Search

Knowing the genes involved in quantitative traits provides an entry point to understanding the biological bases of behavior, but there are very few examples where the pathway from genetic locus to behavioral change is known. To explore the role of specific genes in fear behavior, we mapped three fear-related traits, tested fourteen genes at six quantitative trait loci (QTLs) by quantitative complementation, and identified six genes. Four genes, Lamp, Ptprd, Nptx2, and Sh3gl, have known roles in synapse function; the fifth, Psip1, was not previously implicated in behavior; and the sixth is a long non-coding RNA, 4933413L06Rik, of unknown function. Variation in transcriptome and epigenetic modalities occurred preferentially in excitatory neurons, suggesting that genetic variation is more permissible in excitatory than inhibitory neuronal circuits. Our results relieve a bottleneck in using genetic mapping of QTLs to uncover biology underlying behavior and prompt a reconsideration of expected relationships between genetic and functional variation.

Background: Phenotyping of plant traits presents a significant bottleneck in Quantitative Trait Loci (QTL) mapping and genome-wide association studies (GWAS). Computerized phenotyping using digital images promises rapid, robust, and reproducible measurements of dimension, shape, and color traits of plant organs, including grain, leaf, and floral traits. Results: We introduce GRABSEEDS, which is specifically tailored to extract a comprehensive set of features from plant images based on state-of-the-art computer vision and deep learning methods. This command-line enabled tool, which is adept at managing varying light conditions, background disturbances, and overlapping objects, uses digital images to measure plant organ characteristics accurately and efficiently. GRABSEED has advanced features including label recognition and color correction in a batch setting. Conclusion: GRABSEEDS streamlines the plant phenotyping process and is effective in a variety of seed, floral and leaf trait studies for association with agronomic traits and stress conditions. Source code and documentations for GRABSEEDS are available at: https://github.com/tanghaibao/jcvi/wiki/GRABSEEDS. [ABSTRACT FROM AUTHOR]

Introduction: Owing to advances in high-throughput genome sequencing, QTLSeq mapping of salt tolerance traits is a major platform for identifying soil-salinity tolerance QTLs to accelerate marker-assisted selection for salt-tolerant rice varieties. We performed QTL-BSA-Seq in the seedling stage of rice from a genetic cross of the extreme salt-sensitive variety, IR29, and "Jao Khao" (JK), a Thai salt-tolerant variety. Methods: A total of 462 F2 progeny grown in soil and treated with 160 mM NaCl were used as the QTL mapping population. Two high- and low-bulk sets, based on cell membrane stability (CMS) and tiller number at the recovery stage (TN), were equally sampled. The genomes of each pool were sequenced, and statistical significance of QTL was calculated using QTLseq and G prime (G') analysis, which is based on calculating the allele frequency differences or D(SNP index). Results: Both methods detected the overlapping interval region, wherein CMSbulk was mapped at two loci in the 38.41-38.85 Mb region with 336 SNPs on chromosome 1 (qCMS1) and the 26.13-26.80 Mb region with 1,011 SNPs on chromosome 3 (qCMS3); the D(SNP index) peaks were -0.2709 and 0.3127, respectively. TN-bulk was mapped at only one locus in the overlapping 38.26-38.95 Mb region on chromosome 1 with 575 SNPs (qTN1) and a D(SNP index) peak of -0.3544. These identified QTLs in two different genetic backgrounds of segregating populations derived from JK were validated. The results confirmed the colocalization of the qCMS1 and qTN1 traits on chromosome 1. Based on the CMS trait, qCMS1/qTN1 stably expressed 6%-18% of the phenotypic variance in the two validation populations, while qCMS1/qTN1 accounted for 16%-20% of the phenotypic variance in one validation population based on the TN trait. Conclusion: The findings confirm that the CMS and TN traits are tightly linked to the long arm of chromosome 1 rather than to chromosome 3. The validated qCMS-TN1 QTL can be used for gene/QTL pyramiding in marker-assisted selection to expedite breeding for salt resistance in rice at the seedling stage. [ABSTRACT FROM AUTHOR]

Leaf angle (LA) is an important trait of plant architecture, and individuals with narrow LA can better capture canopy light under high-density planting, which is beneficial for increasing the overall yield per unit area. To study the genetic basis and molecular regulation mechanism of leaf angle in rapeseed, we carried out a series of experiments. Quantitative trait loci (QTL) mapping was performed using the RIL population, and seven QTLs were identified. Transcriptome analysis showed that the cell wall formation/biogenesis processes and biosynthesis/metabolism of cell wall components were the most enrichment classes. Most differentially expressed genes (DEGs) involved in the synthesis of lignin, xylan, and cellulose showed down-regulated expression in narrow leaf material. Microscopic analysis suggested that the cell size affected by the cell wall in the junction area of the stem and petiole was the main factor in leaf petiole angle (LPA) differences. Combining QTL mapping and RNA sequencing, five promising candidate genes BnaA01G0125600ZS, BnaA01G0135700ZS, BnaA01G0154600ZS, BnaA10G0154200ZS, and BnaC03G0294200ZS were identified in rapeseed, and most of them were involved in cell wall biogenesis and the synthesis/metabolism of cell wall components. The results of QTL, transcriptome analysis, and cytological analysis were highly consistent, collectively revealing that genes related to cell wall function played a crucial role in regulating the LA trait in rapeseed. The study provides further insights into LA traits, and the discovery of new QTLs and candidate genes is highly beneficial for genetic improvement. [ABSTRACT FROM AUTHOR]

Starch is the main component that determines the yield and quality of Tartary buckwheat. As a quantitative trait, using quantitative trait locus (QTL) mapping to excavate genes associated with starch-related traits is crucial for understanding the genetic mechanisms involved in starch synthesis and molecular breeding of Tartary buckwheat varieties with high-quality starch. Employing a recombinant inbred line population as research material, this study used QTL mapping to investigate the amylose, amylopectin, and total starch contents across four distinct environments. The results identified a total of 20 QTLs spanning six chromosomes, which explained 4.07% to 14.41% of the phenotypic variation. One major QTL cluster containing three stable QTLs governing both amylose and amylopectin content, qClu-4-1, was identified and located in the physical interval of 39.85–43.34 Mbp on chromosome Ft4. Within this cluster, we predicted 239 candidate genes and analyzed their SNP/InDel mutations, expression patterns, and enriched KEGG pathways. Ultimately, five key candidate genes, namely FtPinG0004897100.01, FtPinG0002636200.01, FtPinG0009329200.01, FtPinG0007371600.01, and FtPinG0005109900.01, were highlighted, which are potentially involved in starch synthesis and regulation, paving the way for further investigative studies. This study, for the first time, utilized QTL mapping to detect major QTLs controlling amylose, amylopectin, and total starch contents in Tartary buckwheat. The QTLs and candidate genes would provide valuable insights into the genetic mechanisms underlying starch synthesis and improving starch-related traits of Tartary buckwheat. [ABSTRACT FROM AUTHOR]

Pod quality and yield traits in snap bean (Phaseolus vulgaris L.) influence consumer preferences, crop adoption by farmers, and the ability of the product to be commercially competitive locally and globally. The objective of the study was to identify the quantitative trait loci (QTL) for pod quality and yield traits in a snap Ã-- dry bean recombinant inbred line (RIL) population. A total of 184 F6 RILs derived from a cross between Vanilla (snap bean) and MCM5001 (dry bean) were grown in three field sites in Kenya and one greenhouse environment in Davis, CA, USA. They were genotyped at 5,951 single nucleotide polymorphisms (SNPs), and composite interval mapping was conducted to identify QTL for 16 pod quality and yield traits, including pod wall fiber, pod string, pod size, and harvest metrics. A combined total of 44 QTL were identified in field and greenhouse trials. The QTL for pod quality were identified on chromosomes Pv01, Pv02, Pv03, Pv04, Pv06, and Pv07, and for pod yield were identified on Pv08. Co-localization of QTL was observed for pod quality and yield traits. Some identified QTL overlapped with previously mapped QTL for pod quality and yield traits, with several others identified as novel. The identified QTL can be used in future marker-assisted selection in snap bean. [ABSTRACT FROM AUTHOR]

