Selection For Traits Research Articles

Conversion of superior bread wheat genotype HD3209 carrying Lr19/Sr25 into CMS line for development of rust-resistant wheat hybrids

Hybrid development is one of the most promising strategies for boosting crop yields. Parental lines used to create hybrids must have good per se performance and disease resistance for developing superior hybrids. Indian wheat line HD3209 was developed by introducing the rust resistance genes Lr19/Sr25 into the background of popular wheat variety HD2932. The wheat line HD3209 carrying Lr19/Sr25 has been successfully and rapidly converted to the CMS line A-HD3209, with 96.01% background genome recovery, based on selection for agro-morphological traits, rust resistance, pollen sterility, and foreground and background analyses utilizing SSR markers. The converted CMS line A-HD3209 was completely sterile and nearly identical to the recurrent parent HD3209. Based on high per se performance and rust resistance, the study concludes that the derived CMS line A-HD3209 is promising and can be employed successfully in hybrid development.

Trait selection strategy in multi-trait GWAS: Boosting SNP discoverability

Since the first Genome-Wide Association Studies (GWAS), thousands of variant-trait associations have been discovered. However, comprehensively mapping the genetic determinant of complex traits through univariate testing can require prohibitive sample sizes. Multi-trait GWAS can circumvent this issue and improve statistical power by leveraging the joint genetic architecture of human phenotypes. Although many methodological hurdles of multi-trait testing have been solved, the strategy to select traits has been overlooked. In this study, we conducted multi-trait GWAS on approximately 20,000 combinations of 72 traits using an omnibus test as implemented in JASS (Joint Analysis of Summary Statistics). We assessed which genetic features of the sets of traits analysed were associated with an increased detection of variants compared to univariate screening. Several features of the set of traits, including the heritability, the number of traits, and the genetic correlation, drive the multi-trait test gain. Using these features jointly in predictive models captures a large fraction of the power gain of the multi-trait test (Pearson's γ between the observed and predicted gain equals 0.43, P < 1.6 x 10-60). Applying an alternative multi-trait approach (MTAG), we identified similar features of interest, but with an overall 70% lower number of new associations. Finally, selecting sets based on our data-driven models systematically outperformed the common strategy of selecting clinically similar traits. This work provides a unique picture of the determinant of multi-trait GWAS statistical power and outline practical strategies for multi-trait testing.

The Phenotypic Variation in Moso Bamboo and the Selection of Key Traits.

This research aimed to explore the diverse phenotypic characteristics of moso bamboo in China and pinpoint essential characteristics of moso bamboo. In this study, 63 grids were selected using the grid method to investigate 28 phenotypic traits of moso bamboo across the entire distribution area of China. The results suggest that the phenotypic traits of moso bamboo exhibit rich diversity, with coefficients of variation ranging from 5.87% to 36.57%. The phenotypic traits of moso bamboo showed varying degrees of correlation. A principal component analysis was used to identify seven main phenotypic trait indicators: diameter at breast height (DBH), leaf area (LA), leaf weight (LW), branch-to-leaf ratio (BLr), leaf moisture content (Lmc), wall-to-cavity ratio (WCr), and node length at breast height (LN), which accounted for 81.64% of the total information. A random forest model was used, which gave good results to validate the results. The average combined phenotypic trait value (D-value) of most germplasm was 0.563. The highest D-value was found in Wuyi 1 moso in Fujian (0.803), while the lowest D-value was observed in Pingle 2 moso in Guangxi (0.317). The clustering analysis of phenotypic traits classified China's moso bamboo germplasm into four groups. Group I had the highest D-value and is an important candidate germplasm for excellent germplasm screening.

Integration of molecular breeding and multi-resistance screening for developing a promising restorer line Guihui5501 with heavy grain, good grain quality, and endurance to biotic and abiotic stresses.

