Pleiotropic Gene HMGA2 Regulates Myoblast Proliferation and Affects Body Size of Sheep.

Uncovering genes associated with muscle growth and body size will benefit the molecular breeding of meat Hu sheep. HMGA2 has proven to be an important gene in mouse muscle growth and is associated with the body size of various species. However, its roles in sheep are still limited. Using sheep myoblast as a cell model, the overexpression of HMGA2 significantly promoted sheep myoblast proliferation, while interference with HMGA2 expression inhibited proliferation, indicated by qPCR, EdU, and CCK-8 assays. Furthermore, the dual-luciferase reporter system indicated that the region NC_056056.1: 154134300-154134882 (-618 to -1200 bp upstream of the HMGA2 transcription start site) was one of the habitats of the HMGA2 core promoter, given the observation that this fragment led to a ~3-fold increase in luciferase activity. Interestingly, SNP rs428001129 (NC_056056.1:g.154134315 C>A) was detected in this fragment by Sanger sequencing of the PCR product of pooled DNA from 458 crossbred sheep. This SNP was found to affect the promoter activity and was significantly associated with chest width at birth and two months old, as well as chest depth at two and six months old. The data obtained in this study demonstrated the phenotypic regulatory role of the HMGA2 gene in sheep production traits and the potential of rs428001129 in marker-assisted selection for sheep breeding in terms of chest width and chest depth.

Genotype selection identified elite lines through quantitative trait loci mapping of agronomically important traits in wheat.

Wheat is one of the most important staple foods in the world. Genetic characterization of wheat agronomically important traits is crucial for yield improvement through molecular breeding. In this study, a recombinant inbred line (RIL) population was developed by crossing a local adapted high yield variety Jimai 22 (JM22) with an external variety Cunmai no.1 (CM1). A high-density genetic map containing 7,359 single nucleotide polymorphism (SNP) markers was constructed. Quantitative trait loci (QTL) mapping identified 61 QTL for eight yield-related traits under six environments (years). Among them, 17 QTL affecting spike number per plant, grain number per spike and thousand grain weight showed high predictability for theoretical yield per plant (TYP), of which, 12 QTL alleles positively contributed to TYP. Nine promising candidate genes for seven of the 12 QTL were identified including three known wheat genes and six rice orthologs. Four elite lines with TYP increased by 5.6%-15.2% were identified through genotype selection which carried 7-9 favorable alleles from JM22 and 2-3 favorable alleles from CM1 of the 12 QTL. Moreover, the linked SNPs of the 12 QTL were converted to high-throughput kompetitive allele-specific PCR (KASP) markers and validated in the population. The mapped QTL, identified promising candidate genes, developed elite lines and KASP markers are highly valuable in future genotype selection to improve wheat yield. Supplementary Information: The online version contains supplementary material available at 10.1007/s11032-024-01496-3.

Rapid breeding of an early maturing, high-quality, and high-y.ielding rice cultivar using marker­assisted selection coupled with optimized anther culture.

With the global shift towards healthier eating habits, the focus of the rice industry has evolved from quantity to quality. In China, the Yangtze River Basin is the main area consuming long-grain and high-quality indica rice. Hubei Province, a significant rice-producing area, currently cultivates a limited range of rice varieties, risking degradation and diminishing economic returns. Therefore, it is imperative to cultivate elite rice varieties tailored to the local production conditions and can significantly enhance the added value. This study bred the novel rice cultivar "Runxiangyu", characterized by early maturity, high quality, and high yield. It is a hybrid of Ezhong 5, known for its moderate height and excellent quality, albeit with a long growth period and lack of fragrance, and Yuzhenxiang, renowned for its high quality, short growth period, and fragrance but limited by its tall stature and poor tillering ability. The breeding process utilized optimized anther culture coupled with molecular marker-assisted selection (MAS) and phenotype analysis. In the field, the developed cultivar was 120.9 cm tall and had an entire growth period of 117.5 days, demonstrating moderate disease resistance and excellent heat tolerance. Its grains are fragrant, meeting the national standard of grade two high-quality rice set by the Food Quality Supervision and Inspection Center of the Ministry of Agriculture and Rural Areas). Exhibiting superior agronomic traits, such as plant type, height, growth period, and stress resistance, along with and quality attributes, including grain shape, chalkiness, fragrance, and taste, "Runxiangyu" was certified by the Agricultural Crop Variety Certification Commission of Hubei in 2022. These findings suggested that molecular MAS coupled with optimized anther culture and multi-site phenotype analysis is an efficient and rapid method for crop breeding. Supplementary Information: The online version contains supplementary material available at 10.1007/s11032-024-01495-4.

