Inbred Lines Research Articles

Alleles on locus chromosome 4B from different parents confer tiller number and the yield-associated traits in wheat

Pleiotropy is frequently detected in agronomic traits of wheat (Triticum aestivum). A locus on chromosome 4B, QTn/Ptn/Sl/Sns/Al/Tgw/Gl/Gw.caas-4B, proved to show pleiotropic effects on tiller, spike, and grain traits using a recombinant inbred line (RIL) population of Qingxinmai × 041133. The allele from Qingxinmai increased tiller numbers, and the allele from line 041133 produced better performances of spike traits and grain traits. Another 52 QTL for the eight traits investigated were detected on 18 chromosomes, except for chromosomes 5D, 6D, and 7B. Several genes in the genomic interval of the locus on chromosome 4B were differentially expressed in crown and inflorescence samples between Qingxinmai and line 041133. The development of the KASP marker specific for the locus on chromosome 4B is useful for molecular marker-assisted selection in wheat breeding.

Predicting superior crosses in winter wheat using genomics: A retrospective study to assess accuracy

AbstractIn plant breeding, selecting cross‐combinations that are more likely to result in superior lines for cultivar development is critical. This step, however, is subjective with decisions being based on available genomic and phenotypic data for prospective parents. Genomic prediction (GP) provides new opportunities to accelerate genetic gain for a target trait by identifying superior crosses through simulation of progeny performance. In this context, this study deployed GP using the phenotype and genotype of potential parents to predict the progeny genetic variance (VG) and means of overall, inferior 10%, and superior 10% (μ, μip, and μsp, respectively). This retrospective experimental design investigated whether the crosses that produced superior soft red winter wheat breeding lines would have been made if progeny simulations had guided crossing decisions of breeding programs. Here, data from historical wheat breeding lines were used to train GP models and predict VG and means for yield, test weight, heading date, and plant height for all combinations of 217 parents. Predicted and observed data for 670 lines derived from biparental crosses were compared to assess the accuracy of progeny simulations, and low‐to‐moderate prediction accuracy was observed for the four traits (0.25–0.52). Of the pedigrees that produced lines that were selected and advanced into later stage nurseries, 76% were predicted to give rise to progeny with above‐average yield. The moderate correlation found between predicted progeny means and observed line per se performance justifies using cross‐combination prediction as a tool to reduce crossing number and focus on segregating populations that harbor future cultivars.

Genome-wide association analysis of the resistance to infectious hematopoietic necrosis virus in two rainbow trout aquaculture lines confirms oligogenic architecture with several moderate effect quantitative trait loci

Infectious hematopoietic necrosis (IHN) is a disease of salmonid fish that is caused by the IHN virus (IHNV), which can cause substantial mortality and economic losses in rainbow trout aquaculture and fisheries enhancement hatchery programs. In a previous study on a commercial rainbow trout breeding line that has undergone selection, we found that genetic resistance to IHNV is controlled by the oligogenic inheritance of several moderate and many small effect quantitative trait loci (QTL). Here we used genome wide association analyses in two different commercial aquaculture lines that were naïve to previous exposure to IHNV to determine whether QTL were shared across lines, and to investigate whether there were major effect loci that were still segregating in the naïve lines. A total of 1,859 and 1,768 offspring from two commercial aquaculture strains were phenotyped for resistance to IHNV and genotyped with the rainbow trout Axiom 57K SNP array. Moderate heritability values (0.15–0.25) were estimated. Two statistical methods were used for genome wide association analyses in the two populations. No major QTL were detected despite the naïve status of the two lines. Further, our analyses confirmed an oligogenic architecture for genetic resistance to IHNV in rainbow trout. Overall, 17 QTL with notable effect (≥1.9% of the additive genetic variance) were detected in at least one of the two rainbow trout lines with at least one of the two statistical methods. Five of those QTL were mapped to overlapping or adjacent chromosomal regions in both lines, suggesting that some loci may be shared across commercial lines. Although some of the loci detected in this GWAS merit further investigation to better understand the biological basis of IHNV disease resistance across populations, the overall genetic architecture of IHNV resistance in the two rainbow trout lines suggests that genomic selection may be a more effective strategy for genetic improvement in this trait.

