Nested Association Research Articles

Origin Specific Genomic Selection: A Simple Process To Optimize the Favorable Contribution of Parents to Progeny.

Modern crop breeding is in constant demand for new genetic diversity as part of the arms race with genetic gain. The elite gene pool has limited genetic variation and breeders are trying to introduce novelty from unadapted germplasm, landraces and wild relatives. For polygenic traits, currently available approaches to introgression are not ideal, as there is a demonstrable bias against exotic alleles during selection. Here, we propose a partitioned form of genomic selection, called Origin Specific Genomic Selection (OSGS), where we identify and target selection on favorable exotic alleles. Briefly, within a population derived from a bi-parental cross, we isolate alleles originating from the elite and exotic parents, which then allows us to separate out the predicted marker effects based on the allele origins. We validated the usefulness of OSGS using two nested association mapping (NAM) datasets: barley NAM (elite-exotic) and maize NAM (elite-elite), as well as by computer simulation. Our results suggest that OSGS works well in its goal to increase the contribution of favorable exotic alleles in bi-parental crosses, and it is possible to extend the approach to broader multi-parental populations.

Diverse reproductive patterns of Bluehead Chub (Nocomis leptocephalus) and their relationships with nest size and interactions with an associate, Yellowfin Shiner (Notropis lutipinnis)

Nest construction by males is a common reproductive strategy in fishes, but little is known about intra-specific variation in nesting behavior and reproductive interactions with other species. In the southeastern USA, reproductive interactions between bluehead chub (Nocomis leptocephalus) and their nest associate, such as yellowfin shiner (Notropis lutipinnis), are mutualistic because the shiner requires chub nests to spawn but the chub also benefits from additional shiner eggs by reducing predation risk on their own eggs (i.e., dilution effect). As proxies for reproductive success of bluehead chub, we studied factors affecting their nest size variation and utilization by yellowfin shiner in three streams in the upper Piedmont region of South Carolina, USA. A total of 92 nests (71 spawned and 21 abandoned) were located, and we recorded spawning activity, nest size, number and size of male bluehead chub, number of yellowfin shiner, and environmental variables for 89 consecutive days in 2016. Path analysis showed that larger males spawned earlier in the season than smaller males, and instances of pebble re-use for nest construction increased through the spawning season, which extended from April to June. Larger males more likely shared the same nest with each other than smaller males, and larger or more males constructed larger nests and attracted more yellowfin shiner. Nest size also increased when males re-used substrate materials from old nests, and nests built in this manner (36 nests) were equally prevalent as newly constructed nests (35 nests). This study suggests that complex mechanisms mediate host nest size and interactions with nest associates, and individual variation likely shapes dynamics of the mutualistic reproductive interaction.

Dissecting Adaptive Traits with Nested Association Mapping: Genetic Architecture of Inflorescence Morphology in Sorghum.

In the cereal crop sorghum (Sorghum bicolor) inflorescence morphology variation underlies yield variation and confers adaptation across precipitation gradients, but its genetic basis is poorly understood. We characterized the genetic architecture of sorghum inflorescence morphology using a global nested association mapping (NAM) population (2200 recombinant inbred lines) and 198,000 phenotypic observations from multi-environment trials for four inflorescence morphology traits (upper branch length, lower branch length, rachis length, and rachis diameter). Trait correlations suggest that lower and upper branch length are under somewhat independent control, while lower branch length and rachis diameter are highly pleiotropic. Joint linkage and genome-wide association mapping revealed an oligogenic architecture with 1–22 QTL per trait, each explaining 0.1–5.0% of variation across the entire NAM population. There is a significant enrichment (2.twofold) of QTL colocalizing with grass inflorescence gene homologs, notably with orthologs of maize Ramosa2 and rice Aberrant Panicle Organization1 and TAWAWA1. Still, many QTL do not colocalize with inflorescence gene homologs. In global georeferenced germplasm, allelic variation at the major inflorescence QTL is geographically patterned but only weakly associated with the gradient of annual precipitation. Comparison of NAM with diversity panel association suggests that naive association models may capture some true associations not identified by mixed linear models. Overall, the findings suggest that global inflorescence diversity in sorghum is largely controlled by oligogenic, epistatic, and pleiotropic variation in ancestral regulatory networks. The findings also provide a basis for genomics-enabled breeding of locally-adapted inflorescence morphology.

