Genome-wide association mapping of root traits in a japonica rice panel

A comparative study of population structure and genetic diversity of commercial and indigenous chickens from different agro-ecological zones in Ghana using SilicoDArT and SNP markers

Chicken production, both in the local and commercial sectors, contributes significantly to human livelihood and food security. Precise use of diverse genetic resources is primary in breeding programs. The study analyzed the genetic diversity and population structure of commercial chickens and indigenous chicken ecotypes from three different agro-ecological zones (Semi-Deciduous Rainforest Zone, Guinea Savannah, and Coastal Savannah) using SilicoDArT and SNP markers, utilizing whole-genome sequencing and phenotypic data. Phenotypic data were collected from 72 indigenous chicken ecotypes across the three AEZs, and 32 commercial birds kept at the Kwame Nkrumah University of Science and Technology (KNUST). DNA samples used for sequencing were obtained from 88 chickens (62 indigenous chicken ecotypes and 26 commercial chickens). A total of 54,995 SilicoDArT and 85,396 SNPs markers were generated from DArTseq genotyping. After filtering, 44,784 SilicoDArT and 58,353 SNP were used for genetic diversity and population structure analysis. Both markers showed high reproducibility and call rate. Polymorphic information content (PIC) values ranged from 0.00 to 0.50, while ≥ 50 % showed PIC values more than the median. Furthermore, we obtained FST values, Nei's genetic distance, dendrogram analysis, and principal component analysis (PCA) of commercial and indigenous chickens. The FST and Nei's genetic distance showed that there is high genetic diversity between the commercial chickens and the indigenous chicken ecotypes. However, there was low genetic diversity among the indigenous chicken ecotypes. The PCA analysis indicated a clear separation between the commercial and indigenous chicken ecotypes, while no clear separation was observed between the indigenous chicken ecotypes. The phenotypic data and the dendrogram indicated that naked and frizzle genes do not markedly alter the genetics of indigenous and commercial birds, and their influence on economic traits may be solely determined by the prevailing environmental conditions. The results indicate that there is high genetic differentiation between commercial and indigenous chickens based on SilicoDArT and SNP markers. The indigenous chickens from the agro-ecological zones have low genetic diversity and might have a common origin. Naked neck and frizzle genes do not markedly alter the genetic performance of birds in terms of economic traits. Therefore, the superiority of birds carrying these genes in economic traits may be solely due to environmental variation.

Glacial vicariance and secondary contact shape demographic histories in a freshwater mussel species complex

Characterizing the mechanisms influencing the distribution of genetic variation in aquatic species can be difficult due to the dynamic nature of hydrological landscapes. In North America's Central Highlands, a complex history of glacial dynamics, long-term isolation, and secondary contact have shaped genetic variation in aquatic species. Although the effects of glacial history have been demonstrated in many taxa, responses are often lineage- or species-specific and driven by organismal ecology. In this study, we reconstruct the evolutionary history of a freshwater mussel species complex using a suite of mitochondrial and nuclear loci to resolve taxonomic and demographic uncertainties. Our findings do not support Pleurobema rubrum as a valid species, which is proposed for listing as threatened under the U.S. Endangered Species Act. We synonymize P. rubrum under Pleurobema sintoxia-a common and widespread species found throughout the Mississippi River Basin. Further investigation of patterns of genetic variation in P. sintoxia identified a complex demographic history, including ancestral vicariance and secondary contact, within the Eastern Highlands. We hypothesize these patterns were shaped by ancestral vicariance driven by the formation of Lake Green and subsequent secondary contact after the last glacial maximum. Our inference aligns with demographic histories observed in other aquatic taxa in the region and mirrors patterns of genetic variation of a freshwater fish species (Erimystax dissimilis) confirmed to serve as a parasitic larval host for P. sintoxia. Our findings directly link species ecology to observed patterns of genetic variation and may have significant implications for future conservation and recovery actions of freshwater mussels.

Uncovering the Genomic Regions Associated with Yield Maintenance in Rice Under Drought Stress Using an Integrated Meta-Analysis Approach

The complex trait of yield is controlled by several quantitative trait loci (QTLs). Given the global water deficit issue, the development of rice varieties suitable for non-flooded cultivation holds significant importance in breeding programs. The powerful approach of Meta-QTL (MQTL) analysis can be used for the genetic dissection of complicated quantitative traits. In the current study, a comprehensive MQTL analysis was conducted to identify consistent QTL regions associated with drought tolerance and yield-related traits under water deficit conditions in rice. In total, 1087 QTLs from 134 rice populations, published between 2000 to 2021, were utilized in the analysis. Distinct MQTL analysis of the relevant traits resulted in the identification of 213 stable MQTLs. The confidence interval (CI) for the detected MQTLs was between 0.12 and 19.7 cM. The average CI of the identified MQTLs (4.68 cM) was 2.74 times narrower compared to the average CI of the initial QTLs. Interestingly, 63 MQTLs coincided with SNP peak positions detected by genome-wide association studies for yield and drought tolerance-associated traits under water deficit conditions in rice. Considering the genes located both in the QTL-overview peaks and the SNP peak positions, 19 novel candidate genes were introduced, which are associated with drought response index, plant height, panicle number, biomass, and grain yield. Moreover, an inclusive MQTL analysis was performed on all the traits to obtain "Breeding MQTLs". This analysis resulted in the identification of 96 MQTLs with a CI ranging from 0.01 to 9.0 cM. The mean CI of the obtained MQTLs (2.33 cM) was 4.66 times less than the mean CI of the original QTLs. Thirteen MQTLs fulfilling the criteria of having more than 10 initial QTLs, CI < 1 cM, and an average phenotypic variance explained greater than 10%, were designated as "Breeding MQTLs". These findings hold promise for assisting breeders in enhancing rice yield under drought stress conditions.

Genome-wide association study of fiber yield-related traits uncovers the novel genomic regions and candidate genes in Indian upland cotton (Gossypium hirsutum L.)

Upland cotton (Gossypium hirsutum L.) is a major fiber crop that is cultivated worldwide and has significant economic importance. India harbors the largest area for cotton cultivation, but its fiber yield is still compromised and ranks 22nd in terms of productivity. Genetic improvement of cotton fiber yield traits is one of the major goals of cotton breeding, but the understanding of the genetic architecture underlying cotton fiber yield traits remains limited and unclear. To better decipher the genetic variation associated with fiber yield traits, we conducted a comprehensive genome-wide association mapping study using 117 Indian cotton germplasm for six yield-related traits. To accomplish this, we generated 2,41,086 high-quality single nucleotide polymorphism (SNP) markers using genotyping-by-sequencing (GBS) methods. Population structure, PCA, kinship, and phylogenetic analyses divided the germplasm into two sub-populations, showing weak relatedness among the germplasms. Through association analysis, 205 SNPs and 134 QTLs were identified to be significantly associated with the six fiber yield traits. In total, 39 novel QTLs were identified in the current study, whereas 95 QTLs overlapped with existing public domain data in a comparative analysis. Eight QTLs, qGhBN_SCY_D6-1, qGhBN_SCY_D6-2, qGhBN_SCY_D6-3, qGhSI_LI_A5, qGhLI_SI_A13, qGhLI_SI_D9, qGhBW_SCY_A10, and qGhLP_BN_A8 were identified. Gene annotation of these fiber yield QTLs revealed 2,509 unique genes. These genes were predominantly enriched for different biological processes, such as plant cell wall synthesis, nutrient metabolism, and vegetative growth development in the gene ontology (GO) enrichment study. Furthermore, gene expression analysis using RNAseq data from 12 diverse cotton tissues identified 40 candidate genes (23 stable and 17 novel genes) to be transcriptionally active in different stages of fiber, ovule, and seed development. These findings have revealed a rich tapestry of genetic elements, including SNPs, QTLs, and candidate genes, and may have a high potential for improving fiber yield in future breeding programs for Indian cotton.

Dissecting the genetic architecture of root-related traits in a grafted wild Vitis berlandieri population for grapevine rootstock breeding

In woody perennial plants, quantitative genetics and association studies remain scarce for root-related traits, due to the time required to obtain mature plants and the complexity of phenotyping. In grapevine, a grafted cultivated plant, most of the rootstocks used are hybrids between American Vitis species (V. rupestris, V. riparia, and V. berlandieri). In this study, we used a wild population of an American Vitis species (V. berlandieri) to analyze the genetic architecture of the root-related traits of rootstocks in a grafted context. We studied a population consisting of 211 genotypes, with one to five replicates each (n = 846 individuals), plus four commercial rootstocks as control genotypes (110R, 5BB, Börner, and SO4). After two independent years of experimentation, the best linear unbiased estimates method revealed root-related traits with a moderate-to-high heritability (0.36-0.82) and coefficient of genetic variation (0.15-0.45). A genome-wide association study was performed with the BLINK model, leading to the detection of 11 QTL associated with four root-related traits (one QTL was associated with the total number of roots, four were associated with the number of small roots (< 1 mm in diameter), two were associated with the number of medium-sized roots (1 mm < diameter < 2 mm), and four were associated with mean diameter) accounting for up to 25.1% of the variance. Three genotypes were found to have better root-related trait performances than the commercial rootstocks and therefore constitute possible new candidates for use in grapevine rootstock breeding programs.