Genome-Wide Association Studies and QTL Mapping Reveal a New Locus Associated with Resistance to Bacterial Pustule Caused by Xanthomonas citri pv. glycines in Soybean.

Bacterial pustule (BP), caused by Xanthomonas citri pv. glycines, is an important disease that, under favorable conditions, can drastically affect soybean production. We performed a genome-wide association study (GWAS) with a panel containing Brazilian and American cultivars, which were screened qualitatively and quantitatively against two Brazilian X. citri isolates (IBS 333 and IBS 327). The panel was genotyped using a genotyping by sequencing (GBS) approach, and we identified two main new regions in soybeans associated with X. citri resistance on chromosomes 6 (IBS 333) and 18 (IBS 327), different from the traditional rxp gene located on chromosome 17. The region on chromosome 6 was also detected by QTL mapping using a biparental cross between Williams 82 (R) and PI 416937 (S), showing that Williams 82 has another recessive resistance gene besides rxp, which was also detected in nine BP-resistant ancestors of the Brazilian cultivars (including CNS, S-100), based on haplotype analysis. Furthermore, we identified additional SNPs in strong LD (0.8) with peak SNPs by exploring variation available in WGS (whole genome sequencing) data among 31 soybean accessions. In these regions in strong LD, two candidate resistance genes were identified (Glyma.06g311000 and Glyma.18g025100) for chromosomes 6 and 18, respectively. Therefore, our results allowed the identification of new chromosomal regions in soybeans associated with BP disease, which could be useful for marker-assisted selection and will enable a reduction in time and cost for the development of resistant cultivars.

Gene pyramiding improved cell membrane stability under heat stress in cotton (Gossypium hirsutum L.).

Climate change has been drastically affecting cotton not only in Pakistan but also all over the world. Normally cotton is known as heat tolerant when compared with other crops, but if the high temperature occurs during flowering period the yield decreases significantly. Marker assisted gene pyramiding provides a sustainable solution to improve heat tolerance. A total of seven genotypes were developed by a series of crossing seven tolerant genotypes over the period of three years. Tolerant genotypes were selected by screening for important transcription factors (GHSP26, HSP3, HSFA2, DREB1A, HSP101, DREB2A, GhNAC2, HSPCB, GhWRKY41, TPS, GbMYB5, ANNAT8, GhMPK17, GhMKK1, GhMKK3, GhMPK2, HSC70, APX1 and GhPP2A1). The seven genotypes were evaluated under normal and heat stress in a multi-year trial. The traits related to heat tolerance, such as cell membrane stability, relative water content, excised leaf water loss, plant height, number of nodes, internodal length, number of buds, number of bolls and leaf area was observed under normal and heat stress conditions. The developed genotypes showed improvement in cell membrane stability and relative water content under heat stress. The genotypes [(VH-305×MNH-886)×MNH-1035)×NIAB-78)], [(MNH-1035×MNH-886)×MNH-886)×SM-431] and [(MNH-1035×MNH-886)×MNH-886)×SS-32] depicted heat tolerance and could be used as heat tolerant material for variety development in breeding programs.

QTL-Seq identified a genomic region on chromosome 1 for soil-salinity tolerance in F2 progeny of Thai salt-tolerant rice donor line "Jao Khao".