Photosynthesis in the fleeting shadows: an overlooked opportunity for increasing crop productivity?

SummaryPhotosynthesis measurements are traditionally taken under steady‐state conditions; however, leaves in crop fields experience frequent fluctuations in light and take time to respond. This slow response reduces the efficiency of carbon assimilation. Transitions from low to high light require photosynthetic induction, including the activation of Rubisco and the opening of stomata, whereas transitions from high to low light require the relaxation of dissipative energy processes, collectively known as non‐photochemical quenching (NPQ). Previous attempts to assess the impact of these delays on net carbon assimilation have used simplified models of crop canopies, limiting the accuracy of predictions. Here, we use ray tracing to predict the spatial and temporal dynamics of lighting for a rendered mature Glycine max (soybean) canopy to review the relative importance of these delays on net cumulative assimilation over the course of both a sunny and a cloudy summer day. Combined limitations result in a 13% reduction in crop carbon assimilation on both sunny and cloudy days, with induction being more important on cloudy than on sunny days. Genetic variation in NPQ relaxation rates and photosynthetic induction in parental lines of a soybean nested association mapping (NAM) population was assessed. Short‐term NPQ relaxation (<30 min) showed little variation across the NAM lines, but substantial variation was found in the speeds of photosynthetic induction, attributable to Rubisco activation. Over the course of a sunny and an intermittently cloudy day these would translate to substantial differences in total crop carbon assimilation. These findings suggest an unexplored potential for breeding improved photosynthetic potential in our major crops.

Species traits predict stream‐fish invaders in an Appalachian (U.S.A.) river basin

Abstract We compared the influence of biological traits (morphology, physiology, reproduction, and life history), ecological traits (geographic distribution, habitat associations, food habits), and introduction attributes (propagule pressure, human use of a species, residence time) on invasion success of native and introduced stream fishes during the colonisation and spread stages in an Appalachian (U.S.A.) river basin. Colonisation success was positively related to residence time, benthic feeding, an equilibrium life‐history strategy, and nest spawning. Successful spread was associated with tolerance to increased temperature and an equilibrium life‐history strategy. The spread of introduced fishes was negatively related to gamefish status. No effect of propagule pressure was detected. Traits linked to invasion success were consistent with the hypothesis that human land‐use practices increase the invasibility of highland catchments by creating novel conditions better suited to lowland and equilibrium invaders. We found biological traits to be more useful than ecological traits in predicting invasion success and suggesting invasion mechanisms. Parental care and nest association can facilitate invasions over large spatial extents for both native and introduced fishes. Analyses of suites of traits can reveal mechanisms of invasions and tactics for controlling them; such mechanisms and tactics may be system‐specific and scale‐dependent.

Spawning periodicity and synchrony of bluehead chub (Nocomis leptocephalus) and a nest associate, yellowfin shiner (Notropis lutipinnis), across local streams

AbstractWe studied daily spawning periodicity of a nest‐building species, bluehead chub (Nocomis leptocephalus), and a nest associate, yellowfin shiner (Notropis lutipinnis), in three streams in the upper Piedmont region of South Carolina, USA. Field observations were conducted for 89 consecutive days in 2016 by recording the number of active nests and environmental variables. A total of 71 nests were located across study streams; bluhead chub and yellowfin shiner spawned between April and June. Spawning was observed periodically at intervals of 4–6 days within the same stream and across different streams, indicating broad‐scale influences of the same environmental factors leading to synchrony. A generalized linear auto‐regressive and moving average model showed that the periodic spawning pattern was likely caused by changes in water temperature, with effects of water level varying by stream. Specifically, spawning was triggered by a short‐term (2‐day) increase in water temperature and was observed under stable flow conditions (i.e. a lack of precipitation). This study showed that spawning periodicity of bluehead chub and yellowfin shiner tracked daily variation in in‐stream conditions, indicating that their reproduction might be affected by anthropogenic disturbances that affect the rate of change in thermal and flow regimes at the fine temporal scale (e.g. hydroelectric dams and impervious cover).