Rice, a critical staple on a global scale, faces escalating challenges in yield preservation due to the rising prevalence of abiotic and biotic stressors, exacerbated by frequent climatic fluctuations in recent years. Moreover, the scorching climate prevalent in the rice-growing regions of South China poses obstacles to the cultivation of good-quality, heavy-grain varieties. Addressing this dilemma requires the development of resilient varieties capable of withstanding multiple stress factors. To achieve this objective, our study employed the broad-spectrum blast-resistant line Digu, the brown planthopper (BPH)-resistant line ASD7, and the heavy-grain backbone restorer lines Fuhui838 (FH838) and Shuhui527 (SH527) as parental materials for hybridization and multiple crossings. The incorporation of molecular markers facilitated the rapid pyramiding of six target genes (Pi5, Pita, Pid2, Pid3, Bph2, and Wxb ). Through a comprehensive evaluation encompassing blast resistance, BPH resistance, cold tolerance, grain appearance, and quality, alongside agronomic trait selection, a promising restorer line, Guihui5501 (GH5501), was successfully developed. It demonstrated broad-spectrum resistance to blast, exhibiting a resistance frequency of 77.33% against 75 artificially inoculated isolates, moderate resistance to BPH (3.78 grade), strong cold tolerance during the seedling stage (1.80 grade), and characteristics of heavy grains (1,000-grain weight reaching 35.64 g) with good grain quality. The primary rice quality parameters for GH5501, with the exception of alkali spreading value, either met or exceeded the second-grade national standard for premium edible rice varieties, signifying a significant advancement in the production of good-quality heavy-grain varieties in the southern rice-growing regions. Utilizing GH5501, a hybrid combination named Nayou5501, characterized by high yield, good quality, and resistance to multiple stresses, was bred and received approval as a rice variety in Guangxi in 2021. Furthermore, genomic analysis with gene chips revealed that GH5501 possessed an additional 20 exceptional alleles, such as NRT1.1B for efficient nitrogen utilization, SKC1 for salt tolerance, and STV11 for resistance to rice stripe virus. Consequently, the restorer line GH5501 could serve as a valuable resource for the subsequent breeding of high-yielding, good-quality, and stress-tolerant hybrid rice varieties.

Whole-genome sequencing analysis of soybean diversity across different countries and selection signature of Korean soybean accession.

Soybean is an important agricultural crop known for its high protein and oil content, contributing to essential nutritional and health benefits for humans. Domesticated in China over 5,000 years ago, soybean has since adapted to diverse environments and spread worldwide. This study aimed to investigate the genomic characteristics and population structures of 2,317 publicly available soybean whole-genome sequences from diverse geographical regions, including China, Korea, Japan, Europe, North America, and South America. We used large-scale whole-genome sequencing data to perform high-resolution analyses to reveal the genetic characteristics of soybean accessions. Soybean accessions from China and Korea exhibited landrace characteristics, indicating higher genetic diversity and adaptation to local environments. On the other hand, soybean accessions from Japan, the European Union, and South America were found to have low genetic diversity due to artificial selection and breeding for agronomic traits. We also identified key variants and genes associated with the ability to adapt to different environments. In Korean soybean accessions, we observed strong selection signals for isoflavone synthesis, an adaptive trait critical for improving soybean adaptability, survival, and reproductive success by mitigating environmental stress. Identifying specific genomic regions showing unique patterns of selective sweeps for genes such as HIDH, CYP73A11, IFS1, and CYP81E11 associated with isoflavone synthesis provided valuable insights into potential adaptation mechanisms. Our research has significantly improved our understanding of soybean diversity at the genetic level. We have identified key genetic variants and genes influencing adaptability, laying the foundation for future advances in genomics-based breeding programs and crop improvement efforts.

Dual-Model GWAS Analysis and Genomic Selection of Maize Flowering Time-Related Traits.