Transcriptome Analysis of Stigmas of Vicia faba L. Flowers.

Pollination in angiosperms depends on complex communication between pollen grains and stigmas, classified as wet or dry, depending on the presence or absence of secretions at the stigma surface, respectively. In species with wet stigma, the cuticle is disrupted and the presence of exudates is indicative of their receptivity. Most stigma studies are focused on a few species and families, many of them with self-incompatibility systems. However, there is scarce knowledge about the stigma composition in Fabaceae, the third angiosperm family, whose stigmas have been classified as semidry. Here we report the first transcriptome profiling and DEGs of Vicia faba L. styles and stigmas from autofertile (flowers able to self-fertilize in the absence of manipulation, whose exudate is released spontaneously) and autosterile (flowers that need to be manipulated to break the cuticle and release the exudates to be receptive) inbred lines. From the 76,269 contigs obtained from the de novo assembly, only 45.1% of the sequences were annotated with at least one GO term. A total of 115,920, 75,489, and 70,801 annotations were assigned to Biological Process (BP), Cellular Component (CC), and Molecular Function (MF) categories, respectively, and 5918 differentially expressed genes (DEGs) were identified between the autofertile and the autosterile lines. Among the most enriched metabolic pathways in the DEGs subset were those related with amino acid biosynthesis, terpenoid metabolism, or signal transduction. Some DEGs have been related with previous QTLs identified for autofertility traits, and their putative functions are discussed. The results derived from this work provide an important transcriptomic reference for style-stigma processes to aid our understanding of the molecular mechanisms involved in faba bean fertilization.

Evaluation of the genotypes of the Kazakh-Siberian nursery (KASIB) in the conditions of the Novosibirsk region

The paper presents the results of evaluation of the KASIB-22 nursery soft wheat samples resistance to the main wheat pathogens. The research material was 44 wheat samples obtained from different regions of Russia and Kazakhstan within the framework of the KASIB shuttle breeding program (A.I. Barayev Research and Production Centre for Grain Farming, Omsk State Agrarian University, ICiG SB RAS, Karabalyk AES, Karaganda AES, North-Kazakhstan AES, FSBSI "Omsk ASC", HE SAU of the Northern Trans-Urals, Aktyubinsk AES, Kurgan Research Institute of Agriculture, Pavlodar AES, agrokomplex "Kurgansemena", Samara Research Institute of Agriculture, Chelyabinsk Research Institute of Agriculture). The following breeding lines were identified as highly productive and possessing high and medium resistance to brown rust, powdery mildew and loose smut: Line Pt-311 (Kurgan Research Institute of Agriculture), Lutescens 1462, Lutescens 1486, Line1616ae14 (Samara Research Institute of Agriculture), Lutescens 1356 (ICiG SB RAS). The yield of the selected samples averaged 42.1–51.2 c/ha. Genotypes Novosibirskaya 41, Line 435/12 and Lutescens 1364 are of interest for selection for quality. The gluten content of the nursery genotypes ranged from 24.1 (Line 23/07 in 2022) to 38.0% (variety Astana 2 in 2021), protein ranged from 13.4 (variety Tertia in 2022) to 19.5% (Lutescens 1364 in 2022). Each of the selected lines is of practical value for breeding, and the samples from the KASIB-22 nursery allow to expand the genetic diversity of spring soft wheat by selecting the most resistant forms to local populations of powdery mildew, leaf rust and loose smut pathogens.

