Marker-trait Association Analysis Research Articles

Transcriptome-wide association mapping provides insights into the genetic basis and candidate genes governing flowering, maturity and seed weight in rice bean (Vigna umbellata)

BackgroundRice bean (Vigna umbellata), an underrated legume, adapts to diverse climatic conditions with the potential to support food and nutritional security worldwide. It is used as a vegetable, minor food crop and a fodder crop, being a rich source of proteins, minerals, and essential fatty acids. However, little effort has been made to decipher the genetic and molecular basis of various useful traits in this crop. Therefore, we considered three economically important traits i.e., flowering, maturity and seed weight of rice bean and identified the associated candidate genes employing an associative transcriptomics approach on 100 diverse genotypes out of 1800 evaluated rice bean accessions from the Indian National Genebank.ResultsThe transcriptomics-based genotyping of one-hundred diverse rice bean cultivars followed by pre-processing of genotypic data resulted in 49,271 filtered markers. The STRUCTURE, PCA and Neighbor-Joining clustering of 100 genotypes revealed three putative sub-populations. The marker-trait association analysis involving various genome-wide association study (GWAS) models revealed significant association of 82 markers on 48 transcripts for flowering, 26 markers on 22 transcripts for maturity and 22 markers on 21 transcripts for seed weight. The transcript annotation provided information on the putative candidate genes for the considered traits. The candidate genes identified for flowering include HSC80, P-II PsbX, phospholipid-transporting-ATPase-9, pectin-acetylesterase-8 and E3-ubiquitin-protein-ligase-RHG1A. Further, the WRKY1 and DEAD-box-RH27 were found to be associated with seed weight. Furthermore, the associations of PIF3 and pentatricopeptide-repeat-containing-gene with maturity and seed weight, and aldo–keto-reductase with flowering and maturity were revealed.ConclusionThis study offers insights into the genetic basis of key agronomic traits in rice bean, including flowering, maturity, and seed weight. The identified markers and associated candidate genes provide valuable resources for future exploration and targeted breeding, aiming to enhance the agronomic performance of rice bean cultivars. Notably, this research represents the first transcriptome-wide association study in pulse crop, uncovering the candidate genes for agronomically useful traits.

Genetic dissection of green pod yield in dolichos bean, an orphan vegetable legume, using new molecular markers.

In the era of genomic-assisted breeding for crop improvement, developing new molecular markers and validating them for use in breeding programs are the prelude. Dolichos bean is one of the most important vegetable legume crops owing to its nutrient-rich green pods used as vegetables. Limitations in genomic resources, including molecular markers, restrict the accelerated improvement of the crop. In the present investigation, a set of 430 new simple sequence repeat markers was developed from sequence information of a reference variety. These markers included di- and tri-nucleotide repeats. The markers were assayed on an association panel, which was evaluated for green pod yield over 5years. A multi-locus model, FarmCPU, was used to assess the marker-trait association analysis. A total of 106 marker-trait associations were identified using an efficient mixed-model approach. Tri-nucleotide repeats were more informative and predominantly associated with trait. Among these markers, 17 were associated with a high level of significance. Markers LP-D-68 and LP-D-14 were identified with a high level of significance in 5-year pooled data and explained 12.70% and 12% of the phenotypic variance, respectively. These markers associated with a high level of confidence have significant scope for use in marker-assisted selection programmes. Other associated markers may be utilized for improving parents through marker-assisted recurrent selection or genomic selection programs.

Marker trait association analysis to unravel genomic regions associated with Stemphylium disease reaction in lentil

This study investigates the response of lentil genotypes to Stemphylium blight disease over two cropping years, 2021 and 2022. In addition, this research aims to assess the marker-trait association between Stemphylium disease progress and the selected SSRs. Visual symptoms were assessed using Hashemi's disease scoring system, leading to the calculation of disease parameters such as Percent Disease Index (PDI) and Area Under Disease Progress Curve (AUDPC). The results revealed variations in disease progress among genotypes, with some exhibiting low disease indices, particularly genotype IC241072. Genetic diversity analysis using SSR markers identified 30 alleles and grouped genotypes into four clusters. Principal Coordinate Analysis (PCoA) confirmed the genetic distances among genotypes. Marker-trait association analysis linked the microsatellite locus LCSSR04_130362_118bp to Stemphylium blight resistance, supported by the identification of a TCP family transcription factor in close proximity. The validation of the association indicated a significant difference between resistant and susceptible alleles. This comprehensive approach combining field screening, genetic diversity analysis, and marker-trait associations provides valuable insights into the genetic basis of Stemphylium blight resistance in lentil genotypes, offering potential candidates for future breeding programs.