Phenotyping and metabolome analysis reveal the role of AdoMetDC and Di19 genes in determining acquired tolerance to drought in rice

Water-saving attempts for rice cultivation often reduce yields. Maintaining productivity under drought is possible when rice genotypes are bred with improved metabolism and spikelet fertility. Although attempts have been made to introgress water mining and water use efficiency traits, combining acquired tolerance traits (ATTs), that is, specific traits induced or upregulated to better tolerate severe stress, appears equally important. In our study, we screened 90 rice germplasm accessions that represented the molecular and phenotypic variations of 851 lines of the 3 K rice panel. Utilising phenomics, we identified markers linked to ATTs through association analysis of over 0.2 million SNPs derived from whole-genome sequences. Propensity to respond to 'induction' stress varied significantly among genotypes, reflecting differences in cellular protection against oxidative stress. Among the ATTs, the hydroxyl radical and proline contents exhibited the highest variability. Furthermore, these significant variations in ATTs were strongly correlated with spikelet fertility. The 43 significant markers associated with ATTs were further validated using a different subset of contrasting genotypes. Gene expression studies and metabolomic profiling of two well-known contrasting genotypes, APO (tolerant) and IR64 (sensitive), identified two ATT genes: AdoMetDC and Di19. Our study highlights the relevance of polyamine biosynthesis in modulating ATTs in rice. Genotypes with superior ATTs and the associated markers can be effectively employed in breeding rice varieties with sustained spikelet fertility and grain yield under drought.

Genome-wide association study as a powerful tool for dissecting competitive traits in legumes

Legumes are extremely valuable because of their high protein content and several other nutritional components. The major challenge lies in maintaining the quantity and quality of protein and other nutritional compounds in view of climate change conditions. The global need for plant-based proteins has increased the demand for seeds with a high protein content that includes essential amino acids. Genome-wide association studies (GWAS) have evolved as a standard approach in agricultural genetics for examining such intricate characters. Recent development in machine learning methods shows promising applications for dimensionality reduction, which is a major challenge in GWAS. With the advancement in biotechnology, sequencing, and bioinformatics tools, estimation of linkage disequilibrium (LD) based associations between a genome-wide collection of single-nucleotide polymorphisms (SNPs) and desired phenotypic traits has become accessible. The markers from GWAS could be utilized for genomic selection (GS) to predict superior lines by calculating genomic estimated breeding values (GEBVs). For prediction accuracy, an assortment of statistical models could be utilized, such as ridge regression best linear unbiased prediction (rrBLUP), genomic best linear unbiased predictor (gBLUP), Bayesian, and random forest (RF). Both naturally diverse germplasm panels and family-based breeding populations can be used for association mapping based on the nature of the breeding system (inbred or outbred) in the plant species. MAGIC, MCILs, RIAILs, NAM, and ROAM are being used for association mapping in several crops. Several modifications of NAM, such as doubled haploid NAM (DH-NAM), backcross NAM (BC-NAM), and advanced backcross NAM (AB-NAM), have also been used in crops like rice, wheat, maize, barley mustard, etc. for reliable marker-trait associations (MTAs), phenotyping accuracy is equally important as genotyping. Highthroughput genotyping, phenomics, and computational techniques have advanced during the past few years, making it possible to explore such enormous datasets. Each population has unique virtues and flaws at the genomics and phenomics levels, which will be covered in more detail in this review study. The current investigation includes utilizing elite breeding lines as association mapping population, optimizing the choice of GWAS selection, population size, and hurdles in phenotyping, and statistical methods which will analyze competitive traits in legume breeding.

Haplotype-Based Genome-Wide Association Analysis Using Exome Capture Assay and Digital Phenotyping Identifies Genetic Loci Underlying Salt Tolerance Mechanisms in Wheat

Soil salinity can impose substantial stress on plant growth and cause significant yield losses. Crop varieties tolerant to salinity stress are needed to sustain yields in saline soils. This requires effective genotyping and phenotyping of germplasm pools to identify novel genes and QTL conferring salt tolerance that can be utilised in crop breeding schemes. We investigated a globally diverse collection of 580 wheat accessions for their growth response to salinity using automated digital phenotyping performed under controlled environmental conditions. The results show that digitally collected plant traits, including digital shoot growth rate and digital senescence rate, can be used as proxy traits for selecting salinity-tolerant accessions. A haplotype-based genome-wide association study was conducted using 58,502 linkage disequilibrium-based haplotype blocks derived from 883,300 genome-wide SNPs and identified 95 QTL for salinity tolerance component traits, of which 54 were novel and 41 overlapped with previously reported QTL. Gene ontology analysis identified a suite of candidate genes for salinity tolerance, some of which are already known to play a role in stress tolerance in other plant species. This study identified wheat accessions that utilise different tolerance mechanisms and which can be used in future studies to investigate the genetic and genic basis of salinity tolerance. Our results suggest salinity tolerance has not arisen from or been bred into accessions from specific regions or groups. Rather, they suggest salinity tolerance is widespread, with small-effect genetic variants contributing to different levels of tolerance in diverse, locally adapted germplasm.

Utilizing Genomics to Characterize the Common Oat Gene Pool—The Story of More than a Century of Polish Breeding

This study was undertaken to investigate the diversity and population structure of 487 oat accessions, including breeding lines from the ongoing programs of the three largest Polish breeding companies, along with modern and historical Polish and foreign cultivars. The analysis was based on 7411 DArTseq-derived SNPs distributed among three sub-genomes (A, C, and D). The heterogeneity of the studied material was very low, as only cultivars and advanced breeding lines were examined. Principal component analysis (PCA), principal coordinate analysis (PCoA), and cluster and STRUCTURE analyses found congruent results, which show that most of the examined cultivars and materials from Polish breeding programs formed major gene pools, that only some accessions derived from Strzelce Plant Breeding, and that foreign cultivars were outside of the main group. During the 120 year oat breeding process, only 67 alleles from the old gene pool were lost and replaced by 67 new alleles. The obtained results indicate that no erosion of genetic diversity was observed within the Polish native oat gene pool. Moreover, current oat breeding programs have introduced 673 new alleles into the gene pool relative to historical cultivars. The analysis also showed that most of the changes in relation to historical cultivars occurred within the A sub-genome with emphasis on chromosome 6A. The targeted changes were the rarest in the C sub-genome. This study showed that Polish oat breeding based mainly on traditional breeding methods—although focused on improving traits typical to this crop, i.e., enhancing the grain yield and quality and improving adaptability—did not significantly narrow the oat gene pool and in fact produced cultivars that are not only competitive in the European market but are also reservoirs of new alleles that were not found in the analyzed foreign materials.

Evaluating the genetic consequences of population subdivision as it unfolds and how to best mitigate them: A rare story about koalas

The genetic consequences of the subdivision of populations are regarded as significant to long-term evolution, and research has shown that the scale and speed at which this is now occurring is critically reducing the adaptive potential of most species which inhabit human-impacted landscapes. Here, we provide a rare and, to our knowledge, the first analysis of this process while it is happening and demonstrate a method of evaluating the effect of mitigation measures such as fauna crossings. We did this by using an extensive genetic data set collected from a koala population which was intensely monitored during the construction of linear transport infrastructure which resulted in the subdivision of their population. First, we found that both allelic richness and effective population size decreased through the process of population subdivision. Second, we predicted the extent to which genetic drift could impact genetic diversity over time and showed that after only 10 generations the resulting two subdivided populations could experience between 12% and 69% loss in genetic diversity. Lastly, using forward simulations we estimated that a minimum of eight koalas would need to disperse from each side of the subdivision per generation to maintain genetic connectivity close to zero but that 16 koalas would ensure that both genetic connectivity and diversity remained unchanged. These results have important consequences for the genetic management of species in human-impacted landscapes by showing which genetic metrics are best to identify immediate loss in genetic diversity and how to evaluate the effectiveness of any mitigation measures.

Multi-stage resistance to Zymoseptoria tritici revealed by GWAS in an Australian bread wheat diversity panel

Septoria tritici blotch (STB) has been ranked the third most important wheat disease in the world, threatening a large area of wheat production. Although major genes play an important role in the protection against Zymoseptoria tritici infection, the lifespan of their resistance unfortunately is very short in modern wheat production systems. Combinations of quantitative resistance with minor effects, therefore, are believed to have prolonged and more durable resistance to Z. tritici. In this study, new quantitative trait loci (QTLs) were identified that are responsible for seedling-stage resistance and adult-plant stage resistance (APR). More importantly was the characterisation of a previously unidentified QTL that can provide resistance during different stages of plant growth or multi-stage resistance (MSR). At the seedling stage, we discovered a new isolate-specific QTL, QSt.wai.1A.1. At the adult-plant stage, the new QTL QStb.wai.6A.2 provided stable and consistent APR in multiple sites and years, while the QTL QStb.wai.7A.2 was highlighted to have MSR. The stacking of multiple favourable MSR alleles was found to improve resistance to Z. tritici by up to 40%.

Response of Southeast Asian rice root architecture and anatomy phenotypes to drought stress

Drought stress in Southeast Asia greatly affects rice production, and the rice root system plays a substantial role in avoiding drought stress. In this study, we examined the phenotypic and genetic correlations among root anatomical, morphological, and agronomic phenotypes over multiple field seasons. A set of >200 rice accessions from Southeast Asia (a subset of the 3000 Rice Genomes Project) was characterized with the aim to identify root morphological and anatomical phenotypes related to productivity under drought stress. Drought stress resulted in slight increases in the basal metaxylem and stele diameter of nodal roots. Although few direct correlations between root phenotypes and grain yield were identified, biomass was consistently positively correlated with crown root number and negatively correlated with stele diameter. The accessions with highest grain yield were characterized by higher crown root numbers and median metaxylem diameter and smaller stele diameter. Genome-wide association study (GWAS) revealed 162 and 210 significant SNPs associated with root phenotypes in the two seasons which resulted in identification of 59 candidate genes related to root development. The gene OsRSL3 was found in a QTL region for median metaxylem diameter. Four SNPs in OsRSL3 were found that caused amino acid changes and significantly associated with the root phenotype. Based on the haplotype analysis for median metaxylem diameter, the rice accessions studied were classified into five allele combinations in order to identify the most favorable haplotypes. The candidate genes and favorable haplotypes provide information useful for the genetic improvement of root phenotypes under drought stress.