Introduction: Owing 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. 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 Δ(SNP index). Results: Both 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. 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.

Assessing the carotenoid profiles and allelic diversity of yellow maize inbred lines adapted to mid-altitude subhumid maize agroecology in Ethiopia.

Biofortification of provitamin A in maize is an attractive and sustainable remedy to the problem of vitamin A deficiency in developing countries. The utilization of molecular markers represents a promising avenue to facilitate the development of provitamin A (PVA)-enriched maize varieties. We screened 752 diverse tropical yellow/orange maize lines using kompetitive allele-specific PCR (KASP) makers to validate the use of KASP markers in PVA maize breeding. To this end, a total of 161 yellow/orange inbred lines, selected from among the 752 lines, were evaluated for their endosperm PVA and other carotenoid compounds levels in two separate trials composed of 63 and 98 inbred lines in 2020 and 2021, respectively. Significant differences (p < 0.001) were observed among the yellow maize inbred lines studied for all carotenoid profiles. An inbred line TZMI1017, introduced by the International Institute of Tropical Agriculture (IITA) showed the highest level of PVA (12.99 µg/g) and ß-carotene (12.08 µg/g). The molecular screening showed 43 yellow maize inbred lines carrying at least three of the favorable alleles of the KASP markers. TZMI1017 inbred line also carried the favorable alleles of almost all markers. In addition, nine locally developed inbred lines had medium to high PVA concentrations varying from 5.11 µg/g to 10.76 µg/g and harbored the favorable alleles of all the KASP PVA markers. Association analysis between molecular markers and PVA content variation in the yellow/orange maize inbred lines did not reveal a significant, predictable correlation. Further investigation is warranted to elucidate the underlying genetic architecture of the PVA content in this germplasm. However, we recommend strategic utilization of the maize-inbred lines with higher PVA content to enhance the PVA profile of the breeding program's germplasm.

Soybean pod shattering resistance allele pdh1 and marker-assisted selection.

Pod shattering is a major production constraint of soybean [Glycine max (L.)]. The objectives of this study were to (i) estimate heritability for pod shattering resistance, (ii) determine the frequency of the pod shattering resistance allele pdh1 in the International Institute for Tropical Agriculture (IITA) soybean germplasm and Zambian commercial varieties, and (iii) determine the effectiveness of the DNA marker for the pod shattering resistance allele pdh1. A total of 59 genotypes were evaluated for pod shattering in field trials conducted in Malawi and Zambia and genotyped with a marker for pdh1. TGx2002-8FM and TGx2002-9FM were the most resistant among genotypes in early and medium maturity classes and can be used for genetic enhancement of pod shattering resistance in these specific maturity classes. Narrow sense heritability estimates for pod shattering ranged from 0.27 to 0.80. Of the 59 genotypes, 57 (96.6%) carried the resistance allele pdh1 while only two genotypes (3.6%) carried the susceptible allele, suggesting near-fixation of the resistance allele pdh1 in the IITA germplasm. The marker for pdh1 was highly effective in selecting resistant genotypes.

Genetic mapping of stripe rust resistance in a geographically diverse barley collection and selected biparental populations.