The main objective of mapping quantitative trait loci (QTL) and genome-wide association studies (GWAS) is to identify and locate QTLs on the genome. Estimating the sizes of QTL is equally important as identifying the QTLs. The size of a QTL is often measured by the QTL variance, or the proportion of phenotypic variance explained by the QTL, known as the QTL heritability. The reported QTL heritability is biased upward for small-sized QTLs estimated from small samples, especially in GWAS with a very small P -value threshold accommodating to Bonferroni correction for multiple tests. The phenomenon is called the Beavis effect. Methods of correcting the Beavis effect have been developed for additive effect models. Corresponding methods are not available for QTLs with more than one effect, such as QTLs including dominance and other genetic effects. In this study, we developed explicit formulas for estimating the variances and heritability for QTL with multiple effects. We also developed a method to remove nuisance parameters via an annihilator matrix. Finally, biases in estimated QTL variances caused by the Beavis effect are investigated and corrected. The new method is demonstrated by analyzing the 1000 grain weight (KGW) trait in a hybrid rice population. [ABSTRACT FROM AUTHOR]

Superior fiber quality is one of the most important objectives in cotton breeding. To detect the genetic basis underlying fiber quality, an F2 population containing 413 plants was constructed by crossing Jifeng 914 and Jifeng 173, both of which have superior fiber quality, with Jifeng 173 being better. Five fiber quality traits were investigated in the F2, F2:3, F2:4, and F2:5 populations. Quantitative trait loci (QTL) mapping was conducted based on a high-density genetic map containing 11,488 single nucleotide polymorphisms (SNPs) and spanning 4202.12 cM in length. Transgressive segregation patterns and complex correlations in the five tested traits were observed. A total of 108 QTLs were found, including 13 major effect QTLs that contributed more than 10% toward phenotypic variation (PV) and 9 stable QTLs that could be repeatedly mapped in different generations. Chromosome A7 contained 12 QTL, ranking the first. No QTL was found on chromosomes D1 and D11. Two QTLs could be repeatedly detected in three populations, including qFL-D3-2 in F2, F2:4, and F2:5 with 9.18–21.45% of PV and qFS-A11-1 in F2:3, F2:4, and F2:5 with 6.05–10.41% of PV. Another seven stable QTLs could be detected in two populations, including four major effect QTLs: qFL-A12-3, qFS-D10-2, qMC-D6-2, and qMC-D8-1. Fourteen QTL-overlapping regions were found, which might explain the complex correlations among the five phenotypic traits. Four regions on chromosome A11, D3, D6, and D10 covered by both stable and major effect QTLs are promising for further fine mapping. The genomic regions of the two QTLs detected in three populations and the four major effect QTLs contain 810 genes. Gene functional analysis revealed that the annotated genes are mainly involved in protein binding and metabolic pathways. Fifteen candidate genes in the qFL-D3-2 region are highly expressed in fiber or ovules during fiber initiation, elongation, secondary cell wall thickening, or maturation stages. qRT-PCR revealed that Ghir_D03G005440.1 and Ghir_D03G011310.1 may play a role in promoting fiber initiation, while Ghir_D03G006470.1 may be beneficial for promoting fiber elongation. This study provides more information for revealing the molecular genetic basis underlying cotton fiber quality. [ABSTRACT FROM AUTHOR]

With the rapid emergence and distribution of red crown rot (RCR) across countries, durable sources of resistance against Calonectria ilicicola in soybean [Glycine max (L.) Merrill] is required to control the disease. We employed two RIL populations for the experiment. We identified 15 and 14 QTLs associated with RCR resistance in ZM6 and MN populations, respectively, totaling 29 QTLs. Six and eight QTLs had phenotypic variation above 10% in ZM6 and MN populations, respectively. We identified six (6) "QTL hotspots" for resistance to RCR from the ZM6 and MN RIL populations on chromosomes 1, 7, 10, 11, 13, and 18. Gene annotations, gene ontology enhancement, and RNA sequencing assessment detected 23 genes located within six "QTL Hotspots" as potential candidate genes that could govern RCR resistance in soybeans. Our data will generally assist breeders in rapidly and effectively incorporating RCR resistance into high-yielding accession through marker-assisted selection. [ABSTRACT FROM AUTHOR]

Understanding the genetic basis of salt resistance in crops is crucial for agricultural productivity. This study investigates the phenotypic and genetic basis of salt stress response in rice (Oryza sativa L.), focusing on germination and seedling traits. Under salt stress conditions, significant differences were observed in seed germination and seedling traits between parental LH99 (Indica rice LuHui 99) and SN265 (japonica rice ShenNong 265). Transgressive segregation was evident within the RIL population, indicating complex genetic interactions. Nine QTLs were detected at germination and seedling stages under salt stress, namely qSGE5 and qSGE7 for seed germination energy (SGE); qSGP7 for seed germination percentage (SGP); qSSH7, qSSH9-1, and qSSH9-2 for seeding height (SSH); qSRN6 for root number (SRN); and qSDW6 and qSDW9 for dry weight (SDW). Among them, qSSH9-1 and qSDW9 were localized in the same interval, derived from the salt-resistant parent SN265. PCA revealed distinct trait patterns under salt stress, captured by six PCs explaining 81.12% of the total variance. PC composite scores were used to localize a QTL associated with early salt resistance in rice qESC9, which was located in the same interval as qSSH9-1 and qSDW9, and was subsequently unified under the name qESC9, an important QTL for early-growth salt tolerance in rice. Correlation analysis also confirmed a relationship between alleles of qESC9 and the resistance to salt, underscoring the critical role this locus plays in the determination of overall salt tolerance in rice. Physiological analyses of extreme phenotype lines highlighted the importance of ion exclusion mechanisms in salt-resistant lines, while salt-susceptible lines exhibited elevated oxidative stress and impaired antioxidant defense, contributing to cellular damage. This comprehensive analysis sheds light on the genetic and physiological mechanisms underlying salt stress response in rice, providing valuable insights for breeding programs aimed at enhancing salt resistance in rice. [ABSTRACT FROM AUTHOR]

Fruit weight is an important agronomic trait in pepper production and is closely related to yield. At present, many quantitative trait loci (QTL) related to fruit weight have been found in pepper; however, the genes affecting fruit weight remain unknown. We analyzed the fruit weight-related quantitative traits in an intraspecific Capsicum annuum cross between the cultivated species blocky-type pepper, cv. Qiemen, and the bird pepper accession, "129−1" (Capsicum annuum var. glatriusculum), which was the wild progenitor of C. annuum. Using the QTL-seq combined with the linkage-based QTL mapping approach, QTL detection was performed; and two major effects of QTL related to fruit weight, qFW2.1 and qFW3.1, were identified on chromosomes 2 and 3. The qFW2.1 maximum explained 12.28% of the phenotypic variance observed in two F2 generations, with the maximum LOD value of 11.02, respectively; meanwhile, the qFW3.1 maximum explained 15.50% of the observed phenotypic variance in the two F2 generations, with the maximum LOD value of 11.36, respectively. qFW2.1 was narrowed down to the 1.22 Mb region using homozygous recombinant screening from BC2S2 and BC2S3 populations, while qFW3.1 was narrowed down to the 4.61Mb region. According to the transcriptome results, a total of 47 and 86 differentially expressed genes (DEGs) in the candidate regions of qFW2.1 and qFW3.1 were identified. Further, 19 genes were selected for a qRT-PCR analysis based on sequence difference combined with the gene annotation. Finally, Capana02g002938 and Capana02g003021 are the most likely candidate genes for qFW2.1, and Capana03g000903 may be a candidate gene for qFW3.1. Taken together, our results identified and fine-mapped two major QTL for fruit weight in pepper that will facilitate marker-assistant breeding for the manipulation of yield in pepper. [ABSTRACT FROM AUTHOR]

Improving low nitrogen (LN) tolerance in barley (Hordeum vulgare L.) increases global barley yield and quality. In this study, a recombinant inbred line (RIL) population crossed between "Baudin × CN4079" was used to conduct field experiments on twenty traits of barley yield, agronomy, and nitrogen(N)-related traits under LN and normal nitrogen (NN) treatments for two years. This study identified seventeen QTL, comprising eight QTL expressed under both LN and NN treatments, eight LN-specific QTL, and one NN-specific QTL. The localized C2 cluster contained QTL controlling yield, agronomic, and N-related traits. Of the four novel QTL, the expression of the N-related QTL Qstna.sau-5H and Qnhi.sau-5H was unaffected by N treatment. Qtgw.sau-2H for thousand-grain weight, Qph.sau-3H for plant height, Qsl.sau-7H for spike length, and Qal.sau-7H for awn length were identified to be the four stable expression QTL. Correlation studies revealed a significant negative correlation between grain N content and harvest index (p < 0.01). These results are essential for barley marker-assisted selection (MAS) breeding. [ABSTRACT FROM AUTHOR]