Identification of efficient inbred testers to strengthen established heterotic groups in pearl millet (Pennisetum glaucum [L.] R. Br)

AbstractPearl millet has two major heterotic groups, HGB (Heterotic Group B) and HGR (Heterotic Group R), each with unique genetic backgrounds and traits. Leveraging appropriate genetic resources is crucial for enhancing the potential of these heterotic groups in hybrid breeding programmes. Testers are essential in this context, determining the combining ability of new breeding lines and accurately assessing the performance and potential of parental lines in hybrid combinations. Two sets of test crosses were produced using line × tester mating design: Set 1 with six HGB testers crossed with new restorer lines and Set 2 with six HGR testers crossed with new seed parental lines, evaluated at multiple locations in India. Testers were evaluated for their effectiveness using multiple criteria, such as rank correlation analysis for line performance in hybrid combinations, discrimination ability, general combining ability, per se performance and Biplot analysis. These assessments determined their relative ranking, with HGB1‐T3, HGB2‐T3, HGR1‐T1 and HGR2‐T1 identified as efficient testers. The genetic analysis helps identify efficient testers for selecting superior genotypes, thereby enhancing heterotic group performance by incorporating appropriate new breeding material.

Identification and Validation of Quantitative Trait Loci Associated with Fruit Puffiness in a Processing Tomato Population.

Physiological disorders impact the yield and quality of marketable fruit in tomato. Puffy fruit caused by cavities inside the locule can be problematic for processing and fresh market quality. In this paper, we used a recombinant inbred line (RIL) and three derived processing tomato populations to map and validate quantitative trait loci (QTLs) for fruit puffiness across environments. Binary interval mapping was used for mapping the incidence of fruit puffiness, and non-parametric interval mapping and parametric composite interval mapping were used for mapping severity. Marker-trait regressions were carried out to validate putative QTLs in subsequent crosses. QTLs were detected on chromosome (Chr) 1, 2, and 4. Only the QTL on Chr 1 was validated in progeny from subsequent crosses. This QTL explained up to 22.5% of the variance in the percentage of puffy fruit, with a significant interaction between loci on Chr 2 and 4, increasing the percentage of puffy fruit by an additional 15%. The allele responsible for puffy fruit on Chr 1 was inherited from parent FG02-188 and was dominant towards increased incidence and severity. Marker-assisted selection (MAS) for the QTL on Chr 1 was as efficient as genomic selection (GS) in reducing the incidence and severity of puffy fruit, despite the potential contribution of other loci.

New Frontiers in Potato Breeding: Tinkering with Reproductive Genes and Apomixis.

Potato is the most important non-cereal crop worldwide, and, yet, genetic gains in potato have been traditionally delayed by the crop's biology, mostly the genetic heterozygosity of autotetraploid cultivars and the intricacies of the reproductive system. Novel site-directed genetic modification techniques provide opportunities for designing climate-smart cultivars, but they also pose new possibilities (and challenges) for breeding potato. As potato species show a remarkable reproductive diversity, and their ovules have a propensity to develop apomixis-like phenotypes, tinkering with reproductive genes in potato is opening new frontiers in potato breeding. Developing diploid varieties instead of tetraploid ones has been proposed as an alternative way to fill the gap in genetic gain, that is being achieved by using gene-edited self-compatible genotypes and inbred lines to exploit hybrid seed technology. In a similar way, modulating the formation of unreduced gametes and synthesizing apomixis in diploid or tetraploid potatoes may help to reinforce the transition to a diploid hybrid crop or enhance introgression schemes and fix highly heterozygous genotypes in tetraploid varieties. In any case, the induction of apomixis-like phenotypes will shorten the time and costs of developing new varieties by allowing the multi-generational propagation through true seeds. In this review, we summarize the current knowledge on potato reproductive phenotypes and underlying genes, discuss the advantages and disadvantages of using potato's natural variability to modulate reproductive steps during seed formation, and consider strategies to synthesize apomixis. However, before we can fully modulate the reproductive phenotypes, we need to understand the genetic basis of such diversity. Finally, we visualize an active, central role for genebanks in this endeavor by phenotyping properly genotyped genebank accessions and new introductions to provide scientists and breeders with reliable data and resources for developing innovations to exploit market opportunities.

Combining Ability, Heritability, and Heterosis for Seed Weight and Oil Content Traits of Castor Bean (Ricinus communis L.)

Hybridization is an important evolutionary force, and heterosis describes the phenomenon where hybrids exhibit superior traits compared to their parents. This study aimed to evaluate the one-hundred-seed weight and fatty acid content in F1 generations, investigating the effects of different parental crosses using a 9 × 3 incomplete diallel design (NCII). One of the challenges faced in this study was the complexity of accurately determining the influence of both genetic and environmental factors on trait inheritance. A total of 36 F1 crosses were analyzed for general combining ability (GCA), specific combining ability (SCA), and heritability. The results showed that the level of each index in F1 is closely related to its parents. Significant differences in GCA and SCA were observed among parental traits in most crosses. The ratio of GCA to SCA ranged from 0 to 3, indicating the pivotal role of SCA over GCA in castor breeding efforts. High narrow-sense heritability was recorded in palmitic acid (30.98%), oleic acid (28.68%), and arachidonic acid (21.34%), suggesting that these traits are predominantly under the control of additive gene action, and hence these characters can be improved by selection. Additionally, heterosis exhibited diverse patterns across traits. Based on the evaluated combining ability, heritability, and heterosis, the inbred lines CSR181 and 20111149 were recommended for castor crossbreeding due to their potential to yield progeny with optimal oil-related traits. This research contributes valuable knowledge to the field of castor breeding, providing a foundation for developing superior castor cultivars.

Promising potato hybrids in Siberia

The results of studying potato hybrids in the nurseries of preliminary and competitive variety trials are presented. The research was conducted in 2018–2022 in the Krasnoyarsk Territory in grain and fallow crop rotation. The soil of the experimental plot is represented by leached chernozem, low- and medium-moist heavy loam of granulometric composition. Experiment design, yield recording and data processing were carried out in accordance with the generally accepted recommendations for work with the crop. Based on the Selyaninov hydrothermal coefficient, the weather conditions of the vegetation periods of the years of research can be characterized as slightly arid. The HTC was 1.1 in 2019 and 2021, in 2020, 2022 – 1,3. According to the results of the preliminary variety trials, lines A-114, A-326, A-529, A-635a exceeded or were at the level of the standard variety Krasnoyarsky Ranniy by the number of marketable tubers and yield. During 4 years of research in the nursery of competitive varietal trial, the studied breeding lines on average formed yields at the level or higher than the standard varieties. According to the elements of the yield structure in the competitive variety trial lines A-114, A-529 significantly exceeded the standard variety in marketability, as well as had a smaller number and weight of unmarketable tubers. Based on the results of the evaluation in 2019–2021 of the chemical composition of tubers for dietary and functional food, lines with low starch content (up to 14%) are proposed: A-114 (12.2%), А-672а (9.9), А-635а (12.7%). Based on the study in 2019–2022 of the line A-114 in competitive trials, preliminary and production multiplication, ecological assessment, application materials for admission to use and protection of the new potato variety Akrux were submitted to the State Variety Commission.

Selection for Phytophthora Root Rot Resistance in Chickpea Crosses Affects Yield Potential of Chickpea × Cicer echinospermum Backcross Derivatives.