An appropriate flowering period is an important selection criterion in maize breeding. It plays a crucial role in the ecological adaptability of maize varieties. To explore the genetic basis of flowering time, GWAS and GS analyses were conducted using an associating panel consisting of 379 multi-parent DH lines. The DH population was phenotyped for days to tasseling (DTT), days to pollen-shedding (DTP), and days to silking (DTS) in different environments. The heritability was 82.75%, 86.09%, and 85.26% for DTT, DTP, and DTS, respectively. The GWAS analysis with the FarmCPU model identified 10 single-nucleotide polymorphisms (SNPs) distributed on chromosomes 3, 8, 9, and 10 that were significantly associated with flowering time-related traits. The GWAS analysis with the BLINK model identified seven SNPs distributed on chromosomes 1, 3, 8, 9, and 10 that were significantly associated with flowering time-related traits. Three SNPs 3_198946071, 9_146646966, and 9_152140631 showed a pleiotropic effect, indicating a significant genetic correlation between DTT, DTP, and DTS. A total of 24 candidate genes were detected. A relatively high prediction accuracy was achieved with 100 significantly associated SNPs detected from GWAS, and the optimal training population size was 70%. This study provides a better understanding of the genetic architecture of flowering time-related traits and provides an optimal strategy for GS.

Commercial maize hybrids have smaller root systems after 80 Years of breeding

Roots have gained attention for their role in improving plant function in high-stress environments and providing ecosystem services such as soil organic carbon storage. An important step in breeding for enhanced root phenotypes is understanding how root traits have changed historically due to selection for yield and other aboveground traits. However, among the few era panel studies focused on roots, there are conflicting findings about how breeding has altered traits such as root system length and biomass, while other traits such as root depth distribution, root size class distribution, and tissue quality remain largely unexplored. Our aim was to assess breeding-driven changes in root traits that are relevant to resource acquisition and soil carbon sequestration. We grew twelve maize (Zea mays L.) hybrids from the Corteva/Pioneer ERA panel, spanning from 1936 to 2014, in 1.5 m deep mesocosms. At the eight-leaf stage, intact root systems were imaged and analyzed using a custom root phenotyping platform, and roots and shoots were subjected to carbon and nitrogen analysis and Diffuse Reflectance FTIR to assess variation in tissue composition. We found that the newest hybrids produced 40% less root biomass and 36% less root length than the oldest hybrids, with declines of 0.024 g year−1 (s.e.: 0.005, p < 0.01) and 0.86 m year−1 (s.e.: 0.23, p < 0.01) with no changes in maximum rooting depth, which averaged 113 cm (±5.62). , and no directional shifts in chemical composition. We also found a decline in the root-to-shoot ratio from 0.58 g g−1 to 0.46 g g−1 (s.e.: 0.0006, p < 0.05). Our results suggest that selection for yield has indirectly decreased root system size over 80 years of maize breeding. Smaller root systems of modern hybrids may contribute to the higher optimum plant populations and higher yields of modern maize hybrids.

Fine-mapping and candidate gene analysis of tuber eye depth in potato

Eye depth is an important agronomic trait affecting tubers' appearance, quality, and processing suitability. Hence, cultivating varieties with uniform shapes and shallow eye depth are important goals for potato breeding. In this study, based on the primary mapping of the tuber eye-depth locus using a small primary-segregating population, a large secondary-segregating population with 2,100 individuals was used to map the eye-depth locus further. A major quantitative trait locus for eye-depth on chromosome 10 was identified (designated qEyd10.1) using BSA-seq and traditional QTL mapping method. The qEyd10.1 could explain 55.0% of the eye depth phenotypic variation and was further narrowed to a 309.10 kb interval using recombinant analysis. To predict candidate genes, tissue sectioning and RNA-seq of the specific tuber tissues were performed. Genes encoding members of the peroxidase superfamily with likely roles in indole acetic acid regulation were considered the most promising candidates. These results will facilitate marker-assisted selection for the shallow-eye trait in potato breeding and provide a solid basis for eye-depth gene cloning and the analysis of tuber eye-depth regulatory mechanisms.

Improved functional mapping of complex trait heritability with GSA-MiXeR implicates biologically specific gene sets.

While genome-wide association studies are increasingly successful in discovering genomic loci associated with complex human traits and disorders, the biological interpretation of these findings remains challenging. Here we developed the GSA-MiXeR analytical tool for gene set analysis (GSA), which fits a model for the heritability of individual genes, accounting for linkage disequilibrium across variants and allowing the quantification of partitioned heritability and fold enrichment for small gene sets. We validated the method using extensive simulations and sensitivity analyses. When applied to a diverse selection of complex traits and disorders, including schizophrenia, GSA-MiXeR prioritizes gene sets with greater biological specificity compared to standard GSA approaches, implicating voltage-gated calcium channel function and dopaminergic signaling for schizophrenia. Such biologically relevant gene sets, often with fewer than ten genes, are more likely to provide insights into the pathobiology of complex diseases and highlight potential drug targets.