Genome-wide association study reveals that GhTRL1 and GhPIN8 affect cotton root development

Two regions located at chromosome A05 and D04 were found to be significantly associated with 0-0.5 mm and 0.5-2 mm diameter roots, respectively, and two candidate genes related to root development were identified. Roots absorb water and nutrients, and play an important role in plant growth. However, there are few genetic developmental studies on cotton root structural traits. In this study, we used 200 upland cotton (Gossypium hirsutum L.) varieties to analyze the phenotypic variation of 43 traits. A total of 2001 related single-nucleotide polymorphism (SNP) sites located within or near 1046 genes were detected through a genome-wide association study (GWAS). The 32 root traits were linked to SNPs that corresponded to 317 nonrepetitive genes. For SNPs associated with root length and 0-0.5 mm diameter root traits, a significant peak appeared on chromosome A05 (between 21.91 and 22.24 Mb). For SNPs associated with root surface area, root volume and 0.5-2 mm diameter root traits, a significant peak appeared on chromosome D04 (between 7.35 and 7.70 Mb). Within these two key regions, SNPs were detected in the promoter and coding regions of two candidate genes, GhTRL1-A05 and GhPIN8-D04. The expression levels of these two genes also changed significantly according to transcriptome sequencing and quantitative real-time PCR (qRT-PCR). After silencing the GhTRL1 and GhPIN8 genes via virus-induced gene silencing (VIGS), we found that the plants expressing TRV2::GhTRL1 and TRV2::GhPIN8 had a reduced root length, surface area. Moreover, the contents of cis-12-oxo-phytodienoic acid (cis-OPDA), isopentenyl adenosine (iPR) and cis-zeatin (cZ) in the roots of the plants expressing TRV2::GhTRL1 decreased. This study contributes to the cultivation and improvement of cotton varieties.

Root system architecture in rice: impacts of genes, phytohormones and root microbiota

To feed the continuously expanding world's population, new crop varieties have been generated, which significantly contribute to the world's food security. However, the growth of these improved plant varieties relies primarily on synthetic fertilizers, which negatively affect the environment and human health; therefore, continuous improvement is needed for sustainable agriculture. Several plants, including cereal crops, have the adaptive capability to combat adverse environmental changes by altering physiological and molecular mechanisms and modifying their root system to improve nutrient uptake efficiency. These plants operate distinct pathways at various developmental stages to optimally establish their root system. These processes include changes in the expression profile of genes, changes in phytohormone level, and microbiome-induced root system architecture (RSA) modification. Several studies have been performed to understand microbial colonization and their involvement in RSA improvement through changes in phytohormone and transcriptomic levels. This review highlights the impact of genes, phytohormones, and particularly root microbiota in influencing RSA and provides new insights resulting from recent studies on rice root as a model system and summarizes the current knowledge about biochemical and central molecular mechanisms.

Identification of quantitative trait loci for tillering, root, and shoot biomass at the maximum tillering stage in rice

Tillering and plant biomass are key determinants of rice crop productivity. Tillering at the vegetative stage is associated with weed competition, nutrient uptake, and methane emissions. However, little information is available on quantitative trait loci (QTLs) associated with tiller number (qTN), root biomass (qRB), and shoot biomass (qSB) at the active tillering stage which occurs approximately 6 weeks after planting. Here, we mapped tiller and biomass QTLs with ~ 250 recombinant inbred lines derived from a ‘Francis’ by ‘Rondo’ cross using data collected at the maximum tillering stage from two years of greenhouse study, and further compared these QTLs with those mapped at the harvest stage from a field study. Across these three studies, we discovered six qTNs, two qRBs, and three qSBs. Multiple linear regression further indicated that qTN1-2, qTN3-3, qTN4-1, qRB3-1, and qRB5-1 were significant at the maximum tillering stage while qTN3-2 was detected only at the harvest stage. Moreover, qTN3-1 was consistently significant across different developmental stages and growing environments. The genes identified from the peak target qTN regions included a carotenoid metabolism enzyme, a MYB transcription factor, a CBS domain-containing protein, a SAC3/GANP family protein, a TIFY motif containing protein, and an ABC transporter protein. Two genes in the qRB peak target regions included an expressed protein and a WRKY gene. This knowledge of the QTLs, associated markers, candidate genes, and germplasm resources with high TN, RB and SB is of value to rice cultivar improvement programs.

Quantitative trait loci (QTL) for low temperature tolerance at the young microspore stage in rice (Oryza sativa L.) in Australian breeding material

Low temperatures at the young microspore stage (YMS) decreases spikelet fertility and is a major limiting factor to rice production in temperate Australia. Low temperature tolerance is a difficult trait to phenotype, hence there is a strong desire for the identification of quantitative trait loci (QTL) for their use in marker-assisted selection (MAS). Association mapping was used in several breeding populations with a known source of low temperature tolerance, Norin PL8, to identify QTL for low temperature tolerance. A novel QTL for spikelet fertility was identified on chromosome 6, qYMCT6.1, in which the Australian variety, Kyeema, was the donor for increased fertility. Additional five genomics regions were identified that co-located with previously reported QTL, two of which have been previously cloned. Additionally, for the first time a QTL for spikelet fertility qYMCT10.1, has been shown to co-locate with the number of dehisced anthers qYMCTF10.1 which increases the shedding of pollen from the anthers. This study revealed one new QTL for low temperature tolerance at YMS in temperate japonica germplasm and identified an additional five previously reported. These QTL will be utilised for MAS in the Australian rice breeding program and may have merit for temperate breeding programs globally.

Phenotypic variation and genome-wide association studies of main culm panicle node number, maximum node production rate, and degree-days to heading in rice

Background

Grain yield is a complex trait that results from interaction between underlying phenotypic traits and climatic, edaphic, and biotic variables. In rice, main culm panicle node number (MCPNN; the node number on which the panicle is borne) and maximum node production rate (MNPR; the number of leaves that emerge per degree-day > 10°C) are primary phenotypic plant traits that have significant positive direct effects on yield-related traits. Degree-days to heading (DDTH), which has a significant positive effect on grain yield, is influenced by the interaction between MCPNN and MNPR. The objective of this research is to assess the phenotypic variation of MCPNN, MNPR, and DDTH in a panel of diverse rice accessions, determine regions in the rice genome associated with these traits using genome-wide association studies (GWAS), and identify putative candidate genes that control these traits.

Results

Considerable variation was observed for the three traits in a 220-genotype diverse rice population. MCPNN ranged from 8.1 to 20.9 nodes in 2018 and from 9.9 to 21.0 nodes in 2019. MNPR ranged from 0.0097 to 0.0214 nodes/degree day > 10°C in 2018 and from 0.0108 to 0.0193 nodes/degree-day > 10°C in 2019. DDTH ranged from 713 to 2,345 degree-days > 10°C in 2018 and from 778 to 2,404 degree-days > 10°C in 2019.

Thirteen significant (P < 2.91 x 10^-7) trait-single nucleotide polymorphism (SNP) associations were identified using the multilocus mixed linear model for GWAS. Significant associations between MCPNN and three SNPs in chromosome 2 (S02_12032235, S02_11971745, and S02_12030176) were detected with both the 2018 and best linear unbiased prediction (BLUP) datasets. Nine SNPs in chromosome 6 (S06_1970442, S06_2310856, S06_2550351, S06_1968653, S06_2296852, S06_1968680, S06_1968681, S06_1970597, and S06_1970602) were significantly associated with MNPR in the 2019 dataset. One SNP in chromosome 11 (S11_29358169) was significantly associated with the DDTH in the BLUP dataset.

Conclusions

This study identifies SNP markers that are putatively associated with MCPNN, MNPR, and DDTH. Some of these SNPs were located within or near gene models, which identify possible candidate genes involved in these traits. Validation of the putative candidate genes through expression and gene editing analyses are necessary to confirm their roles in regulating MCPNN, MNPR, and DDTH. Identifying the underlying genetic basis for primary phenotypic traits MCPNN and MNPR could lead to the development of fast and efficient approaches for their estimation, such as marker-assisted selection and gene editing, which is essential in increasing breeding efficiency and enhancing grain yield in rice. On the other hand, DDTH is a resultant variable that is highly affected by nitrogen and water management, plant density, and several other factors.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-022-08629-y.

Shaping the root system architecture in plants for adaptation to drought stress

Root system architecture plays an important role in plant adaptation to drought stress. The root system architecture (RSA) consists of several structural features, which includes number and length of main and lateral roots along with the density and length of root hairs. These features exhibit plasticity under water-limited environments and could be critical to developing crops with efficient root systems for adaptation under drought. Recent advances in the omics approaches have significantly improved our understanding of the regulatory mechanisms of RSA remodeling under drought and the identification of genes and other regulatory elements. Plant response to drought stress at physiological, morphological, biochemical, and molecular levels in root cells is regulated by various phytohormones and their crosstalk. Stress-induced reactive oxygen species play a significant role in regulating root growth and development under drought stress. Several transcription factors responsible for the regulation of RSA under drought have proven to be beneficial for developing drought tolerant crops. Molecular breeding programs for developing drought-tolerant crops have been greatly benefitted by the availability of quantitative trait loci (QTLs) associated with the RSA regulation. In the present review, we have discussed the role of various QTLs, signaling components, transcription factors, microRNAs and crosstalk among various phytohormones in shaping RSA and present future research directions to better understand various factors involved in RSA remodeling for adaptation to drought stress. We believe that the information provided herein may be helpful in devising strategies to develop crops with better RSA for efficient uptake and utilization of water and nutrients under drought conditions.