Estimation of iron, zinc, phytic acid concentration and protein content in lentil seeds over locations and their marker-trait association analysis

In the present study, a diverse set of 96 lentil accessions including biofortified variety IPL 220 was used to identify sources of high concentration for Fe and Zn along with low phytic acid concentration and high protein content. Further, Marker Trait Association (MTA) analysis was performed to find molecular markers controlling these nutritional traits. The average Fe, Zn and phytic acid concentration and protein content ranged from 46.5 to 94.8 (mg/kg), 21.5 to 45.3 (mg/kg), 3.7 to 9.3 (mg/kg) and 18.1–28.7 (%), respectively over the locations. This study showed variability for these traits as coefficient of variation was 11.1% for Fe, 18% for Zn, 18.3% for phytic acid and 8.71% for protein content over two locations. The standard error (S.E.) of mean ranged from 0.05 to 21.5 for Fe, 0.15 to 9.71 for Zn, 0.05 to 2.10 for phytic acid and 0.06 to 6.16 for protein content further calculated across the locations. MTA analysis following general linear model resulted in the identification of 31 MTAs for three traits at p < 0.05 explaining 10 to 26% of total phenotypic variation. Association of PBA LC0203 marker with Fe concentration explained the highest proportion of total phenotypic variation (26%) at Kanpur location. However, same marker with different loci also showed association with Fe concentration at Bhopal location explaining 11% of total phenotypic variation. This study also identified association of some genetic markers with more than two nutritional traits that provides opportunity of improving more than two positively associated nutritional traits through marker assisted selection simultaneously. In the present study, EST-SSR markers were used as functional markers for developing high yielding bio-fortified lentils.

GENETIC DIVERSITY AND ASSOCIATION ANALYSIS OF SALT TOLERANCE IN ASIATIC COTTON (GOSSYPIUM ARBOREUM) WITH MOLECULAR MARKERS

Gossypium arboreum possesses favorable characteristics that are valuable for developing superior cotton cultivars. This study was carried out to analyze genetic diversity and identify marker-trait association analysis related to salt tolerance using SSR markers for 215 accessions of G. arboreum. The salt tolerance-related traits like germination rate, fresh weight, stem length, water content, chlorophyll content, electric conductivity, and MDA of the accessions were identified using 150 mM salt for 7 days of seedling growth.&#x0D; According to the comprehensive index of salt tolerance, 215 accessions were categorized mainly into four groups. Twenty four accessions were classified as highly tolerant to salt treatment (&gt;2.5). The natural population was classified into 3 main groups by phylogenetic analysis. The classifications of phylogenetic analysis were largely congruent with the breeding history and ecological region.&#x0D; Twenty-two strong marker-trait associations were obtained with strict significant P value i.e. P&lt; 0.01 and four makers including NAU1023, NAU1099, JESPR222, and NAU2783 were significantly related to salt tolerance. The marker NAU2783 was highest associated (P= 1.98E-12) with relative electric conductivity, and with the highest phenotype variation of 20.87%. Some markers are significantly associated with more than two traits. MUSS020 was significantly (P&lt;0.01) associated with relative fresh weight, and relative MDA, NAU1375 was associated with relative fresh weight and relative stem length, while NAU3468 was significantly associated with relative fresh weight, relative germination rate, and relative water content. The strong marker-trait association results might provide insights for marker-assistant selecting salt-tolerant varieties and will be useful for future cotton breeding programs.

Genetic architecture of adult-plant resistance to stripe rust in bread wheat (Triticum aestivum L.) association panel.