Phytophthora root rot (PRR) of chickpea (Cicer arietinum) caused by Phytophthora medicaginis is an important disease. Partial resistance to PRR is sourced from Cicer echinospermum. In this study, we evaluated if lines with low levels of PRR foliage symptoms in two contrasting recombinant inbred line (RIL) populations parented by chickpea cultivars (Yorker and Rupali) and 04067-81-2-1-1 (C. echinospermum, interspecific breeding line) had a significant drag on yield parameters. For the Yorker × 04067-81-2-1-1 population with the highest level of PRR resistance, in the absence of PRR, low foliage symptom RIL had significantly later flowering and podding, lower grain yields, and lighter seed and shorter plant phenotypes than high foliage symptom RIL. A quantitative trait locus analysis identified significant QTL for flowering, height, 100-seed weight, and yield, and there was a significantly higher frequency of alleles for the negative agronomic traits (i.e., drag) from the 04067-81-2-1-1 parent in low foliage symptom RIL than in high foliage symptom RIL. For the Rupali × 04067-81-2-1-1 population with lower levels of PRR resistance, in the absence of PRR, low foliage symptom RIL had significantly lighter seed and shorter plants than high foliage symptom RIL. Significant QTL were detected, the majority were for the timing of flowering and podding (n = 18), others were for plant height, yield, and 100-seed weight. For this second population, the frequency of alleles for the negative agronomic traits from the 04067-81-2-1-1 parent did not differ between low and high foliage symptom RIL. The 100 seed weight of RIL under moderate PRR disease pressure showed some promise as a yield component trait to identify phenotypes with both high levels of PRR resistance and grain yield potential for further seed number evaluations. We identified that large population sizes are required to enable selection among chickpea × C. echinospermum crosses for high levels of PRR resistance without a significant drag on yield.

The Grain Number Increase 1 alleles GNI‐A1‐105Y and ‐105K increase grain number in spring wheat

AbstractWheat (Triticum aestivum L.) has inflorescences made up of multiple spikelets arranged along a central rachis, with each spikelet producing between one and four grains. The Grain Number Increase 1 (GNI‐A1) gene wheat directly influences grain number per spikelet and grain size. Three naturally occurring alleles have been described previously: GNI‐A1‐105N, 105Y, and 105K. This project's goal was to characterize the impact of these alleles within hard red spring wheat cultivars in Montana, where each of the alleles is common. The 105N allele and the 105K allele were compared through analysis of an F5 Vida by Spring‐Yellowstone recombinant inbred line (RIL) population, and with near isogenic lines (NILs) derived from the same population. The 105N allele and the 105Y allele were compared with NILs derived from an F4 Lanning by Egan RIL population. We analyzed the impact of each of the three alleles and compared their effects on inflorescence architecture, grain size, grain yield, grain quality, and milling quality under Bozeman, MT, field conditions. Data show that either loss‐of‐function alleles (105Y and 105K) increased grain number per spikelet by 5% when compared to the more functional allele (105N) across all years and environments tested. Overall grain size was not significantly reduced and there was also not a significant increase in overall grain yield.

Unlocking genetic insights: Evaluating wheat RILs for physiobiochemical traits under terminal heat stress conditions

BackgroundThe increasing impacts of heat stress on wheat production due to climate change has entailed the development of heat-resilient crop varieties. To address this, two hundred recombinant inbred lines (RILs) derived from a cross between WH711/WH1021 were evaluated in a randomized block design (RBD) with two replications at CCSHAU, Hisar, during 2018-19 under heat stress and non-stress conditions. Heat stress was induced by altering the date of sowing so that the grain filling stage coincide with heat stress.ResultsHeat stress adversely affects RILs performance, as illustrated by alterations in phenotypic traits. Highest coefficients of variations were recorded for TAA, CTD 1, WUE, CTD 2, Cc and A under non-stress and heat stress conditions whereas gs, WUEi and GY under non-stress and SPAD 1, SPAD 2, GY and NDVI 2 under heat-stress conditions recorded moderate estimates of coefficient of variations. CTD 2, TAA, E, WUE and A displayed a significant occurrence of both high heritability and substantial genetic advance under non-stress. Similarly, CTD 2, NDVI 2, A, WUEi, SPAD 2, gs, E, Ci, MDA and WUE exhibited high heritability with high genetic advance under heat-stress conditions.ConclusionsComplementary and duplicate types of interactions with number of controlling genes were observed for different parameters depending on the traits and environments. RILs 41, 42, 59, 74, 75, 180 and 194 were categorized as heat tolerant RILs. Selection preferably for NDVI 1, RWC, TAA, A, E and WUEi to accumulate heat tolerance favorable alleles in the selected RILs is suggested for development of heat resilient genotypes for sustainable crop improvement. The results showed that traits such as such as NDVI, RWC, TAA, A, E, and WUEi, can be effective for developing heat-resilient wheat genotypes and ensuring sustainable crop improvement.