Morpho-physiological and yield traits for selection of drought tolerant Urochloa grass ecotypes.

Drought has become more recurrent and causes a substantial decline in forage yields leading to strain on feed resources for livestock production. This has intensified the search for drought-tolerant forages to promote sustainable livestock production. The objective of this study was to identify drought-tolerant Urochloa grasses and to discern their morpho-physiological and yield traits to water stress as well as the relationship between these traits and indices of drought resistance. The results showed that the ecotypes, water regimes and their interaction significantly influenced all the studied morpho-physiological and yield traits. There was a significant decrease in plant height, number of leaves and tillers, dry matter yield, relative water content, photosystem II and efficiency of photosystem II with an increase in non-photochemical quenching. The principal component analysis revealed that the performance of Urochloa grass ecotypes was different under water sufficient (WS) and water deficit conditions. Drought tolerance indicators (mean productivity, geometric mean productivity, tolerance index and stress tolerance index) were most effective in identifying Urochloa ecotypes with high biomass production under both water deficient and WS conditions. Ecotypes K17, K7, Kisii, Busia and Kakamega were the most drought tolerant, Basilisk, K6, K10, K19 and Toledo were moderately tolerant whereas, CIAT6385, CIAT16449, K13, K5 and K9 were drought sensitive. The five drought-tolerant Urochloa ecotypes should be tested for sustainable biomass production under field conditions and used in breeding programmes to develop high-yielding drought-tolerant varieties.

Evaluation of predictive ability of linear type gonadal traits on reproductive capacity of breeding dairy bulls.

Dimensions of linear type traits facilitate selection of livestock for breeding and rearing. To date, use of linear type traits for selection of breeding bulls is highly concentric to scrotal circumference (SC), with probable overlook to other important traits. Present study reported the importance of various gonadal linear type traits on spermatozoa production, age-related changes in gonadal linear type traits of bulls and predictive ability of these traits on bulls' reproductive potentials. Among all gonadal traits, testicular density (TD), scrotal volume (SV), paired testicular weight (PWT) and SC were found most important predictor variables in order, which can discriminate between good/poor breeding bulls, that is, produced frozen semen doses (FSD) or not. Dimensions of gonadal traits increased significantly up to 36 months age and thereafter, development became slow and negligible. In contrast, TD decreased by 30%, 51%, 64%, 68% and 71% at 12, 24, 36, 48 and >49 months age, respectively, from its base value at 6 months. Bulls of lower TD (≤0.88 g/cm3) had significantly higher ejaculate volume (+9%), sperm motility, sperm concentration (+100 million/mL) and sperm output (+26%)/ejaculate as compared to bulls of higher TD (>0.88 g/cm3). Discriminant function was developed using TD, SV, PWT and SC to identify bulls of superior reproductive potentials. It was concluded that among the investigated traits, TD was the strongest to discriminate between FSD and Non-FSD bulls. Therefore, our findings suggested that TD could be more potential trait than SC for dairy bulls' breeding soundness evaluation and assessment of reproductive ability.

Mite non-reproduction is not a consequence of the brood removal behavior of varroa sensitive hygiene honey bee colonies (Apis mellifera).

A sustainable solution to the global threat of the Varroa destructor mite is the selection of varroa-resistant honey bee (Apis mellifera) colonies. Both "mite non-reproduction" (MNR) and "varroa sensitive hygiene" (VSH) appear to be promising selection traits for achieving the goal of a resistant honey bee. MNR describes colonies that have a high number of non-reproductive mites (no offspring, no males, or delayed development of mite offspring). High numbers of non-reproductive mites have been observed in selected colonies, but the mechanism behind this trait has not yet been identified. The specialized hygienic behavior of selected honey bees, called VSH, is the removal of varroa-infested brood. These traits were thought to be linked by VSH bees preferentially removing reproductive varroa females leaving only non-reproductive mites behind in cells and thus creating colonies with high levels of MNR. To further investigate this link, we used an experimental setup and data sets from a four-year selection project designed to breed for MNR and VSH colonies. In addition, we sought to answer the question of whether non-reproductive mites are a direct consequence of worker removal behavior. To test this, we artificially induced removal behavior, and after providing the mite with enough time to re-enter another cell, we opened all capped cells, relocated the mites, and evaluated their reproduction. As shown in previous studies and in this study, VSH had no effect on MNR levels. Also, the induced removal behavior did not lead to non-reproduction in the subsequent reproductive cycle post interruption. We thus concluded that breeding for non-reproductive mites does not automatically breed for VSH behavior and worker removal behavior does not cause subsequent reproductive failure of the mites forced to flee and find a new cell for reproduction.