Stripe rust, caused by Puccinia striiformis f. sp. tritici, is a severe disease in wheat worldwide, including Ethiopia, causing up to 100% wheat yield loss in the worst season. The use of resistant cultivars is considered to be the most effective and durable management technique for controlling the disease. Therefore, the present study targeted the genetic architecture of adult plant resistance to yellow rust in 178 wheat association panels. The panel was phenotyped for yellow rust adult-plant resistance at three locations. Phonological, yield, yield-related, and agro-morphological traits were recorded. The association panel was fingerprinted using the genotyping-by-sequencing (GBS) platform, and a total of 6,788 polymorphic single nucleotide polymorphisms (SNPs) were used for genome-wide association analysis to identify effective yellow rust resistance genes. The marker-trait association analysis was conducted using the Genome Association and Prediction Integrated Tool (GAPIT). The broad-sense heritability for the considered traits ranged from 74.52% to 88.64%, implying the presence of promising yellow rust resistance alleles in the association panel that could be deployed to improve wheat resistance to the disease. The overall linkage disequilibrium (LD) declined within an average physical distance of 31.44 Mbp at r2=0.2. Marker-trait association (MTA) analysis identified 148 loci significantly (p = 0.001) associated with yellow rust adult-plant resistance. Most of the detected resistance quantitative trait loci (QTLs) were located on the same chromosomes as previously reported QTLs for yellow rust resistance and mapped on chromosomes 1A, 1B, 1D, 2A, 2B, 2D, 3A, 3B, 3D, 4A, 4B, 4D, 5A, 5B, 6A, 6B, 7A, and 7D. However, 12 of the discovered MTAs were not previously documented in the wheat literature, suggesting that they could represent novel loci for stripe rust resistance. Zooming into the QTL regions in IWGSC RefSeq Annotation v1 identified crucial disease resistance-associated genes that are key in plants' defense mechanisms against pathogen infections. The detected QTLs will be helpful for marker-assisted breeding of wheat to increase resistance to stripe rust. Generally, the present study identified putative QTLs for field resistance to yellow rust and some important agronomic traits. Most of the discovered QTLs have been reported previously, indicating the potential to improve wheat resistance to yellow rust by deploying the QTLs discovered by marker-assisted selection.

Genome-wide association study of Asian and European common wheat accessions for yield-related traits and stripe rust resistance.

Identifying novel loci of yield-related traits and resistance to stripe rust (caused by Puccinia striiformis f. sp. tritici) in wheat will help in breeding wheat that can meet projected demands in diverse environmental and agricultural practices. We performed a genome-wide association study with 24,767 SNPs in 180 wheat accessions that originated in 16 Asian or European countries between latitudes 30°N and 45°N. We detected seven accessions with desirable yield-related traits and 42 accessions that showed stable, high degrees of stripe rust resistance in multi-environment field assessments. A marker-trait association analysis of yield-related traits detected 18 quantitative trait loci (QTLs) in at least two test environments and two QTLs related to stripe rust resistance in at least three test environments. Five of these QTLs were identified as potentially novel QTLs by comparing their physical locations with those of known QTLs in the Chinese Spring (CS) reference genome RefSeq v1.1 published by the International Wheat Genome Sequencing Consortium; two were for spike length, one was for grain number per spike, one was for spike number, and one was for stripe rust resistance at adult plant stage. We also identified 14 candidate genes associated with the five novel QTLs. These QTLs and candidate genes will provide breeders with new germplasm and can be used to conduct marker-assisted selection in breeding wheat with improved yield and stripe rust resistance.

Association mapping of total flavonoid content and antioxidant capacities in lentil (Lens culinaris Medik.)