Nest association between two predators as a behavioral response to the low density of rodents

AbstractMany birds nest in association with aggressive birds of other species to benefit from their protection against predators. We hypothesized that the protective effect also could extend to foraging resources, whereby the resultant resource-enriched habitats near a nest of aggressive raptors could be an alternative cause of associations between nesting bird species with non-overlapping foraging niches. In the Arctic, the Rough-legged Hawk (Buteo lagopus) and the Peregrine Falcon (Falco peregrinus) are 2 raptor species with non-overlapping food resources that have been reported to nest sometimes in close proximity. Since nesting Peregrine Falcons are very aggressive, they may protect the small rodent prey near their nests from predation, and Rough-legged Hawks could use these hot spots as a nesting territory. In 2 regions in low Arctic Russia we found that (1) the nesting territories of Peregrine Falcons were indeed enriched with small rodents as compared to control areas, (2) the probability of nest association between the 2 raptors increased when rodent abundance was generally low in the region where hawks did not use alternative prey, and (3) hawk reproductive success increased when nesting close to Peregrine Falcons. These results suggest that implications of aggressive nest site defense in birds in certain cases may involve more mechanisms than previously explored. A key ecological process in tundra, rodent population cycles, may explain the occurrence and adaptive significance of a specific behavior pattern, the nesting association between 2 raptor species.

Genome-wide association of barley plant growth under drought stress using a nested association mapping population

BackgroundBarley (Hordeum vulgare L.) is the fourth most important cereal crop worldwide. Barley production is compromised by many abiotic stresses including drought. Wild barley is a valuable source of alleles that can improve adaptation of cultivated barley to drought stress.ResultsIn the present study, a nested association mapping population named HEB-25, consisting of 1420 BC1S3 lines that were developed by crossing 25 different wild barley accessions to the elite barley cultivar ‘Barke’, was evaluated under both control and drought-stressed conditions in the Australian Plant Phenomics Facility, University of Adelaide. Overall, 14 traits reflecting the performance of individual plants in each treatment were calculated from non-destructive imaging over time and destructive end-of-experiment measurements. For each trait, best linear unbiased estimators (BLUEs) were calculated and used for genome-wide association study (GWAS) analysis. Among the quantitative trait loci (QTL) identified for the 14 traits, many co-localise with known inflorescence and developmental genes. We identified a QTL on chromosome 4H where, under drought and control conditions, wild barley alleles increased biomass by 10 and 17% respectively compared to the Barke allele.ConclusionsAcross all traits, QTL which increased phenotypic values were identified, providing a wider range of genetic diversity for the improvement of drought tolerance in barley.

Registration of the Triticeae‐CAP Spring Wheat Nested Association Mapping Population

The Triticeae‐CAP spring wheat nested association mapping population (Reg. No. MP‐10, NSL 527060 MAP) consisting of recombinant inbred line (RIL) populations derived from 32 spring wheat (Triticum aestivum L.) accessions each crossed to a common spring wheat parent, ‘Berkut’, has been released. The spring wheat accessions consisted of 29 landraces and three cultivars. Each population consists of approximately 75 lines for a total of 2325 RILs (Reg. Nos. GSTR No. 14701–GSTR 17133). The RILs have all been genotyped with the Illumina wheat iSelect 90K single nucleotide polymorphism array using the Infinium assay method and through genotype‐by‐sequencing. This nested association mapping population provides a genotyped germplasm resource for the wheat community. A potential strategy for use of the material is to screen the parents for a trait of interest, followed by analysis of RIL of populations that are likely to be segregating for a target trait or sequence.