Measurement of the Angle between stems and leaves of rice based on key point detection

Stem-leaf angle is an important phenotypic parameter of rice, which is crucial for the growth and development of rice plants and scientific breeding. However, the traditional method is inefficient and subjective. In order to quickly and accurately calculate the stem-leaf pinch angle of rice, this paper proposes a key point-based stem-leaf pinch angle detection method. Experimentally, four periods of rice (Jointing stage, Booting stage, Heading stage and Mature stage) are selected as research objects, image data are collected, key points are extracted by YOLOv7-pose network model, and a lightweight convolution method GSConv is introduced, which is able to reduce the complexity of the model and improve the accuracy of the key point detection, the average accuracy of key point detection was improved from 93.7% to 98.7%, an improvement of 5%. Finally, the angular size of the pinch angle was determined based on the coordinates of the key points located by the model, and the R2 of the pinch angle calculation results to the actual manual measurements was the highest of 0.84, the errors for the four periods were 1.543°, 1.716°, 1.213°, and 0.998°. So the method ensures the accuracy of identification while the model size is reduced, and can effectively measure the angle of rice stem and leaf pinch, and the investigated method can better help farmers to understand the growth and development of plants and provide support for the selection of excellent crop traits.

Transcriptomics of differences in thermal plasticity associated with selection for an exaggerated male sexual trait.

The information about the magnitude of differences in thermal plasticity both between and within populations, as well as identification of the underlying molecular mechanisms are key to understanding the evolution of thermal plasticity. In particular, genes underlying variation in the physiological response to temperature can provide raw material for selection acting on plastic traits. Using RNAseq, we investigate the transcriptional response to temperature in males and females from bulb mite populations selected for the increased frequency of one of two discrete male morphs (fighter- and scrambler-selected populations) that differ in relative fitness depending on temperature. We show that different mechanisms underlie the divergence in thermal response between fighter- and scrambler-selected populations at decreased vs. increased temperature. Temperature decrease to 18 °C was associated with higher transcriptomic plasticity of males with more elaborate armaments, as indicated by a significant selection-by-temperature interaction effect on the expression of 40 genes, 38 of which were upregulated in fighter-selected populations in response to temperature decrease. In response to 28 °C, no selection-by-temperature interaction in gene expression was detected. Hence, differences in phenotypic response to temperature increase likely depended on genes associated with their distinct morph-specific thermal tolerance. Selection of males also drove gene expression patterns in females. These patterns could be associated with temperature-dependent fitness differences between females from fighter- vs. scrambler-selected populations reported in previous studies. Our study shows that selection for divergent male sexually selected morphologies and behaviors has a potential to drive divergence in metabolic pathways underlying plastic response to temperature in both sexes.

Original Research Article Genetic Diversity and Association Analysis for Agronomic and Yield Related Traits in Interspecific Progenies of Pigeonpea (Cajanus cajan)

The limited genetic diversity in existing cultivars emphasizes the need for incorporating potential exotics and wild relatives in breeding programs. This study focussed on assessing genetic variation and correlations among yield traits in F8 and F9 progenies resulting from nine interspecific crosses, involving three cultivated parental lines and three wild species. Results indicate significant genotypic variation for all traits studied. Phenotypic and genotypic coefficients of variation varied across agronomic parameters. Heritability estimates ranged from 22.61% (Primary branches plant-1) to 89.35% (Days to maturity) for different traits, emphasizing the potential for selection in breeding programs. Positive correlations were observed among various traits in both progeny generations, providing insights into the interplay of genetic factors influencing pigeon pea traits. The cluster analysis revealed that, 54 interspecific cross derived lines with three parents were grouped into four clusters, indicating the greater diversity among the lines for the selection of yield related traits for pigeonpea crop improvement.