Ninety-six lentil genotypes were characterized for total flavonoid content (TFC) and antioxidant capacities (AOC). Analysis of variance (ANOVA) indicated significant (p ≤0.01) differences among lentil genotypes for studied traits across three locations. The average content of TFC was relatively higher in advanced breeding lines (12.21 mg QE/g) and low in Indian germplasm lines (10.68 mg QE/g). Mean performances for AOC, using the DPPH (ACD) and CUPRAC(ACC) methods, were relatively higher in advanced breeding lines (ACD-4.32 μmolTE/g and ACC-1.25 μmolTE/100 g) and least in released varieties (ACD-2.79 μmolTE/g and ACC-0.92 μmolTE/100 g). Marker trait association analyses were performed with 87 polymorphic SSR markers. The number of alleles amplified per locus ranged from 2 to 5, with an average of 2.92. The polymorphism information content (PIC) value ranged from 0.04 to 0.67, with a mean of 0.25. SSR markers, LCSSR 363 and PLC 38 were significantly associated with TFC and explained 10% of phenotypic variation. PLC 60, SSR 80, PLC 77, and PBALC 216, associated with ACD, explained 7.5 to 23% of phenotypic variation, whereas PBALC 250 and PBALC 216, associated with ACC, explained 15% of the phenotypic variation. TFC and AOC have a broader range of genetic variations that can be used in lentil breeding programs to develop varieties tailored for nutraceutical and therapeutic applications. The identified markers can be validated in biparental populations and used in lentil breeding programs to improve functional constituents and health benefits.

Genome-wide association studies: an intuitive solution for SNP identification and gene mapping in trees.

Analysis of natural diversity in wild/cultivated plants can be used to understand the genetic basis for plant breeding programs. Recent advancements in DNA sequencing have expanded the possibilities for genetically altering essential features. There have been several recently disclosed statistical genetic methods for discovering the genes impacting target qualities. One of these useful methods is the genome-wide association study (GWAS), which effectively identifies candidate genes for a variety of plant properties by examining the relationship between a molecular marker (such as SNP) and a target trait. Conventional QTL mapping with highly structured populations has major limitations. The limited number of recombination events results in poor resolution for quantitative traits. Only two alleles at any given locus can be studied simultaneously. Conventional mapping approach fails to work in perennial plants and vegetatively propagated crops. These limitations are sidestepped by association mapping or GWAS. The flexibility of GWAS comes from the fact that the individuals being examined need not be linked to one another, allowing for the use of all meiotic and recombination events to increase resolution. Phenotyping, genotyping, population structure analysis, kinship analysis, and marker-trait association analysis are the fundamental phases of GWAS. With the rapid development of sequencing technologies and computational methods, GWAS is becoming a potent tool for identifying the natural variations that underlie complex characteristics in crops. The use of high-throughput sequencing technologies along with genotyping approaches like genotyping-by-sequencing (GBS) and restriction site associated DNA (RAD) sequencing may be highly useful in fast-forward mapping approach like GWAS. Breeders may use GWAS to quickly unravel the genomes through QTL and association mapping by taking advantage of natural variances. The drawbacks of conventional linkage mapping can be successfully overcome with the use of high-resolution mapping and the inclusion of multiple alleles in GWAS.

Genome-wide association and targeted transcriptomic analyses reveal loci and candidate genes regulating preharvest sprouting in barley.

Genome-wide association study of diverse barley genotypes identified loci, single nucleotide polymorphisms and candidate genes that control seed dormancy and therefore enhance resistance to preharvest sprouting. Preharvest sprouting (PHS) causes significant yield and quality loss in barley and it is strongly associated with the level of seed dormancy. This study performed genome-wide association study using a collection of 255 diverse barley genotypes grown over four environments to identify loci controlling dormancy/PHS. Our phenotypic analysis revealed substantial variation in germination index/dormancy levels among the barley genotypes. Marker-trait association and linkage disequilibrium (LD) decay analyses identified 16 single nucleotide polymorphisms (SNPs) and two QTLs associated with dormancy/PHS, respectively, on chromosome 3H and 5H explaining 6.9% to 11.1% of the phenotypic variation. QTL.5H consist of 14 SNPs of which 12 SNPs satisfy the FDR threshold of α = 0.05, and it may represent the SD2 locus. The QTL on 3H consists of one SNP that doesn't satisfy FDR (α = 0.05). Genes harbouring the significant SNPs were analyzed for their expression pattern in the seeds of selected dormant and non-dormant genotypes. Of these genes, HvRCD1, HvPSRP1 and HvF3H exhibited differential expression between the dormant and non-dormant seed samples, suggesting their role in controlling seed dormancy/PHS. Three SNPs located within the differentially expressed genes residing in QTL.5H explained considerable phenotypic variation (≥ 8.6%), suggesting their importance in regulating PHS resistance. Analysis of the SNP marker data in QTL.5H identified a haplotype for PHS resistance. Overall, the study identified loci, SNPs and candidate genes that control dormancy and therefore play important roles in enhancing PHS resistance in barley through marker-assisted breeding.

