, an oilseed small achene line, was evaluated for five achene-size related traits in a single field trial. Using a subset of 178 progeny a framework genetic linkage map, 899.7 cM in length, containing 128 SSR markers and 23 ISSR markers was constructed with 18 linkage groups. Based on the results of a simulated QTL analysis, a modified selective genotyping strategy was employed for QTL analysis with 178 F2 individuals (128 randomly selected, 25 shortest achene F2’s and 25 longest achene F2’s). Altogether 18 achene-size related QTL with small effects were identified. Achene-size related genes characteristically expressed additive gene action although several alleles were partially recessive towards the large achene parent. The 18 identified achene-size related QTL were validated in the same diallel mating experiment mentioned above. Significant marker-trait associations were detected for 15 QTL. In addition to 12 significant alleles detected from the F2 population, 12 additional alleles associated with achene-size traits were revealed after the analysis with the diallel. These markers are ready to be used in MAS for confectionery sunflower breeding. Great steps have been made in obtaining essential knowledge of inheritance and linkage of target traits for breeding confectionery sunflower adapted to Australian production environments. The identified markers can be used in MAS and further enhance the breeding process.

Sunflower is grown worldwide for oil production. In Australia, sunflower is under intense competition from canola as an oil crop. Confectionery sunflower aimed for the overseas snack food market is a potential opportunity for Australian farmers due to its ability to provide off-season supply to the major market located mainly in the northern hemisphere. To serve this aim, new confectionery sunflower hybrids adapted to Australian production system with drought tolerance, large achenes, high self-fertility and rust resistance are of paramount importance. The objectives of this project were to understand the genetic inheritance and genetic linkage relationships of the above traits and also to identify linked DNA markers with the potential for marker-assisted selection (MAS). The inheritance of achene-length was studied in a 12 x 12 diallel and a 14 x 12 North Carolina design II (NC II) mating design. Achene-length was evaluated under three environments for each mating design. Genetic correlation among all five achene-size related traits (achene-length, -width, - thickness and also kernel-length and -width) and 100-achene weight were moderate to high. Narrow-and broad-sense heritability for achene-length was moderate to high and similar for each design. The general combining ability (GCA) and maternal effects were found to be the main genetic factors controlling achene-length and each accounted for around 45% of the total genotypic variance. The inheritance of self-fertility (SF) was assessed with the same 12 x 12 diallel mating design evaluated in two environments. The 12 parents also displayed various levels of SF in addition to a wide range of achene-length. Negative genetic correlations between SF and all five achene-size related traits and 100-achene weight were observed. Modelling achene-length as a covariate revealed that certain pre-pollination floret characteristics represented by achene-length at maturity strongly affects SF in sunflower. When the effect of achene-length was removed statistically as a covariate, the specific combining ability (SCA) effect increased dramatically and became the major factor (other than pre-pollination floret characteristics) for SF determination and accounted for 65% of the total variance. Long achene genotypes tended to have low SF and a positive SCA effect was observed more frequently in F1 hybrids that involved small achene lines. The broad sense heritability was moderate (0.663 ± 0.017), while the estimate of narrow-sense heritability was nearly zero. A segregating F6:7 recombinant inbred line population with 239 progeny was developed from a cross between HaR4, a low delta (Δ), high transpiration efficiency (TE), sunflower line with rust resistance but relatively low SF, and SA52 with all the characteristics in the opposite direction. The population was evaluated in two environments for three TE-related traits including Δ, specific leaf weight (SLW) and chlorophyll content (CC) and four agronomic traits i.e. days to flowering (DTF), plant height (PlantH), SF and rust resistance (RustR). A linkage map 1074.6 cM in length with 138 SSR and 37 ISSR markers consisting of 19 linkage groups was constructed. Spatially adjusted BLUPs were used in QTL analysis for individual and combined environments. Altogether, 10 QTL were identified for Δ, SLW and CC at individual environments, and 7 were detected by a combined analysis. Sixteen QTL were identified for 4 agronomic traits and 14 of them were confirmed by a combined analysis. Significant linkage among all three TE related traits was discovered on linkage group 4 (LG4), where alleles from one parent had the same direction of influence on TE which suggested either coupling phase linkage or pleiotropy. QTL for SF and RustR were closely linked on LG13. An F2 population with 502 progeny developed from a cross between Jumbo, a large achene confectionery sunflower line, and RIL25, an oilseed small achene line, was evaluated for five achene-size related traits in a single field trial. Using a subset of 178 progeny a framework genetic linkage map, 899.7 cM in length, containing 128 SSR markers and 23 ISSR markers was constructed with 18 linkage groups. Based on the results of a simulated QTL analysis, a modified selective genotyping strategy was employed for QTL analysis with 178 F2 individuals (128 randomly selected, 25 shortest achene F2’s and 25 longest achene F2’s). Altogether 18 achene-size related QTL with small effects were identified. Achene-size related genes characteristically expressed additive gene action although several alleles were partially recessive towards the large achene parent. The 18 identified achene-size related QTL were validated in the same diallel mating experiment mentioned above. Significant marker-trait associations were detected for 15 QTL. In addition to 12 significant alleles detected from the F2 population, 12 additional alleles associated with achene-size traits were revealed after the analysis with the diallel. These markers are ready to be used in MAS for confectionery sunflower breeding. Great steps have been made in obtaining essential knowledge of inheritance and linkage of target traits for breeding confectionery sunflower adapted to Australian production environments. The identified markers can be used in MAS and further enhance the breeding process.