Barley stripe or yellow rust (BYR) caused by Puccinia striiformis f. sp. hordei (Psh) is a significant constraint to barley production. The disease is best controlled by genetic resistance, which is considered the most economical and sustainable component of integrated disease management. In this study, we assessed the diversity of resistance to Psh in a panel of international barley genotypes (n = 266) under multiple disease environments (Ecuador, India, and Mexico) using genome-wide association studies (GWASs). Four quantitative trait loci (QTLs) (three on chromosome 1H and one on 7H) associated with resistance to Psh were identified. The QTLs were validated by mapping resistance to Psh in five biparental populations, which detected key genomic regions on chromosomes 1H (populations Pompadour/Zhoungdamei, Pompadour/Zug161, and CI9214/Baudin), 3H (Ricardo/Gus), and 7H (Fumai8/Baronesse). The QTL RpshQ.GWA.1H.1 detected by GWAS and RpshQ.Bau.1H detected using biparental mapping populations co-located were the most consistent and stable across environments and are likely the same resistance region. RpshQ.Bau.1H was saturated using population CI9214/Baudin by enriching the target region, which placed the resistance locus between 7.9 and 8.1 Mbp (flanked by markers sun_B1H_03, 0.7 cM proximal to Rpsh_1H and sun_B1H_KASP_02, 3.2 cM distal on 1HS) in the Morex reference genome v.2. A Kompetitive Allele Specific PCR (KASP) marker sun_B1H_KASP_01 that co-segregated for RpshQ.Bau.1H was developed. The marker was validated on 50 Australian barley cultivars, showing well-defined allelic discrimination and presence in six genotypes (Baudin, Fathom, Flagship, Grout, Sakurastar, and Shepherd). This marker can be used for reliable marker-assisted selection and pyramiding of resistance to Psh and in diversifying the genetic base of resistance to stripe rust.

Triumphs of genomic-assisted breeding in crop improvement.

Conventional breeding approaches have played a significant role in meeting the food demand remarkably well until now. However, the increasing population, yield plateaus in certain crops, and limited recombination necessitate using genomic resources for genomics-assisted crop improvement programs. As a result of advancements in the next-generation sequence technology, GABs have developed dramatically to characterize allelic variants and facilitate their rapid and efficient incorporation in crop improvement programs. Genomics-assisted breeding (GAB) has played an important role in harnessing the potential of modern genomic tools, exploiting allelic variation from genetic resources and developing cultivars over the past decade. The availability of pangenomes for major crops has been a significant development, albeit with varying degrees of completeness. Even though adopting these technologies is essentially determined on economic grounds and cost-effective assays, which create a wealth of information that can be successfully used to exploit the latent potential of crops. GAB has been instrumental in harnessing the potential of modern genomic resources and exploiting allelic variation for genetic enhancement and cultivar development. GAB strategies will be indispensable for designing future crops and are expected to play a crucial role in breeding climate-smart crop cultivars with higher nutritional value.

Validation of Molecular Markers for Low Kunitz Trypsin Inhibitor Content in European Soybean (Glycine max L. Merr.) Germplasm.

Trypsin inhibitors (TI) in raw soybean grain, mainly represented by the Kunitz trypsin inhibitor protein (KTI), prevent the normal activity of the digestive enzymes trypsin and chymotrypsin in humans and monogastric livestock. The inactivation of TI is achieved through costly and time-consuming heat treatment. Thermal processing also impairs the solubility and availability of the soybean grain protein. Therefore, the genetic elimination of KTI has been proposed as a suitable alternative to heat treatment. The aim of this study was to screen the collection of European soybean cultivars with six genetic markers (one SSR marker and five SNP markers) previously proposed as tightly linked to the KTI3 gene encoding the major Kunitz trypsin inhibitor seed protein of soybean and validate their usability for marker-assisted selection (MAS). The six markers were validated on a subset of 38 cultivars with wide variability in KTI content and in the F2 and F3:5 progenies of two crosses between the known high- and low-KTI cultivars. Three genetic markers (SSR Satt228 and two SNP markers, Gm08_45317135_T/G and Gm08_45541906_A/C) were significantly associated with KTI content in a subset of 38 cultivars. Low-KTI alleles were detected in both low- and high-KTI genotypes and vice versa, high-KTI alleles were found in both high- and low-KTI genotypes, indicating a tight but not perfect association of these markers with the KTI3 gene. The genetic marker SSR Satt228 showed a significant association with KTI content in the F2 progeny, while the SNP markers Gm08_45317135_T/G and Gm08_45541906_A/C allowed significant discrimination between progeny with high- vs. low-KTI progenies in the F3:5 generation. These three markers could be applied in MAS for low-KTI content but not without the additional phenotyping step to extract the desired low-KTI genotypes.

Identification of QTL for Alkylresorcinols in Wheat and Development of KASