Quality-related Traits Research Articles

Multi-trait selection for mean performance and stability in purple-fleshed sweet potato

Few purple-fleshed sweet potato (PFSP) cultivars are available for Brazilian growers, urging for the development of new and adapted cultivars. PFSP breeding programs should include multiple traits during the selection process to increase the chances of developing an adequate genotype, specially yield-related and quality-related traits. The objective was to select promising PFSP genotypes based on yield and tuberous-roots-related traits exploring genotype x environment interaction (GEI). Four experiments were carried out, in which 23 pre-selected PFSP genotypes were evaluated based on yield and quality traits, after screening among 2500 experimental genotypes. The first experiment adopted an augmented block design, with ‘Luiza’ interspersed as a control. From this first experiment, the 19 experimental genotypes with the best performance were selected for the following three experiments, which were conducted in a randomized block experimental design, with three replications each, including ‘Luiza’ as control. The best genotypes were selected in the first experiment using the multi-trait genotype-ideotype distance index (MGIDI). For the following experiments, the performance of the genotypes was assessed using deviance analysis, genotypic stability through weighted average of absolute scores (WAASB) index, and the multi-trait stability index (MTSI). In the first experiment, three factors were retained, being associated to commercial production of tuberous roots (‘K-104′, ‘K-25′ and ‘U1–29′), total production of tuberous roots (‘K-110′, ‘C-42′, ‘F-16′, and ‘U1–29′), and quality of tuberous roots (‘F-22′), respectively. Desired gains were observed for all traits. For the experiments II, III, and IV five factors were retained, being four related to quality of tuberous roots and one to yield components. The GEI was significant for yield-related traits and desired gains were observed for most traits. Due to high commercial tuberous root yield and low WAASB values, the genotypes ‘U1–29′, ‘K-98′, ‘F-22′, ‘K-57′, ‘C-36′, ‘U1–15′, ‘K-25′, and ‘U2–12′ were highly productive and stable. The genotypes selected by the MTSI index were ‘U1–15′, ‘U2–10′, ‘U1–29′, ‘K-98′, and ‘K-78′. The multi-trait selection enabled the identification of promising genotypes highlighting their strengths and weaknesses.

Integrated GWAS and transcriptome analysis reveals key genes associated with muscle fibre and fat traits in Gushi chicken

ABSTRACT 1. In the following experiment meat quality traits of a Gushi-Anka F2 resource population were measured, and their heritability estimated. Intramuscular fat (IMF) had medium heritability (0.35) but leg muscle fibre density (LMD), leg muscle fibre diameter (LMF), breast muscle fibre density (BMD), fresh fat content (FFA), and absolute dry fat content (AFC) had low heritability (0–0.2). The IMF presented the most important genetic additive effect among the poultry meat quality-related traits studied. 2. The phenotypic data of meat quality traits in the Gushi-Anka F2 resource population were combined with genotyping by sequencing (GBS) data to obtain genotype data. Six meat quality traits in 734 birds were analysed by GWAS. Based on these variants, 83 significant (–log10(p) > 4.42) single nucleotide polymorphisms and four quantitative trait loci (QTL) regions corresponding to 175 genes were identified. Further linkage disequilibrium (LD) analysis was conducted on chromosome 13 (Chr13) and chromosome 27 (Chr27) QTL regions. 3. Based on the transcriptome data and GWAS results, 12 shared genes - ITGB3, DNAJC27, ETV4, C7orf50, FKBP1B, G3BP1, IGF2BP1, KCNH6, LOC416263, SCARA5, SMIM5 and TBL1XR1 were identified as candidate genes influencing muscle fibre and fat traits.

GWAS and Meta-QTL Analysis of Kernel Quality-Related Traits in Maize.

The quality of corn kernels is crucial for their nutritional value, making the enhancement of kernel quality a primary objective of contemporary corn breeding efforts. This study utilized 260 corn inbred lines as research materials and assessed three traits associated with grain quality. A genome-wide association study (GWAS) was conducted using the best linear unbiased estimator (BLUE) for quality traits, resulting in the identification of 23 significant single nucleotide polymorphisms (SNPs). Additionally, nine genes associated with grain quality traits were identified through gene function annotation and prediction. Furthermore, a total of 697 quantitative trait loci (QTL) related to quality traits were compiled from 27 documents, followed by a meta-QTL analysis that revealed 40 meta-QTL associated with these traits. Among these, 19 functional genes and reported candidate genes related to quality traits were detected. Three significant SNPs identified by GWAS were located within the intervals of these QTL, while the remaining eight significant SNPs were situated within 2 Mb of the QTL. In summary, the findings of this study provide a theoretical framework for analyzing the genetic basis of corn grain quality-related traits and for enhancing corn quality.