Identification and functional marker development of SbPLSH1 conferring purple leaf sheath in sorghum.

We identified a SbPLSH1gene conferring purple leaf sheath in sorghum (sorghumbicolor(L.) Moench)and developed a functional markerfor it. The purple leaf sheath of sorghum, a trait mostly related to anthocyanin deposition, is a visually distinguishable morphological marker widely used to evaluate the purity of crop hybrids. We aimed to dissect the genetic mechanism for leaf sheath color to mine the genes regulating this trait. In this study, two F2 populations were constructed by crossing a purple leaf sheath inbred line (Gaoliangzhe) with two green leaf sheath inbred lines (BTx623 and Silimei). Based on the results of bulked-segregant analysis sequencing, bulk-segregant RNA sequencing, and map-based cloning, SbPLSH1 (Sobic.006G175700), which encodes a bHLH transcription factor on chromosome 6, was identified as the candidate gene for purple leaf sheath in sorghum. Genetic analysis demonstrated that overexpression of SbPLSH1 in Arabidopsis resulted in anthocyanin deposition and purple petiole, while two single-nucleotide polymorphism (SNP) variants on the exon 6 resulted in loss of function. Further haplotype analysis revealed that there were two missense mutations and one cis-acting element mutation in SbPLSH1, which are closely associated with leaf sheath color in sorghum. Based on the variations, a functional marker (LSC4-2) for marker-assisted selection was developed, which has a broad-spectrum capability of distinguishing leaf sheath color in natural variants. In summary, this study lays a foundation for analyzing the genetic mechanism for sorghum leaf sheath color.

Development and evaluation of Fusarium wilt-resistant and high-yielding chickpea advanced breeding line, KCD 11.

Fusarium wilt (FW) is the most severe soil-borne disease of chickpea that causes yield losses up to 100%. To improve FW resistance in JG 11, a high-yielding variety that became susceptible to FW, we used WR 315 as the donor parent and followed the pedigree breeding method. Based on disease resistance and yield performance, four lines were evaluated in station trials during 2017-2018 and 2018-2019 at Kalaburagi, India. Further, two lines, namely, Kalaburagi chickpea desi 5 (KCD 5) and KCD 11, which possesses the resistance allele for a specific single-nucleotide polymorphism marker linked with FW resistance, were evaluated across six different locations (Bidar, Kalaburagi, Raichur, Siruguppa, Bhimarayanagudi and Hagari) over a span of 3 years (2020-2021, 2021-2022 and 2022-2023). KCD 11 exhibited notable performance, showcasing yield advantages of 8.67%, 11.26% and 23.88% over JG 11, and the regional checks Super Annigeri 1 (SA 1) and Annigeri 1, respectively, with enhanced FW resistance in wilt sick plot. Further, KCD 11 outperformed JG 11, SA 1 and Annigeri 1 in multi-location trials conducted across three seasons in the North Eastern Transition Zone, North Eastern Dry Zone, and North Dry Zones of Karnataka. KCD 11 was also tested in trials conducted by All India Coordinated Research Project on chickpea and was also nominated for state varietal trials for its release as a FW-resistant and high-yielding variety. The selected line is anticipated to cater the needs of chickpea growers with the dual advantage of yield increment and disease resistance.