Detection of beneficial genes from wild accessions of cultivated crops is becoming increasingly important for crop improvement, especially for traits lost during domestication. A set of wild introgression lines derived from advanced back cross breeding of Swarna with Oryza nivara species were characterized for grain size and seedling vigor related traits. Grain length in the population varied between 7.23 and 8.22 mm, while width varied from 2.66 to 3.13 mm. The length-to-width ratio (LWR) ranged from 2.41 to 3.06 mm, showing various grain shapes in the population. Simultaneously, seedling vigor-related traits were studied, and a significant correlation was observed between seedling vigor traits and grain size parameters. Further mapping of quantitative trait loci (QTL) using simple sequence repeat (SSR) and single nucleotide polymorphism (SNP) genotyping identified 18 QTL for seedling vigor- and grain size-related traits. Among these QTL, three major QTL (qAS7.1, qPL7.1 and qL7.1) were detected for grain size-related traits on chromosome 7, explaining 21.44%, 19.11% and 22.60% of phenotypic variation, respectively. Similarly, for seedling vigor traits, seven major QTL, viz., qSDW3.1, qTDW3.1, qSVI2-3.1, qSL3.1, qTL3.1, qSVI1-6.1, and qRDW8.1, were detected, explaining 18.3–26.38% of phenotypic variation. These QTL were on chromosomes 6 and 7 for seedling vigor and grain size traits and were collocated with common flanking markers. Hence, the results are useful for marker assisted breeding programmes for introgression and simultaneous improvement of seedling vigor and grain size, and further fine mapping of the related genes. [ABSTRACT FROM AUTHOR]

Background: Rapeseed (Brassica napus L.) is one of the most important oil crops and a wildly cultivated horticultural crop. The petals of B. napus serve to protect the reproductive organs and attract pollinators and tourists. Understanding the genetic basis of petal morphology regulation is necessary for B. napus breeding. Results: In the present study, the quantitative trait locus (QTL) analysis for six B. napus petal morphology parameters in a double haploid (DH) population was conducted across six microenvironments. A total of 243 QTLs and five QTL hotspots were observed, including 232 novel QTLs and three novel QTL hotspots. The spatiotemporal transcriptomic analysis of the diversiform petals was also conducted, which indicated that the expression of plant hormone metabolic and cytoskeletal binding protein genes was variant among diversiform petals. Conclusions: The integration of QTL and RNA-seq analysis revealed that plant hormones (including cytokinin, auxin, and gibberellin) and cytoskeleton were key regulators of the petal morphology. Subsequently, 61 high-confidence candidate genes of petal morphology regulation were identified, including Bn.SAUR10, Bn.ARF18, Bn.KIR1, Bn.NGA2, Bn.PRF1, and Bn.VLN4. The current study provided novel QTLs and candidate genes for further breeding B. napus varieties with diversiform petals. [ABSTRACT FROM AUTHOR]

Bakanae disease is mainly caused by Fusarium fujikuroi and is a significant fungal disease with a number of disastrous consequences. It causes great losses in rice production. However, few studies have focused on the details of bakanae disease resistance in rice. Here, we summarize and discuss the progress of bakanae disease resistance in rice. Besides rice germplasm screening and resistance-related gene/quantitative trait locus (QTL) exploration, the route of pathogen invasion in rice plants was determined. We further discussed the regulation of phytohormone-related genes and changes in endogenous phytohormones in rice plants that are induced by the pathogen. To achieve better control of bakanae disease, the use of natural fungicides was assessed in this review. During rice—F. fujikuroi interactions, the infection processes and spatial distribution of F. fujikuroi in infected seedlings and adult plants exhibit different trends. Fungal growth normally occurs both in resistant and susceptible cultivars, with less abundance in the former. Generally, bakanae disease is seed-borne, and seed disinfection using effective fungicides should always be the first and main option to better control the disease. Besides the friendly and effective measure of using natural fungicides, breeding and utilization of resistant rice cultivars is also an effective control method. To some extent, rice cultivars with low grain quality, indica subspecies, and some dwarf or semi-dwarf rice germplasms are more resistant to bakanae disease. Although no highly resistant germplasms were obtained, 37 QTLs were located, with almost half of the QTLs being located on chromosome 1. Using omics methods, WRKYs and MAPKs were usually found to be regulated during rice—F. fujikuroi interactions. The regulation of certain phytohormone-related genes and changes in some endogenous phytohormones induced by the pathogen were clear, i.e., it downregulated gibberellin-related genes and repressed endogenous gibberellins in resistant genotypes, but the opposite results were noted in susceptible rice genotypes. Overall, exploring resistant germplasms or resistance-related genes/QTLs for the breeding of rice with bakanae disease resistance, expanding research on the complex mechanism of rice—F. fujikuroi interactions, and using cost-effective and eco-friendly innovative control methods against the disease are necessary for present and future bakanae disease management. [ABSTRACT FROM AUTHOR]

Peanut stem rot, also known as white mold, poses a significant threat to peanut production. It is typically managed using fungicides and moderately resistant cultivars. Cultivars with higher resistance can reduce fungicide dependency and increase sustainability. This study explores the potential of wild peanut species in stem rot resistance breeding programs by enhancing genetic diversity in cultivated peanut. Through greenhouse and field evaluations, 13 allotetraploid hybrids with Arachis stenosperma as one of the parents showed superior resistance compared to other wild genotypes. The genomic regions that confer the stem rot resistance were further identified by genotyping and phenotyping an F2 population derived from the allotetraploid ValSten1 (A. valida × A. stenosperma)4× and A. hypogaea cv. TifGP-2. A linkage map was constructed from 1926 SNP markers. QTL analysis revealed both beneficial and deleterious loci, with two resistance-associated QTLs derived from A. stenosperma and four susceptibility loci, two from A. stenosperma and two from A. valida. This is the first study that evaluated peanut-compatible wild-derived allotetraploids for stem rot resistance and that identified wild-derived QTLs for resistance to this pathogen. The allotetraploid hybrid ValSten1, that has A. stenosperma as one of the parents, offers a resource for resistance breeding. Markers associated with resistance QTLs can facilitate introgression from ValSten1 into cultivated peanut varieties in future breeding efforts, potentially reducing reliance on chemical control measures. [ABSTRACT FROM AUTHOR]

The watermelon (Citrullus lanatus L.) holds substantial economic value as a globally cultivated horticultural crop. However, the genetic architecture of watermelon fruit weight (FW) remains poorly understood. In this study, we used sh14-11 with small fruit and N14 with big fruit to construct 100 recombinant inbred lines (RILs). Based on whole-genome resequencing (WGR), 218,127 single nucleotide polymorphisms (SNPs) were detected to construct a high-quality genetic map. After quantitative trait loci (QTL) mapping, a candidate interval of 31–38 Mb on chromosome 2 was identified for FW. Simultaneously, the bulked segregant analysis (BSA) in the F2 population corroborated the identification of the same interval, encompassing the homologous gene linked to the known FW-related gene fas. Additionally, RNA-seq was carried out across 11 tissues from sh14-11 and N14, revealing expression profiles that identified 1695 new genes and corrected the annotation of 2941 genes. Subsequent differential expression analysis unveiled 8969 differentially expressed genes (DEGs), with 354 of these genes exhibiting significant differences across four key developmental stages. The integration of QTL mapping and differential expression analysis facilitated the identification of 14 FW-related genes, including annotated TGA and NAC transcription factors implicated in fruit development. This combined approach offers valuable insights into the genetic basis of FW, providing crucial resources for enhancing watermelon cultivation. [ABSTRACT FROM AUTHOR]

Sheath blight (ShB) is the most serious disease of rice (Oryza sativa L.), caused by the soil-borne fungus Rhizoctonia solani Kühn (R. solani). It poses a significant threat to global rice productivity, resulting in approximately 50% annual yield loss. Managing ShB is particularly challenging due to the broad host range of the pathogen, its necrotrophic nature, the emergence of new races, and the limited availability of highly resistant germplasm. In this study, we conducted QTL mapping using an F2 population derived from a cross between a partially resistant accession (IRGC81941A) of Oryza nivara and the susceptible rice cultivar Punjab rice 121 (PR121). Our analysis identified 29 QTLs for ShB resistance, collectively explaining a phenotypic variance ranging from 4.70 to 48.05%. Notably, a cluster of four QTLs (qRLH1.1, qRLH1.2, qRLH1.5, and qRLH1.8) on chromosome 1 consistently exhibit a resistant response against R. solani. These QTLs span from 0.096 to 420.1 Kb on the rice reference genome and contain several important genes, including Ser/Thr protein kinase, auxin-responsive protein, protease inhibitor/seed storage/LTP family protein, MLO domain-containing protein, disease-responsive protein, thaumatin-like protein, Avr9/Cf9-eliciting protein, and various transcription factors. Additionally, simple sequence repeats (SSR) markers RM212 and RM246 linked to these QTLs effectively distinguish resistant and susceptible rice cultivars, showing great promise for marker-assisted selection programs. Furthermore, our study identified pre-breeding lines in the advanced backcrossed population that exhibited superior agronomic traits and sheath blight resistance compared to the recurrent parent. These promising lines hold significant potential for enhancing the sheath blight resistance in elite cultivars through targeted improvement efforts. [ABSTRACT FROM AUTHOR]