Dissecting the Root Phenotypic and Genotypic Variability of the Iowa Mung Bean Diversity Panel

Mung bean [Vigna radiata (L.) Wilczek] is a drought-tolerant, short-duration crop, and a rich source of protein and other valuable minerals, vitamins, and antioxidants. The main objectives of this research were (1) to study the root traits related with the phenotypic and genetic diversity of 375 mung bean genotypes of the Iowa (IA) diversity panel and (2) to conduct genome-wide association studies of root-related traits using the Automated Root Image Analysis (ARIA) software. We collected over 9,000 digital images at three-time points (days 12, 15, and 18 after germination). A broad sense heritability for days 15 (0.22-0.73) and 18 (0.23-0.87) was higher than that for day 12 (0.24-0.51). We also reported root ideotype classification, i.e., PI425425 (India), PI425045 (Philippines), PI425551 (Korea), PI264686 (Philippines), and PI425085 (Sri Lanka) that emerged as the top five in the topsoil foraging category, while PI425594 (unknown origin), PI425599 (Thailand), PI425610 (Afghanistan), PI425485 (India), and AVMU0201 (Taiwan) were top five in the drought-tolerant and nutrient uptake "steep, cheap, and deep" ideotype. We identified promising genotypes that can help diversify the gene pool of mung bean breeding stocks and will be useful for further field testing. Using association studies, we identified markers showing significant associations with the lateral root angle (LRA) on chromosomes 2, 6, 7, and 11, length distribution (LED) on chromosome 8, and total root length-growth rate (TRL_GR), volume (VOL), and total dry weight (TDW) on chromosomes 3 and 5. We discussed genes that are potential candidates from these regions. We reported beta-galactosidase 3 associated with the LRA, which has previously been implicated in the adventitious root development via transcriptomic studies in mung bean. Results from this work on the phenotypic characterization, root-based ideotype categories, and significant molecular markers associated with important traits will be useful for the marker-assisted selection and mung bean improvement through breeding.

Prospectus of Genomic Selection and Phenomics in Cereal, Legume and Oilseed Breeding Programs

The last decade witnessed an unprecedented increase in the adoption of genomic selection (GS) and phenomics tools in plant breeding programs, especially in major cereal crops. GS has demonstrated the potential for selecting superior genotypes with high precision and accelerating the breeding cycle. Phenomics is a rapidly advancing domain to alleviate phenotyping bottlenecks and explores new large-scale phenotyping and data acquisition methods. In this review, we discuss the lesson learned from GS and phenomics in six self-pollinated crops, primarily focusing on rice, wheat, soybean, common bean, chickpea, and groundnut, and their implementation schemes are discussed after assessing their impact in the breeding programs. Here, the status of the adoption of genomics and phenomics is provided for those crops, with a complete GS overview. GS’s progress until 2020 is discussed in detail, and relevant information and links to the source codes are provided for implementing this technology into plant breeding programs, with most of the examples from wheat breeding programs. Detailed information about various phenotyping tools is provided to strengthen the field of phenomics for a plant breeder in the coming years. Finally, we highlight the benefits of merging genomic selection, phenomics, and machine and deep learning that have resulted in extraordinary results during recent years in wheat, rice, and soybean. Hence, there is a potential for adopting these technologies into crops like the common bean, chickpea, and groundnut. The adoption of phenomics and GS into different breeding programs will accelerate genetic gain that would create an impact on food security, realizing the need to feed an ever-growing population.

Assessment of Genetic Diversity and Relatedness in an Andean Potato Collection from Argentina by High-Density Genotyping

Native potatoes are the most diverse among cultivated potato species and thus constitute a valuable source for identifying genes for potato improvement. Nevertheless, high-density mapping, needed to reveal allelic diversity, has not been performed for native Argentinian potatoes. We present a study of the genetic variability and population structure of 96 Andigena potatoes from Northwestern Argentina performed using a subset of 5035 SNPs with no missing data and full reproducibility. These high-density markers are distributed across the genome and present a good coverage of genomic regions. A Bayesian approach revealed the presence of: (I) a major group comprised of most of the Andean accessions; (II) a smaller group containing the out-group cv. Spunta and the sequenced genotype DM; and (III) a third group containing colored flesh potatoes. This grouping was also consistent when maximum likelihood trees were constructed and further confirmed by a principal coordinate analysis. A group of 19 accessions stored as Andean varieties clustered consistently with group Tuberosum accessions. This was in agreement with previous studies and we hypothesize that they may be reintroductions of European-bred long day-adapted potatoes. The present study constitutes a valuable source for allele mining of genes of interest and thus provides a tool for association mapping studies.

Pinpointing genomic regions associated with root system architecture in rice through an integrative meta-analysis approach

Applying an integrated meta-analysis approach led to identification of meta-QTLs/ candidate genes associated with rice root system architecture, which can be used in MQTL-assisted breeding/ genetic engineering of root traits. Root system architecture (RSA) is an important factor for facilitating water and nutrient uptake from deep soils and adaptation to drought stress conditions. In the present research, an integrated meta-analysis approach was employed to find candidate genes and genomic regions involved in rice RSA traits. A whole-genome meta-analysis was performed for 425 initial QTLs reported in 34 independent experiments controlling RSA traits under control and drought stress conditions in the previous twenty years. Sixty-four consensus meta-QTLs (MQTLs) were detected, unevenly distributed on twelve rice chromosomes. The confidence interval (CI) of the identified MQTLs was obtained as 0.11-14.23 cM with an average of 3.79 cM, which was 3.88 times narrower than the mean CI of the original QTLs. Interestingly, 52 MQTLs were co-located with SNP peak positions reported in rice genome-wide association studies (GWAS) for root morphological traits. The genes located in these RSA-related MQTLs were detected and explored to find the drought-responsive genes in the rice root based on the RNA-seq and microarray data. Multiple RSA and drought tolerance-associated genes were found in the MQTLs including the genes involved in auxin biosynthesis or signaling (e.g. YUCCA, WOX, AUX/IAA, ARF), root angle (DRO1-related genes), lateral root development (e.g. DSR, WRKY), root diameter (e.g. OsNAC5), plant cell wall (e.g. EXPA), and lignification (e.g. C4H, PAL, PRX and CAD). The genes located within both the SNP peak positions and the QTL-overview peaks for RSA are suggested as novel candidate genes for further functional analysis. The promising candidate genes and MQTLs can be used as basis for genetic engineering and MQTL-assisted breeding of root phenotypes to improve yield potential, stability and performance in a water-stressed environment.

Testing the effectiveness of genetic monitoring using genetic non-invasive sampling

Effective conservation requires accurate data on population genetic diversity, inbreeding, and genetic structure. Increasingly, scientists are adopting genetic non-invasive sampling (gNIS) as a cost-effective population-wide genetic monitoring approach. gNIS has, however, known limitations which may impact the accuracy of downstream genetic analyses. Here, using high-quality single nucleotide polymorphism (SNP) data from blood/tissue sampling of a free-ranging koala population (n = 430), we investigated how the reduced SNP panel size and call rate typical of genetic non-invasive samples (derived from experimental and field trials) impacts the accuracy of genetic measures, and also the effect of sampling intensity on these measures. We found that gNIS at small sample sizes (14% of population) can provide accurate population diversity measures, but slightly underestimated population inbreeding coefficients. Accurate measures of internal relatedness required at least 33% of the population to be sampled. Accurate geographic and genetic spatial autocorrelation analysis requires between 28% and 51% of the population to be sampled. We show that gNIS at low sample sizes can provide a powerful tool to aid conservation decision-making and provide recommendations for researchers looking to apply these techniques to free-ranging systems.

Enhanced heterozygosity from male meiotic chromosome chains is superseded by hybrid female asexuality in termites

Although males are a ubiquitous feature of animals, they have been lost repeatedly in diverse lineages. The tendency for obligate asexuality to evolve is thought to be reduced in animals whose males play a critical role beyond the contribution of gametes, for example, via care of offspring or provision of nuptial gifts. To our knowledge, the evolution of obligate asexuality in such species is unknown. In some species that undergo frequent inbreeding, males are hypothesized to play a key role in maintaining genetic heterozygosity through the possession of neo-sex chromosomes, although empirical evidence for this is lacking. Because inbreeding is a key feature of the life cycle of termites, we investigated the potential role of males in promoting heterozygosity within populations through karyotyping and genome-wide single-nucleotide polymorphism analyses of the drywood termite Glyptotermes nakajimai We showed that males possess up to 15 out of 17 of their chromosomes as sex-linked (sex and neo-sex) chromosomes and that they maintain significantly higher levels of heterozygosity than do females. Furthermore, we showed that two obligately asexual lineages of this species-representing the only known all-female termite populations-arose independently via intraspecific hybridization between sexual lineages with differing diploid chromosome numbers. Importantly, these asexual females have markedly higher heterozygosity than their conspecific males and appear to have replaced the sexual lineages in some populations. Our results indicate that asexuality has enabled females to supplant a key role of males.

Has the introduction of two subspecies generated dispersal barriers among invasive possums in New Zealand?

The introduction of species into new environments provides the opportunity for the evolution of new forms through admixture and novel selection pressures. The common brushtail possum, Trichosurus vulpecula vulpecula from the Australian mainland and T.v.fuliginosus from Tasmania, were introduced multiple times to New Zealand from Australia to become one of New Zealand’s most significant pests. Although derived from two subspecies, possums in New Zealand are generally considered to be a single entity. In a previous analysis, we showed that possums in the Hawkes Bay region of New Zealand appeared to consist of at least two overlapping populations. Here, we extend that analysis using a genotype-by-sequencing approach to examine the origins and population structure of those possums and compare their genetic diversity to animals sampled from Australia. We identify two populations of each subspecies in Hawkes Bay and provide clear evidence of a contact zone between them in which a hybrid form is evident. Our analysis of private alleles shows higher rates of dispersal into the contact zone than away from it, suggesting that the contact zone functions as a sink (and hence as a barrier) between the two subspecies. Given the widespread and overlapping distribution of the two subspecies across both large islands in New Zealand, it is possible that many such contact zones exist. These results suggest an opportunity for a more targeted approach to controlling this pest by recognising sub-specific differences and identifying the contact zones that may form between them.