Identification and fine mapping of a QTL-rich region for yield-and quality-related traits on chromosome 4BS in common wheat (Triticum aestivum L.).

Yield and quality are important for plant breeding. To better understand the genetic basis underlying yield- and quality-related traits in wheat (Triticum aestivum L.), we conducted the quantitative trait locus (QTL) analysis using recombinant inbred lines (RILs) and a high-density genetic linkage map with a 90K array. In this study, a total of 117 QTLs were detected for spike number per area (SNPA), thousand grain weight (TGW), grain number per spike (GNS), plant height (PH), spike length (SL), total spikelet number (TSN), spikelet density (SD), grain protein content (GPC), and grain starch content (GSC). Among these QTLs, 30 environmentally stable QTLs for yield- and quality-related traits were detected. Notably, five QTL-rich regions (Qrr) for yield-and/or quality-related traits were identified, including the QTL-rich region on chromosome 4BS (QQrr.cau-4B) for eight traits (SNPA, GNS, PH, SL, TSN, SD, GPC, and GSC). The stable QTL-rich region QQrr.cau-4B was delimited into a physical interval of approximately 2.47Mb. Based on the annotation information of the Chinese spring wheat genome v1.0 and parental re-sequencing results, the interval included twelve genes with sequence variations. Taken together, these results contribute to further understanding of the genetic basis of SNPA, GNS, PH, SL, TSN, SD, GPC, and GSC, and fine mapping of QQrr.cau-4B will be beneficial for gene cloning and marker-assisted selection in the genetic improvement of wheat varieties.

Agonistic song rate positively correlates with male breeding success and avian malaria infection in Acrocephalus paludicola (Aquatic Warbler), a promiscuous songbird with female-only parental care

Abstract The link between male song and reproductive success has been explored at length in socially monogamous birds, but results were inconsistent and under-represented socially non-monogamous species with uniparental care. Here, we evaluated whether metrics of male song in Acrocephalus paludicola (Aquatic Warbler), a promiscuous songbird with female-only care and large repertoires, are associated with fitness- and quality-related traits. We showed that the number of 9-day-old nestlings fathered and probability of avian malaria infection increased with the rate of agonistic song, produced in male–male interactions, and that male-scaled mass index (proxy for energy reserves) positively correlated with the repertoire size. The male breeding success was not explained by repertoire size and song duty cycle. None of the song variables clearly explained the male return rate or change in the tarsus length (proxy for structural body size) and scaled mass index of the fathered chicks between days 2 and 9 post-hatch. No other relationships between the song characteristics and the inbreeding coefficient, scaled mass index, wing-length and Trypanosoma infection status of the males were supported, and Plasmodium infection was unrelated to the song duty cycle and repertoire size. We conclude that in male A. paludicola the repertoire size could be a signal of early developmental stress or current body condition, and the agonistic song rate could be shaped by sexual selection and signal to females a genetic makeup that enhances survival upon infection by Plasmodium.

Genetic dissection of value-added quality traits and agronomic parameters through genome-wide association mapping in bread wheat (T. aestivum L.).