Copyright of Acta Agronomica Sinica is the property of Crop Science Society of China and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Copyright of Acta Agronomica Sinica is the property of Crop Science Society of China and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Copyright of Acta Agronomica Sinica is the property of Crop Science Society of China and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

The development and deployment of diverse resistance sources in novel wheat cultivars underpin the durable control of stripe rust. The objectives of this study were to identify quantitative trait loci (QTL) associated with stripe rust resistance in the Chinese wheat breeding line YN1813 and to provide wheat breeders with original genes with potentially durable resistance. A total of 306 F7:8 recombinant inbred lines (RIL), derived from a cross between YN1813 (infection type 0–3 and disease severity 1–36%) and the moderately susceptible landrace Chinese Spring (IT 7–9 and DS 41–65%), were assessed for stripe rust disease severity in the field at Qingshui in Gansu and Pixian in Sichuan in 2020 and 2021 following inoculation with a mixture of the currently predominant Pst races. The parents and RIL were genotyped using the Wheat 55K single-nucleotide polymorphism (SNP) array. The total length of the constructed genetic linkage map was 3896.30 cm, with an average interval of 1.30 cm between adjacent markers. Two major QTL were identified on chromosome 7B and 7D across all tested environments. QYr.hau-7B was mapped to a 2.26 cm interval between the SNP markers AX-110908486–AX-89658728–AX-109489314 on chromosome 7B, explaining 0.9% to 16.9% of the phenotypic variation. QYr.hau-7D was positioned in a 0.67 cm interval flanked by the SNP markers AX-111654594 and AX-89378255, explaining 0.4% to 21.4% of the phenotypic variation. The QTL on 7D likely correspond to the previously known gene Yr18, whereas QYr.hau-7B was presumed to be a novel gene adjacent to YrZH84 or the core part of YrZH84. SNP markers closely linked with QYr.hau-7B were converted to allele-specific quantitative PCR-based genotyping assay (AQP) markers and validated in a panel of 712 wheat accessions. The group possessing a positive allele (TT) of AQP_AX-89658728 significantly (p < 0.05) decreased the IT by 45.8% and the DS by 63.2%. QYr.hau-7B and its markers could be useful in breeding programs to improve the level and durability of stripe rust resistance. [ABSTRACT FROM AUTHOR]

Abstract Background Phenotyping of plant traits presents a significant bottleneck in Quantitative Trait Loci (QTL) mapping and genome-wide association studies (GWAS). Computerized phenotyping using digital images promises rapid, robust, and reproducible measurements of dimension, shape, and color traits of plant organs, including grain, leaf, and floral traits. Results We introduce GRABSEEDS, which is specifically tailored to extract a comprehensive set of features from plant images based on state-of-the-art computer vision and deep learning methods. This command-line enabled tool, which is adept at managing varying light conditions, background disturbances, and overlapping objects, uses digital images to measure plant organ characteristics accurately and efficiently. GRABSEED has advanced features including label recognition and color correction in a batch setting. Conclusion GRABSEEDS streamlines the plant phenotyping process and is effective in a variety of seed, floral and leaf trait studies for association with agronomic traits and stress conditions. Source code and documentations for GRABSEEDS are available at: https://github.com/tanghaibao/jcvi/wiki/GRABSEEDS .

Abstract [Objective] The study aims to discover the genetic loci and candidate genes of seed glucosinolate content in Brassica napus, and lay a foundation for the cloning of genes involved in glucosinolate metabolism and improving the breeding of B. napus. [Methods] Using KN DH populations from four different environments as materials, the QTL mapping of seed glucosinolate content and the candidate genes were analyzed. [Results] (1) The variation coefficient of seed glucosinolate content in B. napus was high and stable, which followed the genetic characteristics of quantitative traits. (2) Seven consistent QTLs, including cqGC.A9-5, cqGC.A9-7, cqGC.A9-9, cqGC.C2-9, cqGC.C2-10, cqGC.C9-5 and cqGC.C9-6, were environmentally stable QTLs, of which cqGC.A9-5, cqGC.C2-10, and cqGC.C9-5 were major QTLs. (3) Three candidate genes, including BnaA09g05480D, BnaC09g05620D, and BnaC09g05810D, were identified in the interval of the major QTL cqGC.A9-5 and cqGC.C9-5. Based on their annotation, these candidate genes were involved in the biosynthetic pathway of glucosinolates (the biosynthesis of IAOx and 3-alkyl malic acid) and transport and distribution of glucosinolates. [Conclusion] Seed glucosinolate content in B. napus was quantitative trait. Three major QTLs for seed glucosinolate content were identified, which might be involved in the synthesis of intermediate products and the transport and distribution of glucosinolates.

Abstract Background Rapeseed (Brassica napus L.) is one of the most important oil crops and a wildly cultivated horticultural crop. The petals of B. napus serve to protect the reproductive organs and attract pollinators and tourists. Understanding the genetic basis of petal morphology regulation is necessary for B. napus breeding. Results In the present study, the quantitative trait locus (QTL) analysis for six B. napus petal morphology parameters in a double haploid (DH) population was conducted across six microenvironments. A total of 243 QTLs and five QTL hotspots were observed, including 232 novel QTLs and three novel QTL hotspots. The spatiotemporal transcriptomic analysis of the diversiform petals was also conducted, which indicated that the expression of plant hormone metabolic and cytoskeletal binding protein genes was variant among diversiform petals. Conclusions The integration of QTL and RNA-seq analysis revealed that plant hormones (including cytokinin, auxin, and gibberellin) and cytoskeleton were key regulators of the petal morphology. Subsequently, 61 high-confidence candidate genes of petal morphology regulation were identified, including Bn.SAUR10, Bn.ARF18, Bn.KIR1, Bn.NGA2, Bn.PRF1, and Bn.VLN4. The current study provided novel QTLs and candidate genes for further breeding B. napus varieties with diversiform petals.

Cotton breeding for the development of early-maturing varieties is an effective way to improve multiple cropping indexes and alleviate the conflict between grains and cotton in the cultivated fields in China. In the present study, we aimed to identify upland cotton quantitative trait loci (QTLs) and candidate genes related to early-maturity traits, including whole growth period (WGP), flowering timing (FT), node of the first fruiting branch (NFFB), height of the node of the first fruiting branch (HNFFB), and plant height (PH). An early-maturing variety, CCRI50, and a late-maturing variety, Guoxinmian 11, were crossed to obtain biparental populations. These populations were used to map QTLs for the early-maturity traits for two years (2020 and 2021). With BSA-seq analysis based on the data of population 2020, the candidate regions related to early maturity were found to be located on chromosome D03. We then developed 22 polymorphic insertions or deletions (InDel) markers to further narrow down the candidate regions, resulting in the detection of five and four QTLs in the 2020 and 2021 populations, respectively. According to the results of QTL mapping, two candidate regions (InDel_G286-InDel_G144 and InDel_G24-InDel_G43) were detected. In these regions, three genes (GH_D03G0451, GH_D03G0649, and GH_D03G1180) have non-synonymous mutations in their exons and one gene (GH_D03G0450) has SNP variations in the upstream sequence between CCRI50 and Guoxinmian 11. These four genes also showed dominant expression in the floral organs. The expression levels of GH_D03G0451, GH_D03G0649 and GH_D03G1180 were significantly higher in CCRI50 than in Guoxinmian 11 during the bud differentiation stages, while GH_D03G0450 showed the opposite trend. Further functional verification of GH_D03G0451 indicated that the GH_D03G0451-silenced plants showed a delay in the flowering time. The results suggest that these are the candidate genes for cotton early maturity, and they may be used for breeding early-maturity cotton varieties.