Genome wide inherited modifications of the tomato epigenome by trans-activated bacterial CG methyltransferase

BackgroundEpigenetic variation is mediated by epigenetic marks such as DNA methylation occurring in all cytosine contexts in plants. CG methylation plays a critical role in silencing transposable elements and regulating gene expression. The establishment of CG methylation occurs via the RNA-directed DNA methylation pathway and CG methylation maintenance relies on METHYLTRANSFERASE1, the homologue of the mammalian DNMT1.PurposeHere, we examined the capacity to stably alter the tomato genome methylome by a bacterial CG-specific M.SssI methyltransferase expressed through the LhG4/pOP transactivation system.ResultsMethylome analysis of M.SssI expressing plants revealed that their euchromatic genome regions are specifically hypermethylated in the CG context, and so are most of their genes. However, changes in gene expression were observed only with a set of genes exhibiting a greater susceptibility to CG hypermethylation near their transcription start site. Unlike gene rich genomic regions, our analysis revealed that heterochromatic regions are slightly hypomethylated at CGs only. Notably, some M.SssI-induced hypermethylation persisted even without the methylase or transgenes, indicating inheritable epigenetic modification.ConclusionCollectively our findings suggest that heterologous expression of M.SssI can create new inherited epigenetic variations and changes in the methylation profiles on a genome wide scale. This open avenues for the conception of epigenetic recombinant inbred line populations with the potential to unveil agriculturally valuable tomato epialleles.

Genetic control of root architectural traits under drought stress in spring barley (Hordeum vulgare L.).

Root architectural traits play pivotal roles in plant adaptation to drought stress, and hence they are considered promising targets in breeding programs. Here, we phenotyped eight root architecture traits in response to well-watered and drought stress conditions in 200 spring barley (Hordeum vulgare L.) inbred lines over two consecutive field seasons. Root architecture traits were less developed under drought in both seasons when compared with control treatments. Genetic variation in root architectural traits was dissected employing a genome-wide association study (GWAS) coupled with linkage disequilibrium mapping. GWAS uncovered a total of 186 significant single nucleotide polymorphism-trait associations for eight root traits under control, drought, and drought-related indices. Of these, a few loci for root traits were detected on chromosomes 3 and 5, which co-located with QTL identified in previous studies. Interestingly, 13 loci showed simultaneou associations with multiple root traits under drought and drought-related indices. These loci harbored candidate genes, which included a wide range of drought-responsive components such as transcription factors, binding proteins, protein kinases, nutrient and ion transporters, and stress signaling factors. For instance, two candidate genes, HORVU7Hr3G0713160 and HORVU6H r3G0626550, are orthologous to AtACX3 and AtVAMPs, which have reported functions in root length-mediated drought tolerance and as a key protein in abiotic stress tolerance, respectively. Interestingly, one of these loci underlying a high-confidence candidate gene NEW ENHANCER OF ROOT DWARFISM1 (NERD1) showed involvement with root development. An allelic variation of this locus in non-coding region was significantly associated with increased root length under drought. Collectively, these results offer promising multi-trait affecting loci and candidate genes underlying root phenotypic responses to drought stress, which may provide valuable resources for genetic improvement of drought tolerance in barley.

Implementing multi-trait genomic selection to improve grain milling quality in oats (Avena sativa L.).