Bread wheat (T. aestivum) is one of the world's most widely consumed cereals. Since micronutrient deficiencies are becoming more common among people who primarily depend upon cereal-based diets, a need for better-quality wheat varieties has been felt. An association panel of 154 T. aestivum lines was evaluated for the following quality traits: grain appearance (GA) score, grain hardness (GH), phenol reaction (PR) score, protein percent, sodium dodecyl sulfate (SDS) sedimentation value, and test weight (TWt). In addition, the panel was also phenotyped for grain yield and related traits such as days to heading, days to maturity, plant height, and thousand kernel weight for the year 2017-18 at the Borlaug Institute for South Asia (BISA) Ludhiana and Jabalpur sites. We performed a genome-wide association analysis on this panel using 18,351 genotyping-by-sequencing (GBS) markers to find marker-trait associations for quality and grain yield-related traits. We detected 55 single nucleotide polymorphism (SNP) marker trait associations (MTAs) for quality-related traits on chromosomes 7B (10), 1A (9), 2A (8), 3B (6), 2B (5), 7A (4), and 1B (3), with 3A, 4A, and 6D, having two and the rest, 4B, 5A, 5B, and 1D, having one each. Additionally, 20 SNP MTAs were detected for yield-related traits based on a field experiment conducted in Ludhiana on 7D (4) and 4D (3) chromosomes, while 44 SNP MTAs were reported for Jabalpur on chromosomes 2D (6), 7A (5), 2A (4), and 4A (4). Utilizing these loci in marker-assisted selection will benefit from further validation studies for these loci to improve hexaploid wheat for better yield and grain quality.

Study on Genetic Variability for Forage Yield and Quality Traits in Forage Sorghum [Sorghum bicolor L. Moench

The initial research related to germplasm screening was carried out in the experimental area of Instructional Dairy Farm, GBPUAT Pantnagar during kharif season 2018. The experimental material for this experiment consisted of two hundreds and eighty diverse germplasm lines of sorghum along with six checks viz., SSG 59-3, Pant Chari- 5, Pant Chari- 6, CSV-21 F, CSH-22S, and CSV-24SS. The germplasm lines were evaluated in Augmented Block Design for nineteen forage yield related traits and thirteen quality traits. The statistical analysis for genetic variability was done using analysis of variance (ANOVA), heritability (h2), genotypic coefficient of variation (GCV), phenotypic coefficient of variation (PCV), and genetic advance (GA). The analysis of variance revealed that the genotypes and checks were showing a highly significant differences for all the traits under study indicated existence of inherent genetic differences among genotypes for different characters. Mean performance of forage yield and quality related traits exhibited a wide range of variability. GCV and PCV values were observed low for most of the characters whereas high for anthracnose, zonate leaf spot and shoot fly incidence. The value of genetic advance was observed high for leaf area, green fodder yield per plant, dry fodder yield per plant, hydrocyanic acid content, plant height, anthracnose, and shoot fly incidence were relatively more than other characters. Genetic advance as per cent of mean was observed low for days to maturity, dry matter per cent, in-vitro dry matter disappearance, neutral detergent fiber, acid detergent fiber, cellulose content whereas high for leaf area, flag leaf width, panicle length, panicle width, 1000-grains weight, grain yield per plant, green fodder yield per plant, dry fodder yield per plant, total soluble solids, silica content, anthracnose, zonate leaf spot and shoot fly incidence. Heritability values were found high for all the traits under study. The genotypes bearing the desired values for different genetic variability parameters and mean performance for can be exploited in future breeding programmes for the improving forage genotypes. These genotypes can be used as donor parents in crop improvement programme for improving forage yield and quality related traits along with improved resistance against anthracnose, shooty fly and zonate leaf spot.

Identification and fine mapping of a major QTL, qGPC4D, for grain protein content using wheat–Aegilopstauschii introgression lines

Wheat is a staple cereal crop that is crucial for food security and human health. Improving wheat quality has become an essential task for breeders to meet escalating market demand. In this study, a set of wheat-Aegilops tauschii introgression lines was developed from a cross between the high-yielding wheat variety Jimai 22 and Ae. tauschii Y215. A high-density genetic map containing 2,727 single nucleotide polymorphisms (SNPs) was constructed using a 55K SNP array to conduct quantitative trait loci (QTL) analysis for grain quality-related traits. Eight QTL were identified for grain protein content (GPC), starch content, and wet gluten content in the two environments. Among them, a major and environmentally stable QTL, qGPC4D, for GPC was identified, with favorable alleles contributed by Ae. tauschii Y215. Subsequently, qGPC4D was narrowed down to a 9.88 Mb physical interval through further fine mapping utilizing the introgression lines. Additionally, three linked SNP of qGPC4D were converted into high-throughput kompetitive allele-specific PCR (KASP) markers and validated in the introgression population. These findings offer promising candidate genes, elite introgression lines, and KASP markers for wheat high-quality breeding.