Seed size is an important agronomic trait in melons that directly affects seed germination and subsequent seedling growth. However, the genetic mechanism underlying seed size in melon remains unclear. In the present study, we employed Bulked-Segregant Analysis sequencing (BSA-seq) to identify a candidate region (~1.35 Mb) on chromosome 6 that corresponds to seed size. This interval was confirmed by QTL mapping of three seed size-related traits from an F2 population across three environments. This mapping region represented nine QTLs that shared an overlapping region on chromosome 6, collectively referred to as qSS6.1. New InDel markers were developed in the qSS6.1 region, narrowing it down to a 68.35 kb interval that contains eight annotated genes. Sequence variation analysis of the eight genes identified a SNP with a C to T transition mutation in the promoter region of MELO3C014002, a leucine-rich repeat receptor-like kinase (LRR-RLK) gene. This mutation affected the promoter activity of the MELO3C014002 gene and was successfully used to differentiate the large-seeded accessions (C-allele) from the small-seeded accessions (T-allele). qRT-PCR revealed differential expression of MELO3C014002 between the two parental lines. Its predicted protein has typical LRR-RLK family domains, and phylogenetic analyses reveled its similarity with the homologs in several plant species. Altogether, these findings suggest MELO3C014002 as the most likely candidate gene involved in melon seed size regulation. Our results will be helpful for better understanding the genetic mechanism regulating seed size in melons and for genetically improving this important trait through molecular breeding pathways.

Abstract Background Leaf morphology plays a crucial role in photosynthetic efficiency and yield potential in crops. Cigar tobacco plants, which are derived from common tobacco (Nicotiana tabacum L.), possess special leaf characteristics including thin and delicate leaves with few visible veins, making it a good system for studying the genetic basis of leaf morphological characters. Results In this study, GWAS and QTL mapping were simultaneously performed using a natural population containing 185 accessions collected worldwide and an F2 population consisting of 240 individuals, respectively. A total of 26 QTLs related to leaf morphological traits were mapped in the F2 population at three different developmental stages, and some QTL intervals were repeatedly detected for different traits and at different developmental stages. Among the 206 significant SNPs identified in the natural population using GWAS, several associated with the leaf thickness phenotype were co-mapped via QTL mapping. By analyzing linkage disequilibrium and transcriptome data from different tissues combined with gene functional annotations, 7 candidate genes from the co-mapped region were identified as the potential causative genes associated with leaf thickness. Conclusions These results presented a valuable cigar tobacco resource showing the genetic diversity regarding its leaf morphological traits at different developmental stages. It also provides valuable information for novel genes and molecular markers that will be useful for further functional verification and for molecular breeding of leaf morphological traits in crops in the future.

Bulked-segregant analysis by deep sequencing (BSA-seq) is a widely used method for mapping QTL (quantitative trait loci) due to its simplicity, speed, cost-effectiveness, and efficiency. However, the ability of BSA-seq to detect QTL is often limited by inappropriate experimental designs, as evidenced by numerous practical studies. Most BSA-seq studies have utilized small to medium-sized populations, with F2 populations being the most common choice. Nevertheless, theoretical studies have shown that using a large population with an appropriate pool size can significantly enhance the power and resolution of QTL detection in BSA-seq, with F3 populations offering notable advantages over F2 populations. To provide an experimental demonstration, we tested the power of BSA-seq to identify QTL controlling days from sowing to heading (DTH) in a 7200-plant rice F3 population in two environments, with a pool size of approximately 500. Each experiment identified 34 QTL, an order of magnitude greater than reported in most BSA-seq experiments, of which 23 were detected in both experiments, with 17 of these located near 41 previously reported QTL and eight cloned genes known to control DTH in rice. These results indicate that QTL mapping by BSA-seq in large F3 populations and multi-environment experiments can achieve high power, resolution, and reliability.

Abstract Proper pericarp thickness protects the maize kernel against pests and diseases, moreover, thinner pericarp improves the eating quality in fresh corn. In this study, we aimed to investigate the dynamic changes in maize pericarp during kernel development and identified the major quantitative trait loci (QTLs) for maize pericarp thickness. It was observed that maize pericarp thickness first increased and then decreased. During the growth and formation stages, the pericarp thickness gradually increased and reached the maximum, after which it gradually decreased and reached the minimum during maturity. To identify the QTLs for pericarp thickness, a BC4F4 population was constructed using maize inbred lines B73 (recurrent parent with thick pericarp) and Baimaya (donor parent with thin pericarp). In addition, a high-density genetic map was constructed using maize 10 K SNP microarray. A total of 17 QTLs related to pericarp thickness were identified in combination with the phenotypic data. The results revealed that the heritability of the thickness of upper germinal side of pericarp (UG) was 0.63. The major QTL controlling UG was qPT1-1, which was located on chromosome 1 (212,215,145–212,948,882). The heritability of the thickness of upper abgerminal side of pericarp (UA) was 0.70. The major QTL controlling UA was qPT2-1, which was located on chromosome 2 (2,550,197–14,732,993). In addition, a combination of functional annotation, DNA sequencing analysis and quantitative real-time PCR (qPCR) screened two candidate genes, Zm00001d001964 and Zm00001d002283, that could potentially control maize pericarp thickness. This study provides valuable insights into the improvement of maize pericarp thickness during breeding.

The seed storage materials accumulate during seed development, and are essential for seed germination and seedling establishment. Here we employed two bi-parental populations of an F2:3 population developed from a cross of improved 220 (I220, small seeds with low starch) and PH4CV (large seeds with high starch), as well as recombinant-inbred lines (RILs) of X178 (high starch) and its improved introgression line I178 (low starch), to identify the genes that control seed storage materials. We identified a total of 12 QTLs for starch, protein and oil, which explained 3.44–10.79% of the phenotypic variances. Among them, qSTA2-1 identified in F2:3 and qSTA2-2 identified in the RILs partially overlapped at an interval of 7.314–9.554 Mb, and they explained 3.44–10.21% of the starch content variation, so they were selected for further study. Fine mapping of qSTA2-2 with the backcrossed populations of I220/PH4CV in each generation narrowed it down to a 199.7 kb interval that contains 14 open reading frames (ORFs). Transcriptomic analysis of developing seeds from the near-isogenic lines (NILs) of I220/PH4CV (BC5F2) showed that only 11 ORFs were expressed in 20 days after pollination (DAP) seeds. Five of them were upregulated and six of them were downregulated in NILI220, and the differentially expressed genes (DEGs) between NILI220 and NILPH4CV were enriched in starch metabolism, hormone signal transduction and glycosaminoglycan degradation. Of the eleven NILI220 differential expressed ORFs, ORF4 (Zm00001d002260) and ORF5 (Zm00001d002261) carry 75% protein sequence similarity, both encodes an glycolate oxidase, were the possible candidates of qSTA2-2. Further analysis and validation indicated that mutation of the qSTA2-2 locus resulted in the dysfunction of ABA accumulation, the embryo/endosperm ratio and the starch and hormone levels.

Summary Developing early maturing lentil has the potential to minimize yield losses, mainly during terminal drought. Whole‐genome resequencing (WGRS) based QTL‐seq identified the loci governing earliness in lentil. The genetic analysis for maturity duration provided a good fit to 3:1 segregation (F2), indicating earliness as a recessive trait. WGRS of Globe Mutant (late parent), late‐flowering, and early‐flowering bulks (from RILs) has generated 1124.57, 1052.24 million raw and clean reads, respectively. The QTL‐Seq identified three QTLs (LcqDTF3.1, LcqDTF3.2, and LcqDTF3.3) on chromosome 3 having 246244 SNPs and 15577 insertions/deletions (InDels) and 13 flowering pathway genes. Of these, 11 exhibited sequence variations between bulks and validation (qPCR) revealed a significant difference in the expression of nine candidate genes (LcGA20oxG, LcFRI, LcLFY, LcSPL13a, Lcu.2RBY.3g060720, Lcu.2RBY.3g062540, Lcu.2RBY.3g062760, LcELF3a, and LcEMF1). Interestingly, the LcELF3a gene showed significantly higher expression in late‐flowering genotype and exhibited substantial involvement in promoting lateness. Subsequently, an InDel marker (I‐SP‐383.9; LcELF3a gene) developed from LcqDTF3.2 QTL region showed 82.35% PVE (phenotypic variation explained) for earliness. The cloning, sequencing, and comparative analysis of the LcELF3a gene from both parents revealed 23 SNPs and InDels. Interestingly, a 52 bp deletion was recorded in the LcELF3a gene of L4775, predicted to cause premature termination of protein synthesis after 4 missense amino acids beyond the 351st amino acid due to the frameshift during translation. The identified InDel marker holds significant potential for breeding early maturing lentil varieties. [ABSTRACT FROM AUTHOR]