A large nested association mapping population for breeding and quantitative trait locus mapping in Ethiopian durum wheat.

SummaryThe Ethiopian plateau hosts thousands of durum wheat (Triticum turgidum subsp. durum) farmer varieties (FV) with high adaptability and breeding potential. To harness their unique allelic diversity, we produced a large nested association mapping (NAM) population intercrossing fifty Ethiopian FVs with an international elite durum wheat variety (Asassa). The Ethiopian NAM population (EtNAM) is composed of fifty interconnected bi‐parental families, totalling 6280 recombinant inbred lines (RILs) that represent both a powerful quantitative trait loci (QTL) mapping tool, and a large pre‐breeding panel. Here, we discuss the molecular and phenotypic diversity of the EtNAM founder lines, then we use an array featuring 13 000 single nucleotide polymorphisms (SNPs) to characterize a subset of 1200 EtNAM RILs from 12 families. Finally, we test the usefulness of the population by mapping phenology traits and plant height using a genome wide association (GWA) approach. EtNAM RILs showed high allelic variation and a genetic makeup combining genetic diversity from Ethiopian FVs with the international durum wheat allele pool. EtNAM SNP data were projected on the fully sequenced AB genome of wild emmer wheat, and were used to estimate pairwise linkage disequilibrium (LD) measures that reported an LD decay distance of 7.4 Mb on average, and balanced founder contributions across EtNAM families. GWA analyses identified 11 genomic loci individually affecting up to 3 days in flowering time and more than 1.6 cm in height. We argue that the EtNAM is a powerful tool to support the production of new durum wheat varieties targeting local and global agriculture.

Genomic Prediction Using Canopy Coverage Image and Genotypic Information in Soybean via a Hybrid Model.

Prediction techniques are important in plant breeding as they provide a tool for selection that is more efficient and economical than traditional phenotypic and pedigree based selection. The conventional genomic prediction models include molecular marker information to predict the phenotype. With the development of new phenomics techniques we have the opportunity to collect image data on the plants, and extend the traditional genomic prediction models where we incorporate diverse set of information collected on the plants. In our research, we developed a hybrid matrix model that incorporates molecular marker and canopy coverage information as a weighted linear combination to predict grain yield for the soybean nested association mapping (SoyNAM) panel. To obtain the testing and training sets, we clustered the individuals based on their marker and canopy information using 2 different clustering techniques, and we compared 5 different cross-validation schemes. The results showed that the predictive ability of the models was the highest when both the canopy and marker information was included, and it was the lowest when only the canopy information was included.

Mutualism or parasitism: Partner abundance affects host fitness in a fish reproductive interaction

Abstract Mutualisms are ubiquitous in nature but are understudied in freshwater ecosystems. Mutualisms can be unstable, shifting to commensal or even negative outcomes with context. Quantifying context dependency in mutualisms is critical for understanding how biotic interactions will shift along disturbance gradients in freshwater systems. A common reproductive interaction among stream fishes, nest association occurs when individuals of one species spawn in nests constructed by a host fish. Hosts benefit from a dilution effect: high proportions of associate eggs decrease the odds of host brood predation. Thus, partner abundance can be an important source of biotic context influencing the outcome of an association. We conducted a large in situ experiment manipulating abundance of partner yellowfin shiner (Leuciscidae: Notropis lutipinnis) (absent, low, high) at constant abundance of host bluehead chub (Leuciscidae: Nocomis leptocephalus), and quantified chub reproductive success using genetic tools. Evidence suggests that the nest association switched from mutualistic to parasitic outcomes as shiner abundance decreased. Chub reproductive success was highest at high shiner abundances. However, chub reproductive success was actually higher in the complete absence of shiners than at low shiner densities. This study shows that outcomes of biotic interactions in freshwater systems are context‐dependent, and that partner abundance can be a key source of context‐dependency in nest associations. We encourage future studies on freshwater mutualisms, which are thus far largely overlooked, relative to competition and predation.

Analysis of QTL-allele system conferring drought tolerance at seedling stage in a nested association mapping population of soybean [Glycine max (L.) Merr.] using a novel GWAS procedure.

RTM-GWAS identified 111 DT QTLs, 262 alleles with high proportion of QEI and genetic variation accounting for 88.55-95.92% PV in NAM, from which QTL-allele matrices were established and candidate genes annotated. Drought tolerance (DT) is one of the major challenges for world soybean production. A nested association mapping (NAM) population with 403 lines comprising two recombinant inbred line (RIL) populations: M8206 × TongShan and ZhengYang × M8206 was tested for DT using polyethylene-glycol (PEG) treatment under spring and summer environments. The population was sequenced using restriction-site-associated DNA sequencing (RAD-seq) filtered with minor allele frequency (MAF) ≥ 0.01, 55,936 single nucleotide polymorphisms (SNPs) were obtained and organized into 6137 SNP linkage disequilibrium blocks (SNPLDBs). The restricted two-stage multi-locus genome-wide association studies (RTM-GWAS) identified 73 and 38 QTLs with 174 and 88 alleles contributed main effect 40.43 and 26.11% to phenotypic variance (PV) and QTL-environment interaction (QEI) effect 24.64 and 10.35% to PV for relative root length (RRL) and relative shoot length (RSL), respectively. The DT traits were characterized with high proportion of QEI variation (37.52-41.65%), plus genetic variation (46.90-58.40%) in a total of 88.55-95.92% PV. The identified QTLs-alleles were organized into main-effect and QEI-effect QTL-allele matrices, showing the genetic and QEI architecture of the three parents/NAM population. From the matrices, the possible best genotype was predicted to have a weighted average value over two indicators (WAV) of 1.873, while the top ten optimal crosses among RILs with 95th percentile WAV 1.098-1.132, transgressive over the parents (0.651-0.773) but much less than 1.873, implying further pyramiding potential. From the matrices, 134 candidate genes were annotated involved in nine biological processes. The present results provide a novel way for molecular breeding in QTL-allele-based genomic selection for optimal cross selection.

Genetic Architecture of Nitrogen-Deficiency Tolerance in Wheat Seedlings Based on a Nested Association Mapping (NAM) Population.

Genetic divergence for nitrogen utilization in germplasms is important in wheat breeding programs, especially for low nitrogen input management. In this study, a nested association mapping (NAM) population, derived from “Yanzhan 1” (a Chinese domesticated cultivar) crossed with “Hussar” (a British domesticated cultivar) and another three semi-wild wheat varieties, namely, “Cayazheda 29” (Triticum aestivum ssp. tibetanum Shao), “Yunnan” (T. aestivum ssp. yunnanense King), and “Yutian” (T. aestivum petropavloski Udats et Migusch), was used to detect quantitative trait loci (QTLs) for nitrogen utilization at the seedling stage. An integrated genetic map was constructed using 2,059 single nucleotide polymorphism (SNP) markers from a 90 K SNP chip, with a total coverage of 2,355.75 cM and an average marker spacing of 1.13 cM. A total of 67 QTLs for RDW (root dry weight), SDW (shoot dry weight), TDW (total dry weight), and RSDW (root to shoot ratio) were identified under normal nitrogen conditions (N+) and nitrogen deficient conditions (N−). Twenty-three of these QTLs were only detected under N− conditions. Moreover, 23 favorable QTLs were identified in the domesticated cultivar Yanzhan 1, 15 of which were detected under N+ conditions, while only four were detected under N− conditions. In contrast, the semi-wild cultivars contributed more favorable N−−specific QTLs (eight from Cayazheda 29; nine from Yunnan), which could be further explored for breeding cultivars adapted to nitrogen-deficient conditions. In particular, QRSDW-5A.1 from YN should be further evaluated using high-resolution mapping.