IMPACT OF WATER STRESS CONDITIONS ON ASSOCIATION OF AGRO-MORPHOLOGICAL, PHYSIO-CHEMICAL AND KERNEL QUALITY-RELATED TRAITS IN MAIZE HYBRIDS

Changing climatic conditions, especially high temperatures and droughts are one of the major factors hindering sustainable maize production in major maize-growing areas of the world. The current study was designed to determine the association between different morphological, physiological, biochemical, and kernel quality-related traits in maize hybrids under water-deficient conditions. The experiment material was comprised of seven indigenously developed maize hybrids from Maize and Millets Research Institute, Yusafwala-Sahiwal (YH-5482, YH-5427, YH-5404, YH-1899, FH-949, YH-5577, and YH-5395), one maize hybrid developed by local seed company i.e., Kissan Seed Corporation (SB-9663) and two maize hybrids developed by multinational seed companies i.e., Corteva Seeds Pvt Ltd. (P-1543) and Syngenta Seed Pvt Ltd. (NK-8441). The experiment was executed under a randomized complete block design with four replications. The results revealed that highly significant genetic variations were present among maize hybrids for morphological, physiological, biochemical, and kernel quality traits under water-deficient conditions except for ear length for which variations were found to be non-significant. Moreover, correlation coefficient analysis depicts a strong positive correlation of kernel yield with days to 50% silking, days to 50% tasseling, stomatal conductance, transpiration rate, total chlorophyll contents, 1000-kernel weight, ear length, and plant height. However, kernel yield was found to be negatively correlated with hydrogen peroxide, superoxide dismutase, and proline contents. Similarly, path coefficient analysis showed that days to 50% silking had the highest direct positive effect on kernel yield followed by 1000-grain weight, starch contents percentage, and ear height. Therefore, parental material selection must be done using these yield-associated trades under water-deficient conditions.

Genetic dissection of yield and quality-related traits in a Colombian Andigenum potato collection, revealed by genome-wide association and genomic prediction analyses

Genetic dissection of yield and quality-related traits in a Colombian Andigenum potato collection, revealed by genome-wide association and genomic prediction analyses

Genetic Variability and Interrelationships of Grain, Cooking, and Nutritional Quality Traits in Cowpea: Implications for Cowpea Improvement

Grain quality, cooking quality, and nutritional quality traits are some of the major attributes that enhance the uptake and utilization of improved cowpea varieties. Therefore, there is a need for a better understanding of the genetic variation and inter-relationships among these quality traits in cowpeas to integrate them into cowpea breeding programs. This study was conducted to determine genetic variability among 306 cowpea genotypes for grain quality, cooking quality, and nutritional quality traits and to understand the interrelationships among these traits for exploitation in breeding programs. The results showed highly significant differences (p < 0.001) among genotypes for grain quality, cooking quality, and nutritional quality traits. The mean performance for these quality traits was also very variable. These results suggest that genetic variability exists in the cowpea genotypes studied, which can be exploited in breeding programs aimed at developing high-performing varieties for the said traits. Significant (p < 0.001) positive correlations were detected for protein content with iron and zinc. On the other hand, nutritional quality traits did not exhibit any association with grain quality or cooking quality traits. Cooking quality traits were also shown to be significantly and positively correlated with grain quality traits. This study has identified several genotypes with desirable quality-related traits that could be used in crossing programs to generate improved varieties with consumer-preferred traits to improve the food, income, and nutritional status of many smallholder farmers that largely depend on cowpeas.

QTL Analysis for Rice Quality-Related Traits and Fine Mapping of qWCR3.