Genetic diversity in Sickleweed (Falcaria vulgaris) and using stepwise regression to identify marker associated with traits

One of the well-known medicinal plants in the Falcaria genus is Sickleweed. Falcaria species exhibit a high degree of genetic variability, posing challenges in the examination of genetic diversity due to the significant potential for hybridization and introgression among them. Utilizing morphological traits and molecular markers may prove to be a valuable approach in evaluating and harnessing germplasm, considering the current obstacles faced in breeding this medicinal herb. In 2021, fifteen Sickleweed populations were cultivated in pots under field conditions, employing a randomized complete block design with three replications. This aimed to assess genetic diversity and conduct marker-trait association analyses utilizing morpho-physiological characteristics and SSR markers. The Sickleweed populations displayed considerable genetic diversity across all traits. Through cluster analysis of traits and the utilization of the UPGMA method based on the Gower distance matrix, the population was classified into three distinct clusters. Upon examining all genotypes, 52 polymorphic bands were detected, with an average of 8.68 bands per primer. The average expected heterozygosity across all loci was 0.864, while the average PIC was 0.855. Molecular data analysis employing the Jaccard similarity index and UPGMA method revealed the division of Sickleweed populations into two major groups. Furthermore, the results of molecular variance analysis indicated that variation within the population exceeded that between populations. Thirty-two SSR fragments were found to be significantly associated with genomic regions controlling the studied traits, determined through the application of stepwise regression. Selection based on molecular markers offers a rapid method for breeding programs, with the genetic information obtained from these markers playing a crucial role. Therefore, alongside traits, selecting superior genotypes and populations of high value in breeding programs becomes feasible. The findings highlight that certain markers are linked to multiple traits, emphasizing the critical importance of this characteristic in plant breeding for the simultaneous improvement of numerous traits. The study’s insights regarding markers hold potential for application in Sickleweed breeding programs.

Genetic Diversification of Starch Branching Enzymes during Maize Domestication and Improvement.

Elucidating the genetic basis of starch pasting and gelatinization properties is crucial for enhancing the quality of maize and its utility as feed and industrial raw material. In maize, ZmSBE genes encode important starch branching enzymes in the starch biosynthesis pathway. In this study, we re-sequenced the genomic sequences of ZmSBEI, ZmSBEIIa, ZmSBEIIb, and ZmSBEIII in three lines called 335 inbred lines, 68 landrace lines, and 32 teosinte lines. Analyses of nucleotide polymorphisms and haplotype diversity revealed differences in the selection patterns of ZmSBEI, ZmSBEIIa, ZmSBEIIb, and ZmSBEIII during maize domestication and improvement. A marker-trait association analysis of inbred lines detected 22 significant loci, including 18 SNPs and 4 indels significantly associated with three maize starch physicochemical properties. The allele frequencies of two variants (SNP17249C and SNP5055G) were examined in three lines. The frequency of SNP17249C in ZmSBEIIb was highest in teosinte lines, followed by landrace lines, and inbred lines, whereas there were no significant differences in the frequency of SNP5055G in ZmSBEIII among the three lines. These results suggest that ZmSBE genes play an important role in the phenotypic variations in the starch physicochemical properties in maize. The genetic variants detected in this study may be used to develop functional markers for improving maize starch quality.

SSR marker-based genetic diversity and marker-trait association analysis in aromatic rice (Oryza sativa) landraces