An uneasy alliance: a nesting association between aggressive ants and equally fierce social wasps.

Although the Neotropical territorially dominant arboreal ant Azteca chartifex Forel is very aggressive towards any intruder, its populous colonies tolerate the close presence of the fierce polistine wasp Polybia rejecta (F.). In French Guiana, 83.33% of the 48 P. rejecta nests recorded were found side by side with those of A. chartifex. This nesting association results in mutual protection from predators (i.e., the wasps protected from army ants; the ants protected from birds). We conducted field studies, laboratory-based behavioral experiments and chemical analyses to elucidate the mechanisms allowing the persistence of this association. Due to differences in the cuticular profiles of the two species, we eliminated the possibility of chemical mimicry. Also, analyses of the carton nests did not reveal traces of marking on the envelopes. Because ant forager flows were not perturbed by extracts from the wasps' Dufour's and venom glands, we rejected any hypothetical action of repulsive chemicals. Nevertheless, we noted that the wasps "scraped" the surface of the upper part of their nest envelope using their mandibles, likely removing the ants' scent trails, and an experiment showed that ant foragers were perturbed by the removal of their scent trails. This leads us to use the term "erasure hypothesis." Thus, this nesting association persists thanks to a relative tolerance by the ants towards wasp presence and the behavior of the wasps that allows them to "contain" their associated ants through the elimination of their scent trails, direct attacks, "wing-buzzing" behavior and ejecting the ants.

Increasing Predictive Ability by Modeling Interactions between Environments, Genotype and Canopy Coverage Image Data for Soybeans

Phenomics is a new area that offers numerous opportunities for its applicability in plant breeding. One possibility is to exploit this type of information obtained from early stages of the growing season by combining it with genomic data. This opens an avenue that can be capitalized by improving the predictive ability of the common prediction models used for genomic prediction. Imagery (canopy coverage) data recorded between days 14–71 using two collection methods (ground information in 2013 and 2014; aerial information in 2014 and 2015) on a soybean nested association mapping population (SoyNAM) was used to calibrate the prediction models together with the inclusion of several types of interactions between canopy coverage data, environments, and genomic data. Three different scenarios were considered that breeders might face testing lines in fields: (i) incomplete field trials (CV2); (ii) newly developed lines (CV1); and (iii) predicting lines in unobserved environments (CV0). Two different traits were evaluated in this study: yield and days to maturity (DTM). Results showed improvements in the predictive ability for yield with respect to those models that solely included genomic data. These relative improvements ranged 27–123%, 27–148%, and 65–165% for CV2, CV1, and CV0, respectively. No major changes were observed for DTM. Similar improvements were observed for both traits when the reduced canopy information for days 14–33 was used to build the training-testing relationships, showing a clear advantage of using phenomics in very early stages of the growing season.

Disentangling Reproductive Interactions among Communal Spawning Minnows Using Reproductive Condition and Visual Observations

Understanding the reproductive ecology of stream fishes is critical for their conservation. Nest association is a common reproductive interaction among minnows (Cyprinidae) in which individuals of ‘associate' species spawn in nests of host species. Nest association behavior is nearly obligate for ‘strong' associates, while it is facultative for other species. Facultative associates may begin spawning before host nesting begins and then visit host nests either to continue spawning or to feed. This is particularly evident for Central Stoneroller Campostoma anomalum, which frequently visits nests of host Bluehead Chub Nocomis leptocephalus but also spawns separately. We monitored the reproductive condition (gonadosomatic index, GSI) of minnows at longitudinally-positioned sites in a central Appalachian stream throughout the spring and summer of 2013. We also conducted daily visual nesting surveys to document chub spawning behavior and reproductive interactions that occurred on their nests. We used nonmetric multidimensional scaling (NMDS) to compare weekly GSI patterns of reproductive groups and hypothesized stoneroller GSI would be more similar to facultative associates than chubs. We also used piecewise regression to identify temporal thresholds in GSI (indicating the onset of spawning) in relation to the visually-confirmed onset of chub spawning. NMDS results suggest clear differences in reproductive condition between chubs/strong associates and stoneroller/weak associates. The onset of chub spawning was contained within the GSI thresholds estimate of strong associates but not of other groups. Stonerollers began spawning several weeks before chubs but were documented to be excavating pits on each nest. Paired together, the GSI and behavioral observations suggest stoneroller does not require chub nests for spawning and may exploit nests as a trophic resource if no eggs are contributed. Moreover, these results demonstrate the close reproductive link between some symbiotic species and their hosts that is required for successful reproduction.