An investigation of the impact of imbalance on the analysis of the US crop variety evaluation program data

AbstractMulti‐environment trial data from many crop variety evaluation programs are imbalanced because only a subset of varieties is selected for the following year, which leads to missing variety by year. Inspired by the US National Cotton Variety Test trial, we conducted new simulation studies to investigate selection processes that differ from the existing literature. The followings are our four main contributions. First, we adopted a framework that utilizes a logistic regression to generate imbalanced data that follow missing completely at random, missing at random, or missing not at random (MNAR). Second, our selection process can depend on multiple traits, whereas all existing studies only used a single trait for selection. Third, besides variance components (VCs), long‐term trends that reflect genetic and non‐genetic development are of interest since the simulated data span over 30 years. Last, we evaluated the prediction accuracy for variety's overall and location‐specific performance. The results show that the VC and long‐term trends estimations are the worst under MNAR using the single trait for selection. Compared to VC, the long‐term trends estimation is more influenced by the missing mechanism and missing rate. However, the prediction accuracy for variety's performance is mainly driven by the missing rate and is less sensitive to the selection process. If ignoring the genetic and non‐genetic long‐term trends, both estimation and prediction will deteriorate. More testing years would improve estimation and prediction, despite a higher missing rate.

Characteristics of sheep in the Near Arctic region by microsatellites and reproductive abilities

The microsatellites polymorphism was analyzed in ewe lambs obtained from intra-breed mating of the Pechora semifine-wool sheep and their littermates from crossing with the Kuibyshev rams. Genotyping of the population by STR loci was performed using the COrDIS Sheep reagent kit recommended by the International Society of Animal Genetics (ISAG). The age of the beginning of reproduction, fertility, milk yield, safety and growth intensity of the litter up to three months of age were taken into account in the ewe lambs. In the group of the Pechora sheep sows 74 alleles were detected, and 81 alleles were detected in the crossbred ones. INRA005 and INRA023 loci were the most polymorphic in both groups, while ETH152 was the least polymorphic. The mean genetic distance between the groups for the 12 STR loci was 0.019 ± 0.003. Pechora sheep (P) and their litters with the Kuibyshev rams (1/2 P + 1/2 K) differed significantly in the frequencies of some STR loci genes. Thus, the INRA023212 allele was found with a frequency of 0.174 in the group of P ewes and was absent in the 1/2 P + 1/2 K group, while the INRA172126 allele was found with a frequency of 0.326 and 0.122, respectively. The mean Fis values in both groups were close to zero. The groups did not differ significantly in the main genetic-population parameters. However, some advantage of the Pechora ewe sows in comparison with the crossbred sheep 1/2 P + 1/2 K on selective traits, apparently, is due to a higher genetic contribution to their heredity of the indigenous northern short-tailed sheep. According to the results of the study, it can be assumed that the age of onset of reproduction of the ewe lambs is related to the level of their heterozygosity for STR loci.

The predicted benefits of genomic selection on pig breeding objectives.

The premise was tested that the additional genetic gain was achieved in the overall breeding objective in a pig breeding program using genomic selection (GS) compared to a conventional breeding program, however, some traits achieved larger gain than other traits. GS scenarios based on different reference population sizes were evaluated. The scenarios were compared using a deterministic simulation model to predict genetic gain in scenarios with and without using genomic information as an additional information source. All scenarios were compared based on selection accuracy and predicted genetic gain per round of selection for objective traits in both sire and dam lines. The results showed that GS scenarios increased overall response in the breeding objectives by 9% to 56% and 3.5% to 27% in the dam and sire lines, respectively. The difference in response resulted from differences in the size of the reference population. Although all traits achieved higher selection accuracy in GS, traits with limited phenotypic information at the time of selection or with low heritability, such as sow longevity, number of piglets born alive, pre- and post-weaning survival, as well as meat and carcass quality traits achieved the largest additional response. This additional response came at the expense of smaller responses for traits that are easy to measure, such as back fat and average daily gain in GS compared to the conventional breeding program. Sow longevity and drip loss percentage did not change in a favourable direction in GS with a reference population of 500 pigs. With a reference population of 1000 pigs or onwards, sow longevity and drip loss percentage began to change in a favourable direction. Despite the smaller responses for average daily gain and back fat thickness in GS, the overall breeding objective achieved additional gain in GS.