The quality of rice, evaluated using multiple quality-related traits, is the main determinant of its market competitiveness. In this study, two japonica rice varieties with significant differences in quality-related traits were used as parents to construct two populations, BC3F2 and BC3F2:3, with Kongyu131 (KY131) as the recurrent parent. A genetic linkage map was constructed using the BC3F2 population based on 151 pairs of SSR/InDel polymorphic markers selected between the parents. Grain-shape-related traits (grain length GL, grain width GW, and length-to-width ratio LWR), chalkiness-related traits (white-core rate WCR, white-belly rate WBR, white-back rate BR, and chalkiness rate CR), and amylose content (AC) were investigated in the two populations in 2017 and 2018. Except for BR and CR, the traits showed similar characteristics with a normal distribution in both populations. Genetic linkage analysis was conducted for these quality-related traits, and a total of 37 QTLs were detected in the two populations. Further validation was performed on the newly identified QTLs with larger effects, and three grain shape QTLs and four chalkiness QTLs were successfully validated in different environments. One repeatedly validated QTL, qWCR3, was selected for fine mapping and was successfully narrowed down to a 100 kb region in which only two genes, LOC_0s03g45210 and LOC_0s03g45320, exhibited sequence variations between the parents. Furthermore, the variation of LOC_Os03g45210 leads to a frameshift mutation and premature protein termination. The results of this study provide a theoretical basis for positional cloning of the qWCR3 gene, thus offering new genetic resources for rice quality improvement.

Phenomics and transcriptomic profiling of fruit development in distinct apple varieties

Apple is one of the most economically important and popular temperate fruit trees. The domestication of apple has resulted in substantial phenotypic differences, particularly between wild and cultivated varieties. However, the relationship between gene expression and phenotypic variations in apple remains poorly understood. Here, we present a comprehensive dataset featuring five distinct apple varieties, including two wild varieties and three representative cultivated varieties. The dataset comprises of both phenomics data, encompassing twelve fruit quality-related traits continuously measured over two years, and transcriptomic data obtained at different developmental stages with three biological replicates. We performed basic quality control process, gene expression normalization and differential gene expression analysis to demonstrate the utility and reliability of the dataset. Our findings indicate that gene expression strongly related with phenotypic variations in apple. This dataset serves as a valuable resource, encompassing phenomics and transcriptomic data in multiple formats, thereby facilitating further exploration of the relationships between gene expression and phenotypic traits in apple.

Genetic and molecular mechanisms underlying the parthenocarpic fruit mutation in tomato.

Parthenocarpy allows fruit set independently of fertilization. In parthenocarpic-prone tomato genotypes, fruit set can be achieved under pollen-limiting environmental conditions and in sterile mutants. Parthenocarpy is also regarded as a quality-related trait, when seedlessness is associated with positive fruit quality aspects. Among the different sources of genetic parthenocarpy described in tomato, the parthenocarpic fruit (pat) mutation is of particular interest because of its strong expressivity, high fruit set, and enhanced fruit quality. The complexity of the pat "syndrome" associates a strong competence for parthenocarpy with a complex floral phenotype involving stamen and ovule developmental aberrations. To understand the genetic basis of the phenotype, we mapped the pat locus within a 0.19-cM window of Chr3, comprising nine coding loci. A non-tolerated missense mutation found in the 14th exon of Solyc03g120910, the tomato ortholog of the Arabidopsis HD-Zip III transcription factor HB15 (SlHB15), cosegregated with the pat phenotype. The role of SlHB15 in tomato reproductive development was supported by its expression in developing ovules. The link between pat and SlHB15 was validated by complementation and knock out experiments by co-suppression and CRISPR/Cas9 approaches. Comparing the phenotypes of pat and those of Arabidopsis HB15 mutants, we argued that the gene plays similar functions in species with fleshy and dry fruits, supporting a conserved mechanism of fruit set regulation in plants.

Integrative omics analysis elucidates the genetic basis underlying seed weight and oil content in soybean.

Synergistic optimization of key agronomic traits by traditional breeding has dramatically enhanced crop productivity in the past decades. However, the genetic basis underlying coordinated regulation of yield- and quality-related traits remains poorly understood. Here, we dissected the genetic architectures of seed weight and oil content by combining genome-wide association studies (GWAS) and transcriptome-wide association studies (TWAS) using 421 soybean (Glycine max) accessions. We identified 26 and 33 genetic loci significantly associated with seed weight and oil content by GWAS, respectively, and detected 5,276 expression quantitative trait loci (eQTLs) regulating expression of 3,347 genes based on population transcriptomes. Interestingly, a gene module (IC79), regulated by two eQTL hotspots, exhibited significant correlation with both seed weigh and oil content. Twenty-two candidate causal genes for seed traits were further prioritized by TWAS, including Regulator of Weight and Oil of Seed 1 (GmRWOS1), which encodes a sodium pump protein. GmRWOS1 was verified to pleiotropically regulate seed weight and oil content by gene knockout and overexpression. Notably, allelic variations of GmRWOS1 were strongly selected during domestication of soybean. This study uncovers the genetic basis and network underlying regulation of seed weight and oil content in soybean and provides a valuable resource for improving soybean yield and quality by molecular breeding.