A New Species of Niditinea (Tineidae: Tineinae) with a Preference for Bird Nests, and the Known Larval Habitats of the Species in the United States

We describe and illustrate Niditinea sabroskyi, new species, the larvae of which are associated with bird nests. We provide diagnostic information to distinguish the new species from the other two species occurring in the United States, Niditinea fuscella (Linnaeus, 1758) and Niditinea orleansella (Chambers, 1873). Although there is a considerable amount of published literature on the biology of the most common species, N. fuscella, owing to the difficulty of identifying species of Niditinea, host records are unreliable. We show that N. sabroskyi is predominantly a bird nest associate, and that specimens identified as N. fuscella and previously associated with bird nests are actually misidentified. We also summarize the larval habitat information from specimens with confirmed identifications.

Spawning Community and Egg Deposition for Three Southeastern Nest-associate Minnows

Nest association is a symbiotic reproductive strategy in North American minnows in which a species spawns in the nest substrate of a host species. Host specificity is unknown for the vast majority of nest associates, and presence of a spawning aggregation over a particular nest site has is assumed to be evidence of egg deposition. In this study, we surveyed multiple streams for spawning aggregations throughout the ranges of 3 nestassociate species—Notropis baileyi (Rough Shiner), N. rubricroceus (Saffron Shiner), and N. chlorocephalus (Greenhead Shiner). We paired direct observation of spawning behavior with molecular verification of egg deposition. We observed all spawning aggregations in association with a host nest. We identified eggs from a number of species not directly observed over a particular aggregation site, although all species were known to aggregate as nest associates. On 2 occasions, we documented Saffron Shiner males in aggregations over Semotilus atromaculatus (Creek Chub) pit—ridge nests; however, we recovered no Saffron Shiner eggs from the nests. Our findings demonstrate that field observations of nuptial aggregations alone are not sufficient to confirm spawning associati on.

Genome-Wide Analysis of Grain Yield Stability and Environmental Interactions in a Multiparental Soybean Population.

Genetic improvement toward optimized and stable agronomic performance of soybean genotypes is desirable for food security. Understanding how genotypes perform in different environmental conditions helps breeders develop sustainable cultivars adapted to target regions. Complex traits of importance are known to be controlled by a large number of genomic regions with small effects whose magnitude and direction are modulated by environmental factors. Knowledge of the constraints and undesirable effects resulting from genotype by environmental interactions is a key objective in improving selection procedures in soybean breeding programs. In this study, the genetic basis of soybean grain yield responsiveness to environmental factors was examined in a large soybean nested association population. For this, a genome-wide association to performance stability estimates generated from a Finlay-Wilkinson analysis and the inclusion of the interaction between marker genotypes and environmental factors was implemented. Genomic footprints were investigated by analysis and meta-analysis using a recently published multiparent model. Results indicated that specific soybean genomic regions were associated with stability, and that multiplicative interactions were present between environments and genetic background. Seven genomic regions in six chromosomes were identified as being associated with genotype-by-environment interactions. This study provides insight into genomic assisted breeding aimed at achieving a more stable agronomic performance of soybean, and documented opportunities to exploit genomic regions that were specifically associated with interactions involving environments and subpopulations.