Sunflower is grown worldwide for oil production. In Australia, sunflower is under intense competition from canola as an oil crop. Confectionery sunflower aimed for the overseas snack food market is a potential opportunity for Australian farmers due to its ability to provide off-season supply to the major market located mainly in the northern hemisphere. To serve this aim, new confectionery sunflower hybrids adapted to Australian production system with drought tolerance, large achenes, high self-fertility and rust resistance are of paramount importance. The objectives of this project were to understand the genetic inheritance and genetic linkage relationships of the above traits and also to identify linked DNA markers with the potential for marker-assisted selection (MAS). The inheritance of achene-length was studied in a 12 x 12 diallel and a 14 x 12 North Carolina design II (NC II) mating design. Achene-length was evaluated under three environments for each mating design. Genetic correlation among all five achene-size related traits (achene-length, -width, - thickness and also kernel-length and -width) and 100-achene weight were moderate to high. Narrow-and broad-sense heritability for achene-length was moderate to high and similar for each design. The general combining ability (GCA) and maternal effects were found to be the main genetic factors controlling achene-length and each accounted for around 45% of the total genotypic variance. The inheritance of self-fertility (SF) was assessed with the same 12 x 12 diallel mating design evaluated in two environments. The 12 parents also displayed various levels of SF in addition to a wide range of achene-length. Negative genetic correlations between SF and all five achene-size related traits and 100-achene weight were observed. Modelling achene-length as a covariate revealed that certain pre-pollination floret characteristics represented by achene-length at maturity strongly affects SF in sunflower. When the effect of achene-length was removed statistically as a covariate, the specific combining ability (SCA) effect increased dramatically and became the major factor (other than pre-pollination floret characteristics) for SF determination and accounted for 65% of the total variance. Long achene genotypes tended to have low SF and a positive SCA effect was observed more frequently in F1 hybrids that involved small achene lines. The broad sense heritability was moderate (0.663 ± 0.017), while the estimate of narrow-sense heritability was nearly zero. A segregating F6:7 recombinant inbred line population with 239 progeny was developed from a cross between HaR4, a low delta (Δ), high transpiration efficiency (TE), sunflower line with rust resistance but relatively low SF, and SA52 with all the characteristics in the opposite direction. The population was evaluated in two environments for three TE-related traits including Δ, specific leaf weight (SLW) and chlorophyll content (CC) and four agronomic traits i.e. days to flowering (DTF), plant height (PlantH), SF and rust resistance (RustR). A linkage map 1074.6 cM in length with 138 SSR and 37 ISSR markers consisting of 19 linkage groups was constructed. Spatially adjusted BLUPs were used in QTL analysis for individual and combined environments. Altogether, 10 QTL were identified for Δ, SLW and CC at individual environments, and 7 were detected by a combined analysis. Sixteen QTL were identified for 4 agronomic traits and 14 of them were confirmed by a combined analysis. Significant linkage among all three TE related traits was discovered on linkage group 4 (LG4), where alleles from one parent had the same direction of influence on TE which suggested either coupling phase linkage or pleiotropy. QTL for SF and RustR were closely linked on LG13. An F2 population with 502 progeny developed from a cross between Jumbo, a large achene confectionery sunflower line, and RIL25, an oilseed small achene line, was evaluated for five achene-size related traits in a single field trial. Using a subset of 178 progeny a framework genetic linkage map, 899.7 cM in length, containing 128 SSR markers and 23 ISSR markers was constructed with 18 linkage groups. Based on the results of a simulated QTL analysis, a modified selective genotyping strategy was employed for QTL analysis with 178 F2 individuals (128 randomly selected, 25 shortest achene F2’s and 25 longest achene F2’s). Altogether 18 achene-size related QTL with small effects were identified. Achene-size related genes characteristically expressed additive gene action although several alleles were partially recessive towards the large achene parent. The 18 identified achene-size related QTL were validated in the same diallel mating experiment mentioned above. Significant marker-trait associations were detected for 15 QTL. In addition to 12 significant alleles detected from the F2 population, 12 additional alleles associated with achene-size traits were revealed after the analysis with the diallel. These markers are ready to be used in MAS for confectionery sunflower breeding. Great steps have been made in obtaining essential knowledge of inheritance and linkage of target traits for breeding confectionery sunflower adapted to Australian production environments. The identified markers can be used in MAS and further enhance the breeding process.