Identification of FASN Gene Polymorphisms, Expression and Their Relationship with Body Size Traits in Guizhou White Goat (Capra hircus) with Different Genders.

To investigate the nucleotide variation sites (SNPs) and expression differences of the fatty acid synthase gene (FASN) in Guizhou white goats, the relationship between the variation and body size traits was investigated. In this study, DNA was extracted from the blood of 100 samples of white goats from different regions in Guizhou province, China, and the variation sites were screened using pooled sequencing by mixing DNA samples, and 242 blood samples with body size traits were used for association analysis. The allele frequency, genotype frequency, homozygosity, heterozygosity and effective gene number were calculated by using PopGene 32.0 software, the population polymorphism information content was calculated by using PIC software (Version 0.6), and the state of genetic balance of the genes was analyzed by using the chi-square test. The mRNA of FASN gene expression levels in male and female goats were investigated by using real-time fluorescence quantitative PCR (RT-qPCR). The general linear mixed model of MINTAB software (Version 16.0) was used to analyze the association between FASN gene nucleotide mutation sites and body size traits. The results showed that there was one nucleotide mutation site g.141 C/T in the target fragment of FASN gene amplification, and revealed two alleles, C and T, and three genotypes CC, CT and TT. The genotype frequencies for CC, CT and TT were 0.4308, 0.4205 and 0.1487, respectively. The allele frequencies for C and T were 0.6410 and 0.3590, respectively. The genetic homozygosity (Ho) was higher than the heterozygosity (He). The χ2 test showed that the mutation site was in the Hardy-Weinberg equilibrium state (p > 0.05). The RT-qPCR results showed that the FASN gene had different expression levels in the longissimus dorsi muscle of male and female goats, and its expression was significantly higher in male goats than in female goats. The association analysis results showed that the mutation of the FASN gene had different effects on body size traits of male and female goats, and the presence of the populations of the T allele and the TT genotype recorded higher body size traits (body weight, heart girth and wither height) in female populations. Therefore, the site of the FASN gene can be used as a candidate marker for the early selection of growth traits in Guizhou white goats.

Identifying plant traits to increase wheat yield under irrigated conditions

Crop models have frequently been used to identify desired plant traits for rainfed wheat (Triticum aestivum L.). However, efforts to apply these models to irrigated wheat grown under non-limiting water and nitrogen conditions have been rare. Using simulation models to identify plant traits that impact yield can facilitate more targeted cultivar improvement and reduce time and cost. In this study, the SSM-iCrop model was employed to identify effective plant traits for increasing the yield of irrigated wheat in four distinct environments in Iran. A comprehensive range of traits related to phenology, leaf area development, dry matter production, and yield formation, which exhibited reported genetic variation, were tested. The impact of these traits on yield showed slight variation across different environmental zones due to genetic × environment interaction. However, across all environments, modifying current cultivars to increase radiation use efficiency (RUE) resulted in a 19 % increase in yield, accelerating leaf area development led to a 10 %–15 % increase, lengthening the grain filling period resulted in a 14 % increase, and extending the vegetative period led to a 6 % increase. These improvements were all statistically significant. Considering that longer duration cultivars may disrupt cropping systems and the need to develop simple methods for targeting and phenotyping RUE, faster leaf area development was found as the most promising option to increase irrigated wheat yield under optimal water and nitrogen management within a short time frame. It should be noted that cultivars with modified traits needed higher water and nitrogen inputs to support increased yields. These findings can be applied to select desirable key traits for targeted breeding and expedite the production of high-yielding cultivars of irrigated wheat in various environmental zones. The potential for further improvement through combined traits requires further investigation.