Oats (Avena sativa L.) provide unique nutritional benefits and contribute to sustainable agricultural systems. Breeding high-value oat varieties that meet milling industry standards is crucial for satisfying the demand for oat-based food products. Test weight, thins, and groat percentage are primary traits that define oat milling quality and the final price of food-grade oats. Conventional selection for milling quality is costly and burdensome. Multi-trait genomic selection (MTGS) combines information from genome-wide markers and secondary traits genetically correlated with primary traits to predict breeding values of primary traits on candidate breeding lines. MTGS can improve prediction accuracy and significantly accelerate the rate of genetic gain. In this study, we evaluated different MTGS models that used morphometric grain traits to improve prediction accuracy for primary grain quality traits within the constraints of a breeding program. We evaluated 558 breeding lines from the University of Illinois Oat Breeding Program across 2 years for primary milling traits, test weight, thins, and groat percentage, and secondary grain morphometric traits derived from kernel and groat images. Kernel morphometric traits were genetically correlated with test weight and thins percentage but were uncorrelated with groat percentage. For test weight and thins percentage, the MTGS model that included the kernel morphometric traits in both training and candidate sets outperformed single-trait models by 52% and 59%, respectively. In contrast, MTGS models for groat percentage were not significantly better than the single-trait model. We found that incorporating kernel morphometric traits can improve the genomic selection for test weight and thins percentage.

Dissection of Common Rust Resistance in Tropical Maize Multiparent Population through GWAS and Linkage Studies.

Common rust (CR), caused by Puccina sorghi, is a major foliar disease in maize that leads to quality deterioration and yield losses. To dissect the genetic architecture of CR resistance in maize, this study utilized the susceptible temperate inbred line Ye107 as the male parent crossed with three resistant tropical maize inbred lines (CML312, D39, and Y32) to generate 627 F7 recombinant inbred lines (RILs), with the aim of identifying maize disease-resistant loci and candidate genes for common rust. Phenotypic data showed good segregation between resistance and susceptibility, with varying degrees of resistance observed across different subpopulations. Significant genotype effects and genotype × environment interactions were observed, with heritability ranging from 85.7% to 92.2%. Linkage and genome-wide association analyses across the three environments identified 20 QTLs and 62 significant SNPs. Among these, seven major QTLs explained 66% of the phenotypic variance. Comparison with six SNPs repeatedly identified across different environments revealed overlap between qRUST3-3 and Snp-203,116,453, and Snp-204,202,469. Haplotype analysis indicated two different haplotypes for CR resistance for both the SNPs. Based on LD decay plots, three co-located candidate genes, Zm00001d043536, Zm00001d043566, and Zm00001d043569, were identified within 20 kb upstream and downstream of these two SNPs. Zm00001d043536 regulates hormone regulation, Zm00001d043566 controls stomatal opening and closure, related to trichome, and Zm00001d043569 is associated with plant disease immune responses. Additionally, we performed candidate gene screening for five additional SNPs that were repeatedly detected across different environments, resulting in the identification of five candidate genes. These findings contribute to the development of genetic resources for common rust resistance in maize breeding programs.

Development and validation of a functional molecular marker for a CaAPRR2-like gene that controls green fruit colour in pepper

Fruit colour is a crucial factor influencing both the marketability and quality of pepper (Capsicum annuum), particularly ornamental varieties. Fruit colour is a complex multigenic trait in plant species. Previously, the Arabidopsis pseudo-response regulator 2 (APRR2) gene, one of the regulators that control fruit chlorophyll content and chloroplast development, thereby influencing fruit colour at the green immature stage in tomato (Solanum lycopersicum), cucumber (Cucumis sativus) and pepper, was reported. Functional molecular markers associated with this homologous gene in pepper could be employed to discern fruit colour at the seedling stage, thus improving the efficiency of green/white-fruited pepper breeding. In this study, a derived cleaved amplified polymorphic sequences (dCAPS) marker was developed based on the mutation site in the sequence of a CaAPRR2-like gene that was cloned from the inbred line B1-2, which exhibits milky white fruit at the green immature stage. The marker was subsequently validated in a CaAPRR2-like progeny segregation population. After digestion with the restriction endonuclease TaqI, the amplification product exhibited evident polymorphic bands, enabling it to distinguish between peppers with milky white and green fruit colours. The developed molecular marker displayed remarkable stability and repeatability, thus offering a straightforward and effective tool for enhancing fruit colour in pepper breeding programs.