Background: Leaf morphology plays a crucial role in photosynthetic efficiency and yield potential in crops. Cigar tobacco plants, which are derived from common tobacco (Nicotiana tabacum L.), possess special leaf characteristics including thin and delicate leaves with few visible veins, making it a good system for studying the genetic basis of leaf morphological characters. Results: In this study, GWAS and QTL mapping were simultaneously performed using a natural population containing 185 accessions collected worldwide and an F2 population consisting of 240 individuals, respectively. A total of 26 QTLs related to leaf morphological traits were mapped in the F2 population at three different developmental stages, and some QTL intervals were repeatedly detected for different traits and at different developmental stages. Among the 206 significant SNPs identified in the natural population using GWAS, several associated with the leaf thickness phenotype were co-mapped via QTL mapping. By analyzing linkage disequilibrium and transcriptome data from different tissues combined with gene functional annotations, 7 candidate genes from the co-mapped region were identified as the potential causative genes associated with leaf thickness. Conclusions: These results presented a valuable cigar tobacco resource showing the genetic diversity regarding its leaf morphological traits at different developmental stages. It also provides valuable information for novel genes and molecular markers that will be useful for further functional verification and for molecular breeding of leaf morphological traits in crops in the future. [ABSTRACT FROM AUTHOR]

Introduction: The coconut tree crop (Cocos nucifera L.) provides vital resources for millions of people worldwide. Coconut germplasm is largely classified into 'Tall' (Typica) and 'Dwarf' (Nana) types. While Tall coconuts are outcrossing, stress tolerant, and late flowering, Dwarf coconuts are inbred and flower early with a high rate of bunch emission. Precocity determines the earlier production of a plantation and facilitates management and harvest. Methods: A unique outbred F2 population was used, generated by intercrossing F1 hybrids between Brazilian Green Dwarf from Jiqui (BGDJ) and West African Tall (WAT) cultivars. Single-nucleotide polymorphism (SNP) markers fixed for alternative alleles in the two varieties, segregating in an F2 configuration, were used to build a high-density linkage map with ~3,000 SNPs, anchored to the existing chromosome-level genome assemblies, and a quantitative trait locus (QTL) mapping analysis was carried out. Results: The linkage map established the chromosome numbering correspondence between the two reference genome versions and the relationship between recombination rate, physical distance, and gene density in the coconut genomes. Leveraging the strong segregation for precocity inherited from the Dwarf cultivar in the F2, a major effect QTL with incomplete dominance was mapped for flowering time. FLOWERING LOCUS T (FT) gene homologs of coconut previously described as putatively involved in flowering time by alternative splice variant analysis were colocalized within a ~200-kb window of the major effect QTL [logarithm of the odds (LOD) = 11.86]. Discussion: Our work provides strong phenotype-based evidence for the role of the FT locus as the putative underlying functional variant for the flowering time difference between Dwarf and Tall coconuts. Major effect QTLs were also detected for developmental traits of the palm, plausibly suggesting pleiotropism of the FT locus for other precocity traits. Haplotypes of the two SNPs flanking the flowering time QTL inherited from the Dwarf parent BGDJ caused a reduction in the time to flower of approximately 400 days. These SNPs could be used for high-throughput marker-assisted selection of early-flowering and higher-productivity recombinant lines, providing innovative genetic material to the coconut industry. [ABSTRACT FROM AUTHOR]

The demand for food goods is rising along with the world population growth, which is directly related to the yield of agricultural crops around the world. However, a number of environmental factors, including floods, salinity, moisture, and drought, have a detrimental effect on agricultural production around the world. Among all of these stresses, drought stress (DS) poses a constant threat to agricultural crops and is a significant impediment to global agricultural productivity. Its potency and severity are expected to increase in the future years. A variety of techniques have been used to generate drought-resistant plants in order to get around this restriction. Different crop plants exhibit specific traits that contribute to drought resistance (DR), such as early flowering, drought escape (DE), and leaf traits. We are highlighting numerous methods that can be used to overcome the effects of DS in this review. Agronomic methods, transgenic methods, the use of sufficient fertilizers, and molecular methods such as clustered regularly interspaced short palindromic repeats (CRISPRs)-associated nuclease 9 (Cas9), virus-induced gene silencing (VIGS), quantitative trait loci (QTL) mapping, microRNA (miRNA) technology, and OMICS-based approaches make up the majority of these techniques. CRISPR technology has rapidly become an increasingly popular choice among researchers exploring natural tolerance to abiotic stresses although, only a few plants have been produced so far using this technique. In order to address the difficulties imposed by DS, new plants utilizing the CRISPR technology must be developed. [ABSTRACT FROM AUTHOR]

Crucian carp (Carassius auratus) is widely distributed in the world and has become an economically freshwater fish. The population in Lake Dali Nur can tolerate the extreme alkaline environment with alkalinity over 50 mmol/L (pH 9.6), thus providing a special model for exploring alkali-tolerant molecular markers in an extremely alkaline environment. In this study, we constructed a high-density and high-resolution linkage map with 16,224 SNP markers based on genotyping-by-sequencing (GBS) consisting of 152 progenies and conducted QTL studies for alkali-tolerant traits. The total length of the linkage map was 3918.893 cM, with an average distance of 0.241 cM. Two QTLs for the ammonia-N-tolerant trait were detected on LG27 and LG45. A QTL for the urea-N-tolerant trait was detected on LG27. Interestingly, mapping the two QTLs on LG27 revealed that the mapped genes were both located in the intron of CDC42. GO functional annotation and KEGG enrichment analysis results indicated that the biological functions might be involved in the cell cycle, cellular senescence, MAPK, and Ras signaling pathways. These findings suggest that CDC42 may play an important role in the process of dealing with extremely alkaline environments. [ABSTRACT FROM AUTHOR]

Maize ear related traits are directly related to yield, and the analysis of their genetic basis is of great significance for guiding maize genetic improvement. In this study, the phenotypic characteristics of eight traits were identified in 168 high generation backcross recombinant inbred lines (AB-RILs) in six environments over three years. QTLs for eight traits were mapped with 11,407 SNP markers generated by 10 K liquid chip in maize. A total of 32 QTL related to eight ear traits were identified in this study, including five environmentally consistent QTLs and three pleiotropic QTL. Further, we used the genotypic and phenotypic data of 507 maize inbred lines to analyze the candidate regions of major QTL and identified 19 candidate genes that might be related to ear shape. We finally speculated four genes as candidate genes based on the analysis of evolution and expression of the genes. These results provide the important marker information for the genetic improvement of ear traits in maize breeding and offered guidance for the cloning of genes related to ear traits. [ABSTRACT FROM AUTHOR]

Body shape and size diversity and their evolutionary rates correlate with species richness at the macroevolutionary scale. However, the molecular genetic mechanisms underlying the morphological diversification across related species are poorly understood. In beetles, which account for one-fourth of the known species, adaptation to different trophic niches through morphological diversification appears to have contributed to species radiation. Here, we explored the key genes for the morphological divergence of the slender to stout body shape related to divergent feeding methods on large to small snails within the genus Carabus. We show that the zinc-finger transcription factor encoded by odd-paired (opa) controls morphological variation in the snail-feeding ground beetle Carabus blaptoides. Specifically, opa was identified as the gene underlying the slender to stout morphological difference between subspecies through genetic mapping and functional analysis via gene knockdown. Further analyses revealed that changes in opa cis -regulatory sequences likely contributed to the differences in body shape and size between C. blaptoides subspecies. Among opa cis -regulatory sequences, single nucleotide polymorphisms on the transcription factor binding sites may be associated with the morphological differences between C. blaptoides subspecies. opa was highly conserved in a wide range of taxa, especially in beetles. Therefore, opa may play an important role in adaptive morphological divergence in beetles. [ABSTRACT FROM AUTHOR]