New drought-adaptive loci underlying candidate genes on wheat chromosome 4B with improved photosynthesis and yield responses

Flag leaf serves as an essential source of assimilates during grain filling, thereby contributing to grain yield up to 48%. Thus, high-throughput phenotyping of flag leaves is crucial to determine their physiological and genetic basis of yield formation and drought adaptation. Here, we utilized 200 wheat cultivars to identify drought-adaptive loci underlying candidate genes associated with flag leaf biomass and photosynthesis-related traits using a genome-wide association study (GWAS). GWAS revealed 21 significant marker-trait associations for key photosynthetic traits in response to drought stress. Analysis of linkage disequilibrium (LD) in these SNPs intervals discovered 103 significant SNPs that established distinct LD blocks containing a total of 382 candidate genes putatively involved in physiological processes, including photosynthesis and water responses. Further, in silico transcript analysis identified two candidate genes in locus AX-580365925 on chromosome 4B, those were found to be highly expressed under drought and associated with proton-transporting ATP synthase activity and stress response pathways. Accordingly, we identified significant allelic haplotype differences on this same locus. The tolerant haplotype (higher chlorophyll content under drought) representing major allele was more abundant and stably increased photosynthetic efficiency and yield under drought scenarios. Collectively, this study offers new adaptive loci and beneficial alleles to reshape the flag leaf physiological and associated photosynthetic components for better yield and sustainability to water-deficit stress.

Association mapping of drought tolerance and agronomic traits in rice (Oryza sativa L.) landraces

BACKGROUND

Asian cultivars were predominantly represented in global rice panel selected for sequencing and to identify novel alleles for drought tolerance. Diverse genetic resources adapted to Indian subcontinent were not represented much in spite harboring useful alleles that could improve agronomic traits, stress resilience and productivity. These rice accessions are valuable genetic resource in developing rice varieties suited to different rice ecosystem that experiences varying drought stress level, and at different crop stages. A core collection of rice germplasm adapted to Southwestern Indian peninsular genotyped using SSR markers and characterized by contrasting water regimes to associate genomic regions for physiological, root traits and yield related traits. Genotyping-By-Sequencing of selected accessions within the diverse panel revealed haplotype variation in genic content within genomic regions mapped for physiological, morphological and root traits.

RESULTS

Diverse rice panel (99 accessions) were evaluated in field and measurements on plant physiological, root traits and yield related traits were made over five different seasons experiencing varying drought stress intensity at different crop stages. Traits like chlorophyll stability index, leaf rolling, days to 50% flowering, chlorophyll content, root volume and root biomass were identified as best predictors of grain yield under stress. Association mapping revealed genetic variation among accessions and revealed 14 genomic targets associated with different physiological, root and plant production traits. Certain accessions were found to have beneficial allele to improve traits, plant height, root length and spikelet fertility, that contribute to the grain yield under stress. Genomic characterization of eleven accessions revealed haplotype variation within key genomic targets on chromosomes 1, 4, 6 and 11 for potential use as molecular markers to combine drought avoidance and tolerance traits. Genes mined within the genomic QTL intervals identified were prioritized based on tissue specific expression level in publicly available rice transcriptome data.

CONCLUSION

The genetic and genomic resources identified will enable combining traits with agronomic value to optimize yield under stress and hasten trait introgression into elite cultivars. Alleles associated with plant height, specific leaf area, root length from PTB8 and spikelet fertility and grain weight from PTB26 can be harnessed in future rice breeding program.

Genome-wide association study for morphological, phenological, quality, and yield traits in einkorn (Triticum monococcum L. subsp. monococcum)

Einkorn (Triticum monococcum L. subsp. monococcum, 2n = 2× = 14, AmAm) is a diploid wheat whose cultivation was widespread in the Mediterranean and European area till the Bronze Age, before it was replaced by the more productive durum and bread wheats. Although scarcely cultivated nowadays, it has gained renewed interest due to its relevant nutritional properties and as source of genetic diversity for crop breeding. However, the molecular basis of many traits of interest in einkorn remain still unknown. A panel of 160 einkorn landraces, from different parts of the distribution area, was characterized for several phenotypic traits related to morphology, phenology, quality, and yield for 4 years in two locations. An approach based on co-linearity with the A genome of bread wheat, supported also by that with Triticum urartu genome, was exploited to perform association mapping, even without an einkorn anchored genome. The association mapping approach uncovered numerous marker-trait associations; for 37 of these, a physical position was inferred by homology with the bread wheat genome. Moreover, numerous associated regions were also assigned to the available T. monococcum contigs. Among the intervals detected in this work, three overlapped with regions previously described as involved in the same trait, while four other regions were localized in proximity of loci previously described and presumably refer to the same gene/QTL. The remaining associated regions identified in this work could represent a novel and useful starting point for breeding approaches to improve the investigated traits in this neglected species.

Discovery and Chromosomal Location a Highly Effective Oat Crown Rust Resistance Gene Pc50-5

Crown rust, caused by Puccinia coronata f. sp. avenae, is one of the most destructive fungal diseases of oat worldwide. Growing disease-resistant oat cultivars is the preferred method of preventing the spread of rust and potential epidemics. The object of the study was Pc50-5, a race-specific seedling crown rust resistant gene, highly effective at all growth stages, selected from the differential line Pc50 (Avena sterilis L. CW 486-1 × Pendek). A comparison of crown rust reaction as well as an allelism test showed the distinctiveness of Pc50-5, whereas the proportions of phenotypes in segregating populations derived from a cross with two crown rust-susceptible Polish oat cultivars, Kasztan × Pc50-5 and Bingo × Pc50-5, confirmed monogenic inheritance of the gene, indicating its usefulness in oat breeding programs. Effective gene introgression depends on reliable gene identification in the early stages of plant development; thus, the aim of the study was to develop molecular markers that are tightly linked to Pc50-5. Segregating populations of Kasztan × Pc50-5 were genotyped using DArTseq technology based on next-generation Illumina short-read sequencing. Markers associated with Pc50-5 were located on chromosome 6A of the current version of the oat reference genome (Avena sativa OT3098 v2, PepsiCo) in the region between 434,234,214 and 440,149,046 bp and subsequently converted to PCR-based SCAR (sequence-characterized amplified region) markers. Furthermore, 5426978_SCAR and 24031809_SCAR co-segregated with the Pc50-5 resistance allele and were mapped to the partial linkage group at 0.6 and 4.0 cM, respectively. The co-dominant 58163643_SCAR marker was the best diagnostic and it was located closest to Pc50-5 at 0.1 cM. The newly discovered, very strong monogenic crown rust resistance may be useful for oat improvement. DArTseq sequences converted into specific PCR markers will be a valuable tool for marker-assisted selection in breeding programs.

Combining UAV-RGB high-throughput field phenotyping and genome-wide association study to reveal genetic variation of rice germplasms in dynamic response to drought stress

Accurate and high-throughput phenotyping of the dynamic response of a large rice population to drought stress in the field is a bottleneck for genetic dissection and breeding of drought resistance. Here, high-efficiency and high-frequent image acquisition by an unmanned aerial vehicle (UAV) was utilized to quantify the dynamic drought response of a rice population under field conditions. Deep convolutional neural networks (DCNNs) and canopy height models were applied to extract highly correlated phenotypic traits including UAV-based leaf-rolling score (LRS_uav), plant water content (PWC_uav) and a new composite trait, drought resistance index by UAV (DRI_uav). The DCNNs achieved high accuracy (correlation coefficient R = 0.84 for modeling set and R = 0.86 for test set) to replace manual leaf-rolling rating. PWC_uav values were precisely estimated (correlation coefficient R = 0.88) and DRI_uav was modeled to monitor the drought resistance of rice accessions dynamically and comprehensively. A total of 111 significantly associated loci were detected by genome-wide association study for the three dynamic traits, and 30.6% of them were not detected in previous mapping studies using nondynamic drought response traits. Unmanned aerial vehicle and deep learning are confirmed effective phenotyping techniques for more complete genetic dissection of rice dynamic responses to drought and exploration of valuable alleles for drought resistance improvement.

Genome-Wide Association Mapping of Mixed Linkage (1,3;1,4)-β-Glucan and Starch Contents in Rice Whole Grain

The glucan content of rice is a key factor defining its nutritional and economic value. Starch and its derivatives have many industrial applications such as in fuel and material production. Non-starch glucans such as (1,3;1,4)-β-D-glucan (mixed-linkage β-glucan, MLG) have many benefits in human health, including lowering cholesterol, boosting the immune system, and modulating the gut microbiome. In this study, the genetic variability of MLG and starch contents were analyzed in rice (Oryza sativa L.) whole grain, by performing a new quantitative analysis of the polysaccharide content of rice grains. The 197 rice accessions investigated had an average MLG content of 252 μg/mg, which was negatively correlated with the grain starch content. A new genome-wide association study revealed seven significant quantitative trait loci (QTLs) associated with the MLG content and two QTLs associated with the starch content in rice whole grain. Novel genes associated with the MLG content were a hexose transporter and anthocyanidin 5,3-O-glucosyltransferase. Also, the novel gene associated with the starch content was a nodulin-like domain. The data pave the way for a better understanding of the genes involved in determining both MLG and starch contents in rice grains and should facilitate future plant breeding programs.

Identification of Markers for Root Traits Related to Drought Tolerance Using Traditional Rice Germplasm

Drought is one of the important constraints affecting rice productivity worldwide. The vigorous shoot and deep root system help to improve drought resistance. In present era, genome-wide association study (GWAS) is the preferred method for mapping of QTLs for complex traits such as root and drought tolerance traits. In the present study, 114 rice genotypes were evaluated for various root and shoot traits under water stress conditions. All genotypes showed a significant amount of variation for various root and shoot traits. Correlation analysis revealed that high dry shoot weight and fresh shoot weight is associated with root length, root volume, fresh root weight and dry root weight. A total of 11 significant marker-trait associations were detected for various root, shoot and drought tolerance traits with the coefficient of determination (R²) ranging from 18.99 to 53.41%. Marker RM252 and RM212 showed association with three root traits which suggests their scope for improvement of root system. In the present study, a novel QTL was detected for root length associated with RM127, explaining 19.30% of variation. The marker alleles with increasing phenotypic effects for root and drought-tolerant traits can be exploited for improvement of root and drought tolerance traits using marker-assisted selection.

Peanut Leaf Wilting Estimation From RGB Color Indices and Logistic Models

Peanut (Arachis hypogaea L.) is an important crop for United States agriculture and worldwide. Low soil moisture is a major constraint for production in all peanut growing regions with negative effects on yield quantity and quality. Leaf wilting is a visual symptom of low moisture stress used in breeding to improve stress tolerance, but visual rating is slow when thousands of breeding lines are evaluated and can be subject to personnel scoring bias. Photogrammetry might be used instead. The objective of this article is to determine if color space indices derived from red-green-blue (RGB) images can accurately estimate leaf wilting for breeding selection and irrigation triggering in peanut production. RGB images were collected with a digital camera proximally and aerially by a unmanned aerial vehicle during 2018 and 2019. Visual rating was performed on the same days as image collection. Vegetation indices were intensity, hue, saturation, lightness, a^∗, b^∗, u^∗, v^∗, green area (GA), greener area (GGA), and crop senescence index (CSI). In particular, hue, a^∗, u^∗, GA, GGA, and CSI were significantly (p ≤ 0.0001) associated with leaf wilting. These indices were further used to train an ordinal logistic regression model for wilting estimation. This model had 90% accuracy when images were taken aerially and 99% when images were taken proximally. This article reports on a simple yet key aspect of peanut screening for tolerance to low soil moisture stress and uses novel, fast, cost-effective, and accurate RGB-derived models to estimate leaf wilting.

DArTseq-Based High-Throughput SilicoDArT and SNP Markers Applied for Association Mapping of Genes Related to Maize Morphology

Today, agricultural productivity is essential to meet the needs of a growing population, and is also a key tool in coping with climate change. Innovative plant breeding technologies such as molecular markers, phenotyping, genotyping, the CRISPR/Cas method and next-generation sequencing can help agriculture meet the challenges of the 21st century more effectively. Therefore, the aim of the research was to identify single-nucleotide polymorphisms (SNPs) and SilicoDArT markers related to select morphological features determining the yield in maize. The plant material consisted of ninety-four inbred lines of maize of various origins. These lines were phenotyped under field conditions. A total of 14 morphological features was analyzed. The DArTseq method was chosen for genotyping because this technique reduces the complexity of the genome by restriction enzyme digestion. Subsequently, short fragment sequencing was used. The choice of a combination of restrictases allowed the isolation of highly informative low copy fragments of the genome. Thanks to this method, 90% of the obtained DArTseq markers are complementary to the unique sequences of the genome. All the observed features were normally distributed. Analysis of variance indicated that the main effect of lines was statistically significant (p < 0.001) for all 14 traits of study. Thanks to the DArTseq analysis with the use of next-generation sequencing (NGS) in the studied plant material, it was possible to identify 49,911 polymorphisms, of which 33,452 are SilicoDArT markers and the remaining 16,459 are SNP markers. Among those mentioned, two markers associated with four analyzed traits deserved special attention: SNP (4578734) and SilicoDArT (4778900). SNP marker 4578734 was associated with the following features: anthocyanin coloration of cob glumes, number of days from sowing to anthesis, number of days from sowing to silk emergence and anthocyanin coloration of internodes. SilicoDArT marker 4778900 was associated with the following features: number of days from sowing to anthesis, number of days from sowing to silk emergence, tassel: angle between the axis and lateral branches and plant height. Sequences with a length of 71 bp were used for physical mapping. The BLAST and EnsemblPlants databases were searched against the maize genome to identify the positions of both markers. Marker 4578734 was localized on chromosome 7, the closest gene was Zm00001d022467, approximately 55 Kb apart, encoding anthocyanidin 3-O-glucosyltransferase. Marker 4778900 was located on chromosome 7, at a distance of 45 Kb from the gene Zm00001d045261 encoding starch synthase I. The latter observation indicated that these flanking SilicoDArT and SNP markers were not in a state of linkage disequilibrium.

A novel motif in the 5'-UTR of an orphan gene 'Big Root Biomass' modulates root biomass in sesame

Developing crops with improved root system is crucial in current global warming scenario. Underexploited crops are valuable reservoirs of unique genes that can be harnessed for the improvement of major crops. In this study, we performed genome-wide association studies on seven root traits in sesame (Sesamum indicum L.) and uncovered 409 significant signals, 19 quantitative trait loci containing 32 candidate genes. A peak SNP significantly associated with root number and root dry weight traits was located in the promoter of the gene named 'Big Root Biomass' (BRB), which was subsequently validated in a bi-parental population. BRB has no functional annotation and is restricted to the Lamiales order. We detected the presence of a novel motif 'AACACACAC' located in the 5'-UTR of BRB in single and duplicated copy in accessions with high and small root biomass, respectively. A strong expression level of BRB was negatively correlated with high root biomass, and this was attributed to the gene SiMYB181 which represses the activity of BRB by binding specifically to the single motif but not to the duplicated one. Curiously, the allele that enhanced BRB expression has been intensively selected by modern breeding. Overexpression of BRB in Arabidopsis modulates auxin pathway leading to reduced root biomass, improved yield parameters under normal growth conditions and increased drought stress sensitivity. Overall, BRB represents a solid gene model for improving the performance of sesame and other crops.

Stable and Novel Quantitative Trait Loci (QTL) Confer Narrow Root Cone Angle in an Aerobic Rice (Oryza sativa L.) Production System

BACKGROUND

Aerobic rice production (AP) may be a solution to the looming water crisis by utilising less water compared to traditional flooded culture. As such, development of genotypes with narrow root cone angle (RCA) is considered a key AP adaptation trait as it could lead to deeper rooting and ensure water uptake at depth. Quantitative trait loci (QTL) and genes associated with rooting angle have been identified in rice, but usually in conventional transplanted systems or in upland and drought conditions. This study aimed to identify QTL associated with RCA in AP systems using a recombinant inbred line population derived from IRAT109.

RESULTS

Four experiments conducted in glasshouse and aerobic field conditions revealed significant genotypic variation existed for RCA in the population. Single and multiple QTL models identified the presence of eight QTL distributed in chromosomes 1, 2, 3, 4, and 11. Combined, these QTL explained 36.7-51.2% of the genotypic variance in RCA present in the population. Two QTL, qRCA1.1 and qRCA1.3, were novel and may be new targets for improvement of RCA. Genotypes with higher number of favourable QTL alleles tended to have narrower RCA. qRCA4 was shown to be a major and stable QTL explaining up to 24.3% of the genotypic variation, and the presence of the target allele resulted in as much as 8.6° narrower RCA. Several genes related to abiotic stress stimulus response were found in the qRCA4 region.

CONCLUSION

Stable and novel genomic regions associated with RCA have been identified. Genotypes which had combinations of these QTL, resulted in a narrower RCA phenotype. Allele mining, gene cloning, and physiological dissection should aid in understanding the molecular function and mechanisms underlying RCA and these QTL. Ultimately, our work provides an opportunity for breeding programs to develop genotypes with narrow RCA and deep roots for improved adaptation in an AP system for sustainable rice production.

Assessment of root phenotypes in mungbean mini-core collection (MMC) from the World Vegetable Center (AVRDC) Taiwan

Mungbean (Vigna radiata L.) is an important food grain legume, but its production capacity is threatened by global warming, which can intensify plant stress and limit future production. Identifying new variation of key root traits in mungbean will provide the basis for breeding lines with effective root characteristics for improved water uptake to mitigate heat and drought stress. The AVRDC mungbean mini core collection consisting of 296 genotypes was screened under modified semi-hydroponic screening conditions to determine the variation for fourteen root-related traits. The AVRDC mungbean mini core collection displayed wide variations for the primary root length, total surface area, and total root length, and based on agglomerative hierarchical clustering eight homogeneous groups displaying different root traits could be identified. Germplasm with potentially favorable root traits has been identified for further studies to identify the donor genotypes for breeding cultivars with enhanced adaptation to water-deficit stress and other stress conditions.

Prediction Accuracies of Genomic Selection for Nine Commercially Important Traits in the Portuguese Oyster (Crassostrea angulata) Using DArT-Seq Technology

Genomic selection has been widely used in terrestrial animals but has had limited application in aquaculture due to relatively high genotyping costs. Genomic information has an important role in improving the prediction accuracy of breeding values, especially for traits that are difficult or expensive to measure. The purposes of this study were to (i) further evaluate the use of genomic information to improve prediction accuracies of breeding values from, (ii) compare different prediction methods (BayesA, BayesCπ and GBLUP) on prediction accuracies in our field data, and (iii) investigate the effects of different SNP marker densities on prediction accuracies of traits in the Portuguese oyster (Crassostrea angulata). The traits studied are all of economic importance and included morphometric traits (shell length, shell width, shell depth, shell weight), edibility traits (tenderness, taste, moisture content), and disease traits (Polydora sp. and Marteilioides chungmuensis). A total of 18,849 single nucleotide polymorphisms were obtained from genotyping by sequencing and used to estimate genetic parameters (heritability and genetic correlation) and the prediction accuracy of genomic selection for these traits. Multi-locus mixed model analysis indicated high estimates of heritability for edibility traits; 0.44 for moisture content, 0.59 for taste, and 0.72 for tenderness. The morphometric traits, shell length, shell width, shell depth and shell weight had estimated genomic heritabilities ranging from 0.28 to 0.55. The genomic heritabilities were relatively low for the disease related traits: Polydora sp. prevalence (0.11) and M. chungmuensis (0.10). Genomic correlations between whole weight and other morphometric traits were from moderate to high and positive (0.58–0.90). However, unfavourably positive genomic correlations were observed between whole weight and the disease traits (0.35–0.37). The genomic best linear unbiased prediction method (GBLUP) showed slightly higher accuracy for the traits studied (0.240–0.794) compared with both BayesA and BayesCπ methods but these differences were not significant. In addition, there is a large potential for using low-density SNP markers for genomic selection in this population at a number of 3000 SNPs. Therefore, there is the prospect to improve morphometric, edibility and disease related traits using genomic information in this species.

Evaluation of genetic structure in European wheat cultivars and advanced breeding lines using high-density genotyping-by-sequencing approach

BACKGROUND

The genetic diversity and gene pool characteristics must be clarified for efficient genome-wide association studies, genomic selection, and hybrid breeding. The aim of this study was to evaluate the genetic structure of 509 wheat accessions representing registered varieties and advanced breeding lines via the high-density genotyping-by-sequencing approach.

RESULTS

More than 30% of 13,499 SNP markers representing 2162 clusters were mapped to genes, whereas 22.50% of 26,369 silicoDArT markers overlapped with coding sequences and were linked in 3527 blocks. Regarding hexaploidy, perfect sequence matches following BLAST searches were not sufficient for the unequivocal mapping to unique loci. Moreover, allelic variations in homeologous loci interfered with heterozygosity calculations for some markers. Analyses of the major genetic changes over the last 27 years revealed the selection pressure on orthologs of the gibberellin biosynthesis-related GA2 gene and the senescence-associated SAG12 gene. A core collection representing the wheat population was generated for preserving germplasm and optimizing breeding programs.

CONCLUSIONS

Our results confirmed considerable differences among wheat subgenomes A, B and D, with D characterized by the lowest diversity but the highest LD. They revealed genomic regions that have been targeted by breeding.

Genome-Wide Association Study (GWAS) to Identify Salt-Tolerance QTLs Carrying Novel Candidate Genes in Rice During Early Vegetative Stage

BACKGROUND

Rice is considered as a salt-sensitive plant, particularly at early vegetative stage, and its production is suffered from salinity due to expansion of salt affected land in areas under cultivation. Hence, significant increase of rice productivity on salinized lands is really necessary. Today genome-wide association study (GWAS) is a method of choice for fine mapping of QTLs involved in plant responses to abiotic stresses including salinity stress at early vegetative stage. In this study using > 33,000 SNP markers we identified rice genomic regions associated to early stage salinity tolerance. Eight salinity-related traits including shoot length (SL), root length (RL), root dry weight (RDW), root fresh weight (RFW), shoot fresh weight (SFW), shoot dry weight (SDW), relative water content (RWC) and TW, and 4 derived traits including SL-R, RL-R, RDW-R and RFW-R in a diverse panel of rice were evaluated under salinity (100 mM NaCl) and normal conditions in growth chamber. Genome-wide association study (GWAS) was applied based on MLM(+Q + K) model.

RESULTS

Under stress conditions 151 trait-marker associations were identified that were scattered on 10 chromosomes of rice that arranged in 29 genomic regions. A genomic region on chromosome 1 (11.26 Mbp) was identified which co-located with a known QTL region SalTol1 for salinity tolerance at vegetative stage. A candidate gene (Os01g0304100) was identified in this region which encodes a cation chloride cotransporter. Furthermore, on this chromosome two other candidate genes, Os01g0624700 (24.95 Mbp) and Os01g0812000 (34.51 Mbp), were identified that encode a WRKY transcription factor (WRKY 12) and a transcriptional activator of gibberellin-dependent alpha-amylase expression (GAMyb), respectively. Also, a narrow interval on the same chromosome (40.79-42.98 Mbp) carries 12 candidate genes, some of them were not so far reported for salinity tolerance at seedling stage. Two of more interesting genes are Os01g0966000 and Os01g0963000, encoding a plasma membrane (PM) H⁺-ATPase and a peroxidase BP1 protein. A candidate gene was identified on chromosome 2 (Os02g0730300 at 30.4 Mbp) encoding a high affinity K⁺ transporter (HAK). On chromosome 6 a DnaJ-encoding gene and pseudouridine synthase gene were identified. Two novel genes on chromosome 8 including the ABI/VP1 transcription factor and retinoblastoma-related protein (RBR), and 3 novel genes on chromosome 11 including a Lox, F-box and Na⁺/H⁺ antiporter, were also identified.

CONCLUSION

Known or novel candidate genes in this research were identified that can be used for improvement of salinity tolerance in molecular breeding programmes of rice. Further study and identification of effective genes on salinity tolerance by the use of candidate gene-association analysis can help to precisely uncover the mechanisms of salinity tolerance at molecular level. A time dependent relationship between salt tolerance and expression level of candidate genes could be recognized.

Multi-year pair-bonding in Murray cod (Maccullochella peelii)

Mating strategies in fishes are known to include polygyny, polyandry and monogamy and provide valuable insights regarding powerful evolutionary forces such as sexual selection. Monogamy is a complex of mating systems that has been relatively neglected. Previous work on mating strategies in fishes has often been based on observation and focused on marine species rather than freshwater fishes. SNPs are increasingly being used as a molecular ecology tool in non-model organisms, and methods of probabilistic genetic analysis of such datasets are becoming available for use in the absence of parental genotypes. This approach can be used to infer mating strategies. The long-term pair bonding seen in mammals, reptiles and birds has not been recorded in freshwater fishes-in every other respect an extremely diverse group. This study shows that multi-year pair bonding occurs in an Australian Percichthyid fish that exhibits paternal care of eggs and larvae. Using SNPs, full sibling pairs of larvae were found over multiple years in a three-year study. Stable isotope signatures of the larvae support the genetic inference that full sibling pairs shared a common mother, the ultimate source of that isotopic signature during oogenesis. Spatial and temporal clustering also suggests that the full sibling larvae are unlikely to be false positive identifications of the probabilistic identification of siblings. For the first time, we show multi-year pair bonding in a wild freshwater fish. This will have important conservation and management implications for the species. This approach could provide insights into many behavioural, ecological and evolutionary questions, particularly if this is not a unique case. Our findings are likely to initiate interest in seeking more examples of monogamy and alternative mating strategies in freshwater fishes, particularly if others improve methods of analysis of SNP data for identification of siblings in the absence of parental genotypes.

Genetic Diversity of Landraces and Improved Varieties of Rice (Oryza sativa L.) in Taiwan

BACKGROUND

Rice, the most important crop in Asia, has been cultivated in Taiwan for more than 5000 years. The landraces preserved by indigenous peoples and brought by immigrants from China hundreds of years ago exhibit large variation in morphology, implying that they comprise rich genetic resources. Breeding goals according to the preferences of farmers, consumers and government policies also alter gene pools and genetic diversity of improved varieties. To unveil how genetic diversity is affected by natural, farmers', and breeders' selections is crucial for germplasm conservation and crop improvement.

RESULTS

A diversity panel of 148 rice accessions, including 47 cultivars and 59 landraces from Taiwan and 42 accessions from other countries, were genotyped by using 75 molecular markers that revealed an average of 12.7 alleles per locus with mean polymorphism information content of 0.72. These accessions could be grouped into five subpopulations corresponding to wild rice, japonica landraces, indica landraces, indica cultivars, and japonica cultivars. The genetic diversity within subpopulations was: wild rices > landraces > cultivars; and indica rice > japonica rice. Despite having less variation among cultivars, japonica landraces had greater genetic variation than indica landraces because the majority of Taiwanese japonica landraces preserved by indigenous peoples were classified as tropical japonica. Two major clusters of indica landraces were formed by phylogenetic analysis, in accordance with immigration from two origins. Genetic erosion had occurred in later japonica varieties due to a narrow selection of germplasm being incorporated into breeding programs for premium grain quality. Genetic differentiation between early and late cultivars was significant in japonica (F_ST = 0.3751) but not in indica (F_ST = 0.0045), indicating effects of different breeding goals on modern germplasm. Indigenous landraces with unique intermediate and admixed genetic backgrounds were untapped, representing valuable resources for rice breeding.

CONCLUSIONS

The genetic diversity of improved rice varieties has been substantially shaped by breeding goals, leading to differentiation between indica and japonica cultivars. Taiwanese landraces with different origins possess various and unique genetic backgrounds. Taiwanese rice germplasm provides diverse genetic variation for association mapping to unveil useful genes and is a precious genetic reservoir for rice improvement.

Sequencing depth and genotype quality: accuracy and breeding operation considerations for genomic selection applications in autopolyploid crops

KEY MESSAGE

Polypoid crop breeders can balance resources between density and sequencing depth, dosage information and fewer highly informative SNPs recommended, non-additive models and QTL advantages on prediction dependent on trait architecture. The autopolyploid nature of potato and sweetpotato ensures a wide range of meiotic configurations and linkage phases leading to complex gene-action and pose problems in genotype data quality and genomic selection analyses. We used a 315-progeny biparental F1 population of hexaploid sweetpotato and a diversity panel of 380 tetraploid potato, genotyped using different platforms to answer the following questions: (i) do polyploid crop breeders need to invest more for additional sequencing depth? (ii) how many markers are required to make selection decisions? (iii) does considering non-additive genetic effects improve predictive ability (PA)? (iv) does considering dosage or quantitative trait loci (QTL) offer significant improvement to PA? Our results show that only a small number of highly informative single nucleotide polymorphisms (SNPs; ≤ 1000) are adequate for prediction in the type of populations we analyzed. We also show that considering dosage information and models considering only additive effects had the best PA for most traits, while the comparative advantage of considering non-additive genetic effects and including known QTL in the predictive model depended on trait architecture. We conclude that genomic selection can help accelerate the rate of genetic gains in potato and sweetpotato. However, application of genomic selection should be considered as part of optimizing the entire breeding program. Additionally, since the predictions in the current study are based on single populations, further studies on the effects of haplotype structure and inheritance on PA should be studied in actual multi-generation breeding populations.