The present study on SSR marker-based genetic diversity and marker-trait association analysis in aromatic rice (Oryza sativa L.) landraces was carried out at R. H. Richharia Research Laboratory, Indira Gandhi Krishi Vishwavidyalaya, Raipur, Chhattisgarh during 2020. A total of 25 PCR-based simple sequence repeats (SSR) markers were evaluated in a set of 90 aromatic rice landraces along with 6 checks which includes 1 non-aromatic and 5 aromatic check varieties. Phenotypic data for marker-trait association analysis were taken for 24 yield attributing traits. Polymorphic Information Content (PIC) value ranged from 0.52 (RM316) to 0.79 (RM553) with a mean of0.69 which reveals that all the markers used in this study were highly informative and useful for diversity analysis of a wide range of genotypes. Unweighted Pair Group Method with Arithmetic Mean (UPGMA) and Rho’s similarity based cluster analysis revealed that all 5 aromatic check varieties falls in one cluster while the 1 non-aromatic check variety (Mahamaya) forms a separate cluster. Mixed linear model (MLM) was applied to perform genome-wide association mapping where 41 significant marker-trait associations were observed for 24 yield attributing traits. The potential markers identified in the study may provide new opportunities for rice breeder to improve yield and its attributing traits through marker assisted selection approach.

Genetic diversity, population structure, and genome-wide association study for the flowering trait in a diverse panel of 428 moth bean (Vigna aconitifolia) accessions using genotyping by sequencing

BackgroundMoth bean (Vigna aconitifolia) is an underutilized, protein-rich legume that is grown in arid and semi-arid areas of south Asia and is highly resistant to abiotic stresses such as heat and drought. Despite its economic importance, the crop remains unexplored at the genomic level for genetic diversity and trait mapping studies. To date, there is no report of SNP marker discovery and association mapping of any trait in this crop. Therefore, this study aimed to dissect the genetic diversity, population structure and marker-trait association for the flowering trait in a diversity panel of 428 moth bean accessions using genotyping by sequencing (GBS) approach.ResultsA total of 9078 high-quality single nucleotide polymorphisms (SNPs) were discovered by genotyping of 428 moth bean accessions. Model-based structure analysis and PCA grouped the moth bean accessions into two subpopulations. Cluster analysis revealed accessions belonging to the Northwestern region of India had higher variability than accessions from the other regions suggesting that this region represents its center of diversity. AMOVA revealed more variations within individuals (74%) and among the individuals (24%) than among the populations (2%). Marker-trait association analysis using seven multi-locus models including mrMLM, FASTmrEMMA FASTmrEMMA, ISIS EM-BLASSO, MLMM, BLINK and FarmCPU revealed 29 potential genomic regions for the trait days to 50% flowering, which were consistently detected in three or more models. Analysis of the allelic effect of the major genomic regions explaining phenotypic variance of more than 10% and those detected in at least 2 environments showed 4 genomic regions with significant phenotypic effect on this trait. Further, we also analyzed genetic relationships among the Vigna species using SNP markers. The genomic localization of moth bean SNPs on genomes of closely related Vigna species demonstrated that maximum numbers of SNPs were getting localized on Vigna mungo. This suggested that the moth bean is most closely related to V. mungo.ConclusionOur study shows that the north-western regions of India represent the center of diversity of the moth bean. Further, the study revealed flowering-related genomic regions/candidate genes which can be potentially exploited in breeding programs to develop early-maturity moth bean varieties.

Mapping the Genomic Regions Controlling Germination Rate and Early Seedling Growth Parameters in Rice.

Seed vigor is the key performance parameter of good quality seed. A panel was prepared by shortlisting genotypes from all the phenotypic groups representing seedling growth parameters from a total of 278 germplasm lines. A wide variation was observed for the traits in the population. The panel was classified into four genetic structure groups. Fixation indices indicated the existence of linkage disequilibrium in the population. A moderate to high level of diversity parameters was assessed using 143 SSR markers. Principal component, coordinate, neighbor-joining tree and cluster analyses showed subpopulations with a fair degree of correspondence with the growth parameters. Marker-trait association analysis detected eight novel QTLs, namely qAGR4.1, qAGR6.1, qAGR6.2 and qAGR8.1 for absolute growth rate (AGR); qRSG6.1, qRSG7.1 and qRSG8.1 for relative shoot growth (RSG); and qRGR11.1 for relative growth rate (RGR), as analyzed by GLM and MLM. The reported QTL for germination rate (GR), qGR4-1, was validated in this population. Additionally, QTLs present on chromosome 6 controlling RSG and AGR at 221 cM and RSG and AGR on chromosome 8 at 27 cM were detected as genetic hotspots for the parameters. The QTLs identified in the study will be useful for improvement of the seed vigor trait in rice.

Screening germplasm and detecting QTLs for mesocotyl elongation trait in rice (Oryza sativa L.) by association mapping

BackgroundRice is one of the most important food crops in the world and mainly cultivated in paddy field by transplanting seedlings. However, increasing water scarcity due to climate change, labor cost for transplanting, and competition from urbanization is making this traditional method of rice production unsustainable in the long term. In the present study, we mined favorable alleles for mesocotyl elongation length (MEL) by combining the phenotypic data of 543 rice accessions with genotypic data of 262 SSR markers through association mapping method.ResultsAmong the 543 rice accessions studied, we found 130 accessions could elongate mesocotyl length under dark germination condition. A marker-trait association analysis based on a mixed linear model revealed eleven SSR markers were associated with MEL trait with p-value less than 0.01. Among the 11 association loci, seven were novel. In total, 30 favorable marker alleles for MEL were mined, and RM265-140 bp showed the highest phenotypic effect value of 1.8 cm with Yuedao46 as the carrier accession. The long MEL group of rice accessions had higher seedling emergence rate than the short MEL group in the field. The correlation coefficient (rGCC−FSC = 0.485**) between growth chamber condition (GCC) and field soil condition (FSC) showed positive relationship and highly significant (P < 0.01) indicating that the result obtained in GCC could basically represent that obtained under FSC.ConclusionNot every genotype of the rice possesses the ability to elongate its mesocotyl length under dark or deep sowing condition. Mesocotyl elongation length is a quantitative trait controlled by many gene loci, and can be improved by pyramiding favorable alleles dispersed at different loci in different germplasm into a single genotype.

Marker-trait association analyses revealed major novel QTLs for grain yield and related traits in durum wheat.

The growing global demand for wheat for food is rising due to the influence of population growth and climate change. The dissection of complex traits by employing a genome-wide association study (GWAS) allows the identification of DNA markers associated with complex traits to improve the productivity of crops. We used GWAS with 10,045 single nucleotide polymorphism (SNP) markers to search for genomic regions associated with grain yield and related traits based on diverse panels of Ethiopian durum wheat. In Ethiopia, multi-environment trials of the genotypes were carried out at five locations. The genotyping was conducted using the 25k Illumina Wheat SNP array to explore population structure, linkage disequilibrium (LD), and marker-trait associations (MTAs). For GWAS, the multi-locus Fixed and Random Model Circulating Probability Unification (FarmCPU) model was applied. Broad-sense heritability estimates were high, ranging from 0.63 (for grain yield) to 0.97 (for thousand-kernel weight). The population structure based on principal component analysis, and model-based cluster analysis revealed two genetically distinct clusters with limited admixtures. The LD among SNPs declined within the range of 2.02-10.04 Mbp with an average of 4.28 Mbp. The GWAS scan based on the mean performance of the genotypes across the environments identified 44 significant MTAs across the chromosomes. Twenty-six of these MTAs are novel, whereas the remaining 18 were previously reported and confirmed in this study. We also identified candidate genes for the novel loci potentially regulating the traits. Hence, this study highlights the significance of the Ethiopian durum wheat gene pool for improving durum wheat globally. Furthermore, a breeding strategy focusing on accumulating favorable alleles at these loci could improve durum wheat production in the East African highlands and elsewhere.

Genetic Variation, DIMBOA Accumulation, and Candidate Gene Identification in Maize Multiple Insect-Resistance.