Sunflower is grown worldwide for oil production. In Australia, sunflower is under intense competition from canola as an oil crop. Confectionery sunflower aimed for the overseas snack food market is a potential opportunity for Australian farmers due to its ability to provide off-season supply to the major market located mainly in the northern hemisphere. To serve this aim, new confectionery sunflower hybrids adapted to Australian production system with drought tolerance, large achenes, high self-fertility and rust resistance are of paramount importance. The objectives of this project were to understand the genetic inheritance and genetic linkage relationships of the above traits and also to identify linked DNA markers with the potential for marker-assisted selection (MAS). The inheritance of achene-length was studied in a 12 x 12 diallel and a 14 x 12 North Carolina design II (NC II) mating design. Achene-length was evaluated under three environments for each mating design. Genetic correlation among all five achene-size related traits (achene-length, -width, - thickness and also kernel-length and -width) and 100-achene weight were moderate to high. Narrow-and broad-sense heritability for achene-length was moderate to high and similar for each design. The general combining ability (GCA) and maternal effects were found to be the main genetic factors controlling achene-length and each accounted for around 45% of the total genotypic variance. The inheritance of self-fertility (SF) was assessed with the same 12 x 12 diallel mating design evaluated in two environments. The 12 parents also displayed various levels of SF in addition to a wide range of achene-length. Negative genetic correlations between SF and all five achene-size related traits and 100-achene weight were observed. Modelling achene-length as a covariate revealed that certain pre-pollination floret characteristics represented by achene-length at maturity strongly affects SF in sunflower. When the effect of achene-length was removed statistically as a covariate, the specific combining ability (SCA) effect increased dramatically and became the major factor (other than pre-pollination floret characteristics) for SF determination and accounted for 65% of the total variance. Long achene genotypes tended to have low SF and a positive SCA effect was observed more frequently in F1 hybrids that involved small achene lines. The broad sense heritability was moderate (0.663 ± 0.017), while the estimate of narrow-sense heritability was nearly zero. A segregating F6:7 recombinant inbred line population with 239 progeny was developed from a cross between HaR4, a low delta (Δ), high transpiration efficiency (TE), sunflower line with rust resistance but relatively low SF, and SA52 with all the characteristics in the opposite direction. The population was evaluated in two environments for three TE-related traits including Δ, specific leaf weight (SLW) and chlorophyll content (CC) and four agronomic traits i.e. days to flowering (DTF), plant height (PlantH), SF and rust resistance (RustR). A linkage map 1074.6 cM in length with 138 SSR and 37 ISSR markers consisting of 19 linkage groups was constructed. Spatially adjusted BLUPs were used in QTL analysis for individual and combined environments. Altogether, 10 QTL were identified for Δ, SLW and CC at individual environments, and 7 were detected by a combined analysis. Sixteen QTL were identified for 4 agronomic traits and 14 of them were confirmed by a combined analysis. Significant linkage among all three TE related traits was discovered on linkage group 4 (LG4), where alleles from one parent had the same direction of influence on TE which suggested either coupling phase linkage or pleiotropy. QTL for SF and RustR were closely linked on LG13. An F2 population with 502 progeny developed from a cross between Jumbo, a large achene confectionery sunflower line, and RIL25, an oilseed small achene line, was evaluated for five achene-size related traits in a single field trial. Using a subset of 178 progeny a framework genetic linkage map, 899.7 cM in length, containing 128 SSR markers and 23 ISSR markers was constructed with 18 linkage groups. Based on the results of a simulated QTL analysis, a modified selective genotyping strategy was employed for QTL analysis with 178 F2 individuals (128 randomly selected, 25 shortest achene F2’s and 25 longest achene F2’s). Altogether 18 achene-size related QTL with small effects were identified. Achene-size related genes characteristically expressed additive gene action although several alleles were partially recessive towards the large achene parent. The 18 identified achene-size related QTL were validated in the same diallel mating experiment mentioned above. Significant marker-trait associations were detected for 15 QTL. In addition to 12 significant alleles detected from the F2 population, 12 additional alleles associated with achene-size traits were revealed after the analysis with the diallel. These markers are ready to be used in MAS for confectionery sunflower breeding. Great steps have been made in obtaining essential knowledge of inheritance and linkage of target traits for breeding confectionery sunflower adapted to Australian production environments. The identified markers can be used in MAS and further enhance the breeding process.

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