Comparing Genomic Signatures of Selection Between the Abbassa Strain and Eight Wild Populations of Nile Tilapia (Oreochromis niloticus) in Egypt

Domestication to captive rearing conditions, along with targeted selective breeding have genetic consequences that vary from those in wild environments. Nile tilapia (Oreochromis niloticus) is one of the most translocated and farmed aquaculture species globally, farmed throughout Asia, North and South America, and its African native range. In Egypt, a breeding program established the Abbassa Strain of Nile tilapia (AS) in 2002 based on local broodstock sourced from the Nile River. The AS has been intensively selected for growth and has gone through genetic bottlenecks which have likely shifted levels and composition of genetic diversity within the strain. Consequently, there are questions on the possible genetic impact AS escapees may have on endemic populations of Nile tilapia. However, to date there have been no genetic studies comparing genetic changes in the domesticated AS to local wild populations. This study used 9,827 genome-wide SNPs to investigate population genetic structure and signatures of selection in the AS (generations 9–11) and eight wild Nile tilapia populations from Egypt. SNP analyses identified two major genetic clusters (captive and wild populations), with wild populations showing evidence of isolation-by-distance among the Nile Delta and upstream riverine populations. Between genetic clusters, approximately 6.9% of SNPs were identified as outliers with outliers identified on all 22 O. niloticus chromosomes. A lack of localized outlier clustering on the genome suggests that no genes of major effect were presently detected. The AS has retained high levels of genetic diversity (H_{o_All} = 0.21 ± 0.01; H_{e_All} = 0.23 ± 0.01) when compared to wild populations (H_{o_All} = 0.18 ± 0.01; H_{e_All} = 0.17 ± 0.01) after 11 years of domestication and selective breeding. Additionally, 565 SNPs were unique within the AS line. While these private SNPs may be due to domestication signals or founder effects, it is suspected that introgression with blue tilapia (Oreochromis aureus) has occurred. This study highlights the importance of understanding the effects of domestication in addition to wild population structure to inform future management and dissemination decisions. Furthermore, by conducting a baseline genetic study of wild populations prior to the dissemination of a domestic line, the effects of aquaculture on these populations can be monitored over time.

Phenotyping Root Systems in a Set of Japonica Rice Accessions: Can Structural Traits Predict the Response to Drought?

BACKGROUND

The root system plays a major role in plant growth and development and root system architecture is reported to be the main trait related to plant adaptation to drought. However, phenotyping root systems in situ is not suited to high-throughput methods, leading to the development of non-destructive methods for evaluations in more or less controlled root environments. This study used a root phenotyping platform with a panel of 20 japonica rice accessions in order to: (i) assess their genetic diversity for a set of structural and morphological root traits and classify the different types; (ii) analyze the plastic response of their root system to a water deficit at reproductive phase and (iii) explore the ability of the platform for high-throughput phenotyping of root structure and morphology.

RESULTS

High variability for the studied root traits was found in the reduced set of accessions. Using eight selected traits under irrigated conditions, five root clusters were found that differed in root thickness, branching index and the pattern of fine and thick root distribution along the profile. When water deficit occurred at reproductive phase, some accessions significantly reduced root growth compared to the irrigated treatment, while others stimulated it. It was found that root cluster, as defined under irrigated conditions, could not predict the plastic response of roots under drought.

CONCLUSIONS

This study revealed the possibility of reconstructing the structure of root systems from scanned images. It was thus possible to significantly class root systems according to simple structural traits, opening up the way for using such a platform for medium to high-throughput phenotyping. The study also highlighted the uncoupling between root structures under non-limiting water conditions and their response to drought.

Morphological and genome-wide evidence for natural hybridisation within the genus Stipa (Poaceae)

Hybridisation in the wild between closely related species is a common mechanism of speciation in the plant kingdom and, in particular, in the grass family. Here we explore the potential for natural hybridisation in Stipa (one of the largest genera in Poaceae) between genetically distant species at their distribution edges in Mountains of Central Asia using integrative taxonomy. Our research highlights the applicability of classical morphological and genome reduction approaches in studies on wild plant species. The obtained results revealed a new nothospecies, Stipa × lazkovii, which exhibits intermediate characters to S. krylovii and S. bungeana. A high-density DArTseq assay disclosed that S. × lazkovii is an F1 hybrid, and established that the plastid and mitochondrial DNA was inherited from S. bungeana. In addition, molecular markers detected a hybridisation event between morphologically and genetically distant species S. bungeana and probably S. glareosa. Moreover, our findings demonstrated an uncertainty on the taxonomic status of S. bungeana that currently belongs to the section Leiostipa, but it is genetically closer to S. breviflora from the section Barbatae. Finally, we noticed a discrepancy between the current molecular data with the previous findings on S. capillata and S. sareptana.

Genome-wide association study identifies favorable SNP alleles and candidate genes for frost tolerance in pea

BACKGROUND

Frost is a limiting abiotic stress for the winter pea crop (Pisum sativum L.) and identifying the genetic determinants of frost tolerance is a major issue to breed varieties for cold northern areas. Quantitative trait loci (QTLs) have previously been detected from bi-parental mapping populations, giving an overview of the genome regions governing this trait. The recent development of high-throughput genotyping tools for pea brings the opportunity to undertake genetic association studies in order to capture a higher allelic diversity within large collections of genetic resources as well as to refine the localization of the causal polymorphisms thanks to the high marker density. In this study, a genome-wide association study (GWAS) was performed using a set of 365 pea accessions. Phenotyping was carried out by scoring frost damages in the field and in controlled conditions. The association mapping collection was also genotyped using an Illumina Infinium® BeadChip, which allowed to collect data for 11,366 single nucleotide polymorphism (SNP) markers.

RESULTS

GWAS identified 62 SNPs significantly associated with frost tolerance and distributed over six of the seven pea linkage groups (LGs). These results confirmed 3 QTLs that were already mapped in multiple environments on LG III, V and VI with bi-parental populations. They also allowed to identify one locus, on LG II, which has not been detected yet and two loci, on LGs I and VII, which have formerly been detected in only one environment. Fifty candidate genes corresponding to annotated significant SNPs, or SNPs in strong linkage disequilibrium with the formers, were found to underlie the frost damage (FD)-related loci detected by GWAS. Additionally, the analyses allowed to define favorable haplotypes of markers for the FD-related loci and their corresponding accessions within the association mapping collection.

CONCLUSIONS

This study led to identify FD-related loci as well as corresponding favorable haplotypes of markers and representative pea accessions that might to be used in winter pea breeding programs. Among the candidate genes highlighted at the identified FD-related loci, the results also encourage further attention to the presence of C-repeat Binding Factors (CBF) as potential genetic determinants of the frost tolerance locus on LG VI.

Shifts in Reproductive Investment in Response to Competitors Lower Male Reproductive Success

AbstractIn many species, males exhibit phenotypic plasticity in sexually selected traits when exposed to social cues about the intensity of sexual competition. To date, however, few studies have tested how this plasticity affects male reproductive success. We initially tested whether male mosquitofish, Gambusia holbrooki (Poeciliidae), change their investment in traits under pre- and postcopulatory sexual selection depending on the social environment. For a full spermatogenesis cycle, focal males were exposed to visual and chemical cues of rivals that were either present (competitive treatment) or absent (control). Males from the competitive treatment had significantly slower-swimming sperm but did not differ in sperm count from control males. When two males competed for a female, competitive treatment males also made significantly fewer copulation attempts and courtship displays than control males. Further, paternity analysis of 708 offspring from 148 potential sires, testing whether these changes in reproductive traits affected male reproductive success, showed that males previously exposed to cues about the presence of rivals sired significantly fewer offspring when competing with a control male. We discuss several possible explanations for these unusual findings.

Robbery in progress: Historical museum collections bring to light a mitochondrial capture within a bird species widespread across southern Australia, the Copperback Quail-thrush Cinclosoma clarum

We surveyed mitochondrial, autosomal, and Z chromosome diversity within and between the Copperback Quail-thrush Cinclosoma clarum and Chestnut Quail-thrush C. castanotum, which together span the arid and semi-arid zones of southern Australia, and primarily from specimens held in museum collections. We affirm the recent taxonomic separation of the two species and then focus on diversity within the more widespread of the two species, C. clarum. To guide further study of the system and what it offers to understanding the genomics of the differentiation and speciation processes, we develop and present a hypothesis to explain mitonuclear discordance that emerged in ourdata. Following a period of historical allopatry, secondary contact has resulted in an eastern mitochondrial genome replacing the western mitochondrial genome in western populations. This is predicted under a population-level invasion in the opposite direction, that of the western population invading the range of the eastern one. Mitochondrial captures can be driven by neutral, demographic processes, or adaptive mechanisms, and we favor the hypothesized capture being driven by neutral means. We cannot fully reject the adaptive process but suggest how these alternatives may be further tested. We acknowledge an alternative hypothesis, which finds some support in phenotypic data published elsewhere, namely that outcomes of secondary contact have been more complex than our current genomic data suggest. Discriminating and reconciling these two alternative hypotheses, which may not be mutually exclusive, could be tested with closer sampling at levels of population, individual, and nucleotide than has so far been possible. This would be further aided by knowledge of the genetic basis to phenotypic variation described elsewhere.