Identification of circRNA-associated ceRNA networks in the longissimus dorsi of yak under different feeding systems

BackgroundYaks (Bos grunniens), prized for their ability to thrive in high-altitude environments, are indispensable livestock in the plateau region. Modifying their feeding systems holds significant promise for improving their growth and meat quality. Tenderness, a key determinant of yak meat quality and consumer appeal, is demonstrably influenced by dietary regimen. Indoor feeding regimes have been shown to enhance tenderness by lowering shear stress and optimizing pH values. CircRNAs, well-known modulators of circulatory function, also play a crucial role in skeletal muscle development across various animal species. However, their functional significance in yak skeletal muscle remains largely unexplored.ResultsIn this study, we identified a total of 5,534 circRNAs within the longissimus dorsi muscle, and we found 51 differentially expressed circRNAs (20 up-regulated and 31 down-regulated) between the two feeding groups. Constructing a comprehensive ceRNA network illuminated intricate regulatory mechanisms, with PGP and circRNA_0617 converging on bta-miR-2285q, mirrored by KLF15/circRNA_0345/bta-miR-20b and CTSF/circRNA_0348/bta-miR-146a. These findings shed light on the potential of circRNAs to influence yak muscle development and meat quality, offering valuable insights for future research.ConclusionsThis investigation unraveled a complex interaction network between circRNAs、mRNAs and miRNAs in yak skeletal muscle. We further elucidated the target genes regulated by these target genes within the network, offering valuable insights into the potential regulatory mechanisms governing muscle development and meat quality-related traits in yaks.

Dissection of a novel major stable QTL on chromosome 7D for grain hardness and its breeding value estimation in bread wheat.

Grain hardness (Gh) is important for wheat processing and end-product quality. Puroindolines polymorphism explains over 60% of Gh variation and the novel genetic factors remain to be exploited. In this study, a total of 153 quantitative trait loci (QTLs), clustered into 12 genomic intervals (C1-C12), for 13 quality-related traits were identified using a recombinant inbred line population derived from the cross of Zhongkemai138 (ZKM138) and Chuanmai44 (CM44). Among them, C7 (harboring eight QTLs for different quality-related traits) and C8 (mainly harboring QGh.cib-5D.1 for Gh) were attributed to the famous genes, Rht-D1 and Pina, respectively, indicating that the correlation of involved traits was supported by the pleotropic or linked genes. Notably, a novel major stable QTL for Gh was detected in the C12, QGh.cib-7D, with ZKM138-derived allele increasing grain hardness, which was simultaneously mapped by the BSE-Seq method. The geographic pattern and transmissibility of this locus revealed that the increasing-Gh allele is highly frequently present in 85.79% of 373 worldwide wheat varieties and presented 99.31% transmissibility in 144 ZKM138-derivatives, indicating the non-negative effect on yield performance and that its indirect passive selection has happened during the actual breeding process. Thus, the contribution of this new Gh-related locus was highlighted in consideration of improving the efficiency and accuracy of the soft/hard material selection in the molecular marker-assisted process. Further, TraesCS7D02G099400, TraesCS7D02G098000, and TraesCS7D02G099500 were initially deduced to be the most potential candidate genes of QGh.cib-7D. Collectively, this study provided valuable information of elucidating the genetic architecture of Gh for wheat quality improvement.

T2T reference genome assembly and genome-wide association study reveal the genetic basis of Chinese bayberry fruit quality.