Smallholder maize farming systems in sub-Saharan Africa (SSA) are vulnerable to drought-induced yield losses, which significantly impact food security and livelihoods within these communities. Mapping and characterizing genomic regions associated with water stress tolerance in tropical maize is essential for future breeding initiatives targeting this region. In this study, three biparental F3 populations composed of 753 families were evaluated in Kenya and Zimbabwe and genotyped with high-density single nucleotide polymorphism (SNP) markers. Quantitative trait loci maping was performed on these genotypes to dissect the genetic architecture for grain yield (GY), plant height (PH), ear height (EH) and anthesis-silking interval (ASI) under well-watered (WW) and water-stressed (WS) conditions. Across the studied maize populations, mean GY exhibited a range of 4.55--8.55 t/ha under WW and 1.29--5.59 t/ha under WS, reflecting a 31--59% reduction range under WS conditions. Genotypic and genotype-by-environment (G E) variances were significant for all traits except ASI. Overall broad sense heritabilities for GY were low to high (0.25--0.60). For GY, these genetic parameters were decreased under WS conditions. Linkage mapping revealed a significant difference in the number of QTLs detected, with 93 identified under WW conditions and 41 under WS conditions. These QTLs were distributed across all maize chromosomes. For GY, eight and two major effect QTLs (>10% phenotypic variation explained) were detected under WW and WS conditions, respectively. Under WS conditions, Joint Linkage Association Mapping (JLAM) identified several QTLs with minor effects for GY and revealed genomic region overlaps in the studied populations. Across the studied water regimes, five-fold cross-validation showed moderate to high prediction accuracies (0.15--0.90) for GY and other agronomic traits. Our findings demonstrate the polygenic nature of WS tolerance and highlights the immense potential of using genomic selection in improving genetic gain in maize breeding. [ABSTRACT FROM AUTHOR]

A recombinant inbred line (RIL) population derived from wheat landrace Qingxinmai and breeding line 041133 exhibited segregation in resistance to powdery mildew and stripe rust in five and three field tests, respectively. A 16K genotyping by target sequencing (GBTS) single-nucleotide polymorphism (SNP) array-based genetic linkage map was used to dissect the quantitative trait loci (QTLs) for disease resistance. Four and seven QTLs were identified for adult-plant resistance (APR) against powdery mildew and stripe rust. QPm.caas-1B and QPm.caas-5A on chromosomes 1B and 5A were responsible for the APR against powdery mildew in line 041133. QYr.caas-1B, QYr.caas-3B, QYr.caas-4B, QYr.caas-6B.1, QYr.caas-6B.2, and QYr.caas-7B detected on the five Bgenome chromosomes of line 041133 conferred its APR to stripe rust. QPm.caas-1B and QYr.caas.1B were co-localized with the pleiotropic locus Lr46/Yr29/Sr58/Pm39/Ltn2. A Kompetitive Allele Specific Polymorphic (KASP) marker KASP_1B_668028290 was developed to trace QPm/Yr.caas.1B. Four lines pyramiding six major disease resistance loci, PmQ, Yr041133, QPm/Yr.caas-1B, QPm.caas-2B.1, QYr.caas-3B, and QPm.caas-6B, were developed. They displayed effective resistance against both powdery mildew and stripe rust at the seedling and adult-plant stages. [ABSTRACT FROM AUTHOR]

Tobacco (Nicotiana tabacum L.) use is the leading cause of preventable death, due to deleterious chemical components and smoke from tobacco products, and therefore reducing harmful chemical components in tobacco is one of the crucial tobacco breeding targets. However, due to complexity of tobacco smoke and unavailability of high-density genetic maps, the genetic architecture of representative hazardous smoke has not been fully dissected. The present study aimed to explore the genetic architecture of nine hazardous component traits of mainstream smoke through QTL mapping using 271 recombinant inbred lines (RILs) derived from K326 and Y3 in multiple environments. The analysis of genotype and genotype by environment interaction (GE) revealed substantially greater heritability over 95% contributed mostly by GE interaction effects. We also observed strong genetic correlations among most studied hazardous smoke traits, with the highest correlation coefficient of 0.84 between carbon monoxide and crotonaldehyde. Based on a published high-density genetic map, a total of 19 novel QTLs were detected for eight traits using a full QTL model, of which 17 QTLs showed significant additive effects, six showed significant additive-by-environment interaction effects, and one pair showed significant epistasis-by-environment interaction effect. Bioinformatics analysis of sequence in QTL region predicted six genes as candidates for four traits, of which Nt21g04598.1, Nt21g04600.1, and Nt21g04601.1 had pleiotropic effects on PHE and TAR. [ABSTRACT FROM AUTHOR]

Roots are the hidden and most important part of plants. They serve as stabilizers and channels for uptaking water and nutrients and play a crucial role in the growth and development of plants. Here, two-dimensional image data were used to identify quantitative trait loci (QTL) controlling root traits in an interspecific mapping population derived from a cross between wild soybean 'PI366121' and cultivar 'Williams 82'. A total of 2830 single-nucleotide polymorphisms were used for genotyping, constructing genetic linkage maps, and analyzing QTLs. Forty-two QTLs were identified on twelve chromosomes, twelve of which were identified as major QTLs, with a phenotypic variation range of 36.12% to 39.11% and a logarithm of odds value range of 12.01 to 17.35. Two significant QTL regions for the average diameter, root volume, and link average diameter root traits were detected on chromosomes 3 and 13, and both wild and cultivated soybeans contributed positive alleles. Six candidate genes, Glyma.03G027500 (transketolase/glycoaldehyde transferase), Glyma.03G014500 (dehydrogenases), Glyma.13G341500 (leucine-rich repeat receptor-like protein kinase), Glyma.13G341400 (AGC kinase family protein), Glyma.13G331900 (60S ribosomal protein), and Glyma.13G333100 (aquaporin transporter) showed higher expression in root tissues based on publicly available transcriptome data. These results will help breeders improve soybean genetic components and enhance soybean root morphological traits using desirable alleles from wild soybeans. [ABSTRACT FROM AUTHOR]

Proper pericarp thickness protects the maize kernel against pests and diseases, moreover, thinner pericarp improves the eating quality in fresh corn. In this study, we aimed to investigate the dynamic changes in maize pericarp during kernel development and identified the major quantitative trait loci (QTLs) for maize pericarp thickness. It was observed that maize pericarp thickness first increased and then decreased. During the growth and formation stages, the pericarp thickness gradually increased and reached the maximum, after which it gradually decreased and reached the minimum during maturity. To identify the QTLs for pericarp thickness, a BC4F4 population was constructed using maize inbred lines B73 (recurrent parent with thick pericarp) and Baimaya (donor parent with thin pericarp). In addition, a high-density genetic map was constructed using maize 10 K SNP microarray. A total of 17 QTLs related to pericarp thickness were identified in combination with the phenotypic data. The results revealed that the heritability of the thickness of upper germinal side of pericarp (UG) was 0.63. The major QTL controlling UG was qPT1-1, which was located on chromosome 1 (212,215,145–212,948,882). The heritability of the thickness of upper abgerminal side of pericarp (UA) was 0.70. The major QTL controlling UA was qPT2-1, which was located on chromosome 2 (2,550,197–14,732,993). In addition, a combination of functional annotation, DNA sequencing analysis and quantitative real-time PCR (qPCR) screened two candidate genes, Zm00001d001964 and Zm00001d002283, that could potentially control maize pericarp thickness. This study provides valuable insights into the improvement of maize pericarp thickness during breeding. [ABSTRACT FROM AUTHOR]

Introduction: Plant height (PH) and ear height (EH) are key plant architectural traits in maize, which will affect the photosynthetic efficiency, high plant density tolerance, suitability for mechanical harvesting Methods: QTL mapping were conducted for PH and EH using a recombinant inbred line (RIL) population and two corresponding immortalized backcross (IB) populations obtained from crosses between the RIL population and the two parental lines. Results: A total of 17 and 15 QTL were detected in the RIL and IB populations, respectively. Two QTL, qPH1-1 (qEH1-1) and qPH1-2 (qEH1-4) in the RIL, were simultaneously identified for PH and EH. Combing reported genome-wide association and cloned PH-related genes, co-expression network analyses were constructed, then five candidate genes with high confidence in major QTL were identified including Zm00001d011117 and Zm00001d011108, whose homologs have been confirmed to play a role in determining PH in maize and soybean. Discussion: QTL mapping used a immortalized backcross population is a new strategy. These identified genes in this study can provide new insights for improving the plant architecture in maize. [ABSTRACT FROM AUTHOR]

A stable back cross introgression line IL65 (IET22161) (Swarna/O. nivara-BC2F6) of rice was used to map flag leaf related traits in F2 and F3 populations. A total of 12 QTLs were mapped on two chromosomes with each QTL explaining 3 to 21% phenotypic variance (PV). Interestingly, a novel 12 Mb QTL cluster (RM8094—RM9) that controls 7 traits was identified on long arm of chromosome 1 where QTLs qSPAD1.2, qSPAD1.3 for SPAD, qFLL1.1, qFLL1.2 for flag leaf length, qFLW1.1, qFLW1.2 for flag leaf width, qFLA1.1, qFLA1.2 for flag leaf area, qPH1.1, qPH1.2 for plant height, qDTF1.2, qDTF1.3 for days to flowering and qHI1.2, qHI1.3 for harvest index were co-located. Among these, one major effect QTL qFLA1.1 for flag leaf area explaining 12.7% PV was identified in a 9 Mb region between RM8094 and RM5638. There was an adjacent minor effect QTL qFLA1.2 with 7% PV in a 3 Mb region between RM5638 and RM9. Together, these two QTLs from O. nivara explained 19.7% PV of leaf area. The QTL for flag leaf related traits can be fine mapped and considered for breeding rice varieties with higher flag leaf area, photosynthetic rate and grain yield. [ABSTRACT FROM AUTHOR]