Maize seedlings contain high amounts of 2,4-dihydroxy-7-methoxy-1,4-benzoxazin-3-one (DIMBOA), and the effect of DIMBOA is directly associated with multiple insect-resistance against insect pests such as Asian corn borer and corn leaf aphids. Although numerous genetic loci for multiple insect-resistant traits have been identified, little is known about genetic controls regarding DIMBOA content. In this study, the best linear unbiased prediction (BLUP) values of DIMBOA content in two ecological environments across 310 maize inbred lines were calculated; and their phenotypic data and BLUP values were used for marker-trait association analysis. We identified nine SSRs that were significantly associated with DIMBOA content, which explained 4.30-20.04% of the phenotypic variation. Combined with 47 original genetic loci from previous studies, we detected 19 hot loci and approximately 11 hot loci (in Bin 1.04, Bin 2.00-2.01, Bin 2.03-2.04, Bin 4.00-4.03, Bin 5.03, Bin 5.05-5.07, Bin 8.01-8.03, Bin 8.04-8.05, Bin 8.06, Bin 9.01, and Bin 10.04 regions) supported pleiotropy for their association with two or more insect-resistant traits. Within the 19 hot loci, we identified 49 candidate genes, including 12 controlling DIMBOA biosynthesis, 6 involved in sugar metabolism/homeostasis, 2 regulating peroxidases activity, 21 associated with growth and development [(auxin-upregulated RNAs (SAUR) family member and v-myb avian myeloblastosis viral oncogene homolog (MYB)], and 7 involved in several key enzyme activities (lipoxygenase, cysteine protease, restriction endonuclease, and ubiquitin-conjugating enzyme). The synergy and antagonism interactions among these genes formed the complex defense mechanisms induced by multiple insect pests. Moreover, sufficient genetic variation was reported for DIMBOA performance and SSR markers in the 310 tested maize inbred lines, and 3 highly (DIMBOA content was 402.74-528.88 μg g-1 FW) and 15 moderate (DIMBOA content was 312.92-426.56 μg g-1 FW) insect-resistant genotypes were major enriched in the Reid group. These insect-resistant inbred lines can be used as parents in maize breeding programs to develop new varieties.

Genetic Structure and Diversity Study of Cassava (&amp;lt;i&amp;gt;Manihot esculenta&amp;lt;/i&amp;gt;) Germplasm for African Cassava Mosaic Disease and Fresh Storage Root Yield

A better understanding of population structure and genetic diversity among cassava germplasm for African cassava mosaic disease and fresh root yield traits is useful for cassava improvement programme. Phenotype-based selection for these traits is cumbersome due to phenotypic plasticity and difficulty in screening of phenotypic-induced variations. This study assessed quantitative trait loci (QTL) regions associated with African cassava mosaic disease (ACMD) and fresh storage root yield (FSRY) in 131 cassava (Manihot esculenta) genotypes using a genome-wide association study (GWAS). The single nucleotide polymorphism (SNP) loci and associated candidate genes, when validated, would be a valuable resource for marker-assisted selection in the breeding process for development of new cassava genotypes with improved resistance to ACMD and desirable high root yield. Population structure analysis using 12,500 SNPs differentiated the 131 genotypes into five distinct sub-groups (K = 5). Marker-trait association (MTA) analysis using the generalized linear model identified two QTL regions significant for ACMD and three for FSRY. This study demonstrated that DArTseq markers are useful genomic resources for genome-wide association studies of ACMD and FSRY traits in cassava for the acceleration of varietal development and release.

A multi-reference parent nested-association mapping population to dissect the genetics of quantitative traits in durum wheat

Durum wheat (Triticum durum Desf.) breeding programs face many challenges surrounding the development of stable varieties with high quality and yield. Therefore, researchers and breeders are focused on deciphering the genetic architecture of biotic and abiotic traits with the aim of pyramiding desirable traits. These efforts require access to diverse genetic resources, including wild relatives, germplasm collections and mapping populations. Advances in accelerated generation technologies have enabled the rapid development of mapping populations with significant genetic diversity. Here, we describe the development of a durum Nested Association Mapping (dNAM) population, which represents a valuable genetic resource for mapping the effects of different alleles on trait performance. We created this population to understand the quantitative nature of drought-adaptive traits in durum wheat. We developed 920 F6 lines in only 18 months using speed breeding technology, including the F4 generation in the field. Large variation in above- and below-ground traits was observed, which could be harnessed using genetic mapping and breeding approaches. We genotyped the population using 13,393 DArTseq markers. Quality control resulted in 6,785 high-quality polymorphic markers used for structure analysis, linkage disequilibrium decay, and marker-trait association analyses. To demonstrate the effectiveness of dNAM as a resource for elucidating the genetic control of quantitative traits, we took a genome-wide mapping approach using the FarmCPU method for plant height and days to flowering. These results highlight the power of using dNAM as a tool to dissect the genetics of durum wheat traits, supporting the development of varieties with improved adaptation and yield.