Chinese bayberry (Myrica rubra or Morella rubra; 2n = 16) produces fruit with a distinctive flavor, high nutritional, and economic value. However, previous versions of the bayberry genome lack sequence continuity. Moreover, to date, no large-scale germplasm resource association analysis has examined the allelic and genetic variations determining fruit quality traits. Therefore, in this study, we assembled a telomere-to-telomere (T2T) gap-free reference genome for the cultivar 'Zaojia' using PacBio HiFi long reads. The resulting 292.60Mb T2T genome, revealed 8 centromeric regions, 15 telomeres, and 28 345 genes. This represents a substantial improvement in the genome continuity and integrity of Chinese bayberry. Subsequently, we re-sequenced 173 accessions, identifying 6 649 674 single nucleotide polymorphisms (SNPs). Further, the phenotypic analyses of 29 fruit quality-related traits enabled a genome-wide association study (GWAS), which identified 1937 SNPs and 1039 genes significantly associated with 28 traits. An SNP cluster pertinent to fruit color was identified on Chr6: 3407532 to 5 153 151bp region, harboring two MYB genes (MrChr6G07650 and MrChr6G07660), exhibiting differential expression in extreme phenotype transcriptomes, linked to anthocyanin synthesis. An adjacent, closely linked gene, MrChr6G07670 (MLP-like protein), harbored an exonic missense variant and was shown to increase anthocyanin production in tobacco leaves tenfold. This SNP cluster, potentially a quantitative trait locus (QTL), collectively regulates bayberry fruit color. In conclusion, our study presented a complete reference genome, uncovered a suite of allelic variations related to fruit-quality traits, and identified functional genes that could be harnessed to enhance fruit quality and breeding efficiency of bayberries.

Genome-Wide Mapping of Quantitative Trait Loci for Yield-Attributing Traits of Peanut.

Peanuts (Arachis hypogaea L.) are important high-protein and oil-containing legume crops adapted to arid to semi-arid regions. The yield and quality of peanuts are complex quantitative traits that show high environmental influence. In this study, a recombinant inbred line population (RIL) (Valencia-C × JUG-03) was developed and phenotyped for nine traits under two environments. A genetic map was constructed using 1323 SNP markers spanning a map distance of 2003.13 cM. Quantitative trait loci (QTL) analysis using this genetic map and phenotyping data identified seventeen QTLs for nine traits. Intriguingly, a total of four QTLs, two each for 100-seed weight (HSW) and shelling percentage (SP), showed major and consistent effects, explaining 10.98% to 14.65% phenotypic variation. The major QTLs for HSW and SP harbored genes associated with seed and pod development such as the seed maturation protein-encoding gene, serine-threonine phosphatase gene, TIR-NBS-LRR gene, protein kinase superfamily gene, bHLH transcription factor-encoding gene, isopentyl transferase gene, ethylene-responsive transcription factor-encoding gene and cytochrome P450 superfamily gene. Additionally, the identification of 76 major epistatic QTLs, with PVE ranging from 11.63% to 72.61%, highlighted their significant role in determining the yield- and quality-related traits. The significant G × E interaction revealed the existence of the major role of the environment in determining the phenotype of yield-attributing traits. Notably, the seed maturation protein-coding gene in the vicinity of major QTLs for HSW can be further investigated to develop a diagnostic marker for HSW in peanut breeding. This study provides understanding of the genetic factor governing peanut traits and valuable insights for future breeding efforts aimed at improving yield and quality.

Multi-model genome-wide association studies for appearance quality in rice.

Improving the quality of the appearance of rice is critical to meet market acceptance. Mining putative quality-related genes has been geared towards the development of effective breeding approaches for rice. In the present study, two SL-GWAS (CMLM and MLM) and three ML-GWAS (FASTmrEMMA, mrMLM, and FASTmrMLM) genome-wide association studies were conducted in a subset of 3K-RGP consisting of 198 rice accessions with 553,831 SNP markers. A total of 594 SNP markers were identified using the mixed linear model method for grain quality traits. Additionally, 70 quantitative trait nucleotides (QTNs) detected by the ML-GWAS models were strongly associated with grain aroma (AR), head rice recovery (HRR, %), and percentage of grains with chalkiness (PGC, %). Finally, 39 QTNs were identified using single- and multi-locus GWAS methods. Among the 39 reliable QTNs, 20 novel QTNs were identified for the above-mentioned three quality-related traits. Based on annotation and previous studies, four functional candidate genes (LOC_Os01g66110, LOC_Os01g66140, LOC_Os07g44910, and LOC_Os02g14120) were found to influence AR, HRR (%), and PGC (%), which could be utilized in rice breeding to improve grain quality traits.