The excavation and utilization of dormancy loci in breeding are effective endeavors for enhancing the resistance to pre-harvest sprouting (PHS) of wheat varieties. CH1539 is a wheat breeding line with high-level seed dormancy. To clarify the dormant loci carried by CH1539 and obtain linked molecular markers, in this study, a recombinant inbred line (RIL) population derived from the cross of weak dormant SY95-71 and strong dormant CH1539 was genotyped using the Wheat17K single-nucleotide polymorphism (SNP) array, and a high-density genetic map covering 21 chromosomes and consisting of 2437 SNP markers was constructed. Then, the germination percentage (GP) and germination index (GI) of the seeds from each RIL were estimated. Two QTLs for GP on chromosomes 5A and 6B, and four QTLs for GI on chromosomes 5A, 6B, 6D and 7A were identified. Among them, the QTL on chromosomes 6B controlling both GP and GI, temporarily named QGp/Gi.sxau-6B, is a major QTL for seed dormancy with the maximum phenotypic variance explained of 17.66~34.11%. One PCR-based diagnostic marker Ger6B-3 for QGp/Gi.sxau-6B was developed, and the genetic effect of QGp/Gi.sxau-6B on the RIL population and a set of wheat germplasm comprising 97 accessions was successfully confirmed. QGp/Gi.sxau-6B located in the 28.7~30.9 Mbp physical position is different from all the known dormancy loci on chromosomes 6B, and within the interval, there are 30 high-confidence annotated genes. Our results revealed a novel QTL QGp/Gi.sxau-6B whose CH1539 allele had a strong and broad effect on seed dormancy, which will be useful in further PHS-resistant wheat breeding. [ABSTRACT FROM AUTHOR]

Bulked-segregant analysis by deep sequencing (BSA-seq) is a widely used method for mapping QTL (quantitative trait loci) due to its simplicity, speed, cost-effectiveness, and efficiency. However, the ability of BSA-seq to detect QTL is often limited by inappropriate experimental designs, as evidenced by numerous practical studies. Most BSA-seq studies have utilized small to medium-sized populations, with F2 populations being the most common choice. Nevertheless, theoretical studies have shown that using a large population with an appropriate pool size can significantly enhance the power and resolution of QTL detection in BSA-seq, with F3 populations offering notable advantages over F2 populations. To provide an experimental demonstration, we tested the power of BSA-seq to identify QTL controlling days from sowing to heading (DTH) in a 7200-plant rice F3 population in two environments, with a pool size of approximately 500. Each experiment identified 34 QTL, an order of magnitude greater than reported in most BSA-seq experiments, of which 23 were detected in both experiments, with 17 of these located near 41 previously reported QTL and eight cloned genes known to control DTH in rice. These results indicate that QTL mapping by BSA-seq in large F3 populations and multi-environment experiments can achieve high power, resolution, and reliability. [ABSTRACT FROM AUTHOR]

Goji berries are a small-fruited shrub with industrial importance whose fruit considered beneficial in both fresh and dried forms. Current germplasms of goji berries include small fruits with a short shelf life, less sweet and bitter taste, and a lack of appropriate genetic information. This study aimed to employ whole genome resequencing to generate an ultra-dense bin linkage map and to elucidate the genetic basis of goji fruit quality and size using quantitative trait loci (QTL) mapping analysis in a cross-pollinated hybrid population. To achieve this goal, human sensory tests were carried out to determine the bitter taste (BT) and sweet taste (ST), and to quantify the soluble solid content (SSC), fruit firmness (FF), and fruit size-related traits of fresh goji fruits over three or four years. The results revealed that the goji bin linkage map based on resequencing spanned a total length of 966.42 cM and an average bin interval of 0.03 cM. Subsequent variant calling and ordering resulted in 3,058 bins containing 35,331 polymorphic markers across 12 chromosomes. A total of 99 QTLs, with individual loci in different environments explaining a phenotypic variance of 1.21-16.95% were identified for the studied traits. Ten major effects, including colocalized QTLs corresponding to different traits, were identified on chromosomes 1, 3, 5, 6, 7, and 8, with a maximum Logarithm of Odds (LOD) of 29.25 and 16.95% of explained phenotypic variance (PVE). In addition, four stable loci, one for FF, one for fruit weight (FW), and two for fruit shape index (FSI), were mainly mapped on chromosomes 5, 6, and 7, elucidating 2.10-16.95% PVE. These findings offer valuable insights into the genetic architecture of goji fruit traits along with identified specific loci and markers to further improve and develop sweeter, less bitter and larger fruited goji berry cultivars with extended shelf life.

Non-alcoholic fatty liver disease (NAFLD) is the most common chronic liver condition in the United States, encompassing a wide spectrum of liver pathologies including steatosis, steatohepatitis, fibrosis, and cirrhosis. Despite its high prevalence, there are no medications currently approved by the Food and Drug Administration for the treatment of NAFLD. Recent work has suggested that NAFLD has a strong genetic component and identifying causative genes will improve our understanding of the molecular mechanisms contributing to NAFLD and yield targets for future therapeutic investigations. Oxidative stress is known to play an important role in NAFLD pathogenesis, yet the underlying mechanisms accounting for disturbances in redox status are not entirely understood. To better understand the relationship between the glutathione redox system and signs of NAFLD in a genetically-diverse population, we measured liver weight, serum biomarkers aspartate aminotransferase (AST) and alanine aminotransferase (ALT), and graded liver pathology in a large cohort of Diversity Outbred mice. We compared hepatic endpoints to those of the glutathione redox system previously measured in the livers and kidneys of the same mice, and we screened for statistical and genetic associations using the R/qtl2 software. We discovered several novel genetic loci associated with markers of liver health, including loci that were associated with both liver steatosis and glutathione redox status. Candidate genes within each locus point to possible new mechanisms underlying the complex relationship between NAFLD and the glutathione redox system, which could have translational implications for future studies targeting NAFLD pathology.

IntroductionOwing to advances in high-throughput genome sequencing, QTL-Seq mapping of salt tolerance traits is a major platform for identifying soil-salinity tolerance QTLs to accelerate marker-assisted selection for salt-tolerant rice varieties. We performed QTL-BSA-Seq in the seedling stage of rice from a genetic cross of the extreme salt-sensitive variety, IR29, and “Jao Khao” (JK), a Thai salt-tolerant variety.MethodsA total of 462 F2 progeny grown in soil and treated with 160 mM NaCl were used as the QTL mapping population. Two high- and low-bulk sets, based on cell membrane stability (CMS) and tiller number at the recovery stage (TN), were equally sampled. The genomes of each pool were sequenced, and statistical significance of QTL was calculated using QTLseq and G prime (G′) analysis, which is based on calculating the allele frequency differences or Δ(SNP index).ResultsBoth methods detected the overlapping interval region, wherein CMS-bulk was mapped at two loci in the 38.41–38.85 Mb region with 336 SNPs on chromosome 1 (qCMS1) and the 26.13–26.80 Mb region with 1,011 SNPs on chromosome 3 (qCMS3); the Δ(SNP index) peaks were −0.2709 and 0.3127, respectively. TN-bulk was mapped at only one locus in the overlapping 38.26–38.95 Mb region on chromosome 1 with 575 SNPs (qTN1) and a Δ(SNP index) peak of −0.3544. These identified QTLs in two different genetic backgrounds of segregating populations derived from JK were validated. The results confirmed the colocalization of the qCMS1 and qTN1 traits on chromosome 1. Based on the CMS trait, qCMS1/qTN1 stably expressed 6%–18% of the phenotypic variance in the two validation populations, while qCMS1/qTN1 accounted for 16%–20% of the phenotypic variance in one validation population based on the TN trait.ConclusionThe findings confirm that the CMS and TN traits are tightly linked to the long arm of chromosome 1 rather than to chromosome 3. The validated qCMS-TN1 QTL can be used for gene/QTL pyramiding in marker-assisted selection to expedite breeding for salt resistance in rice at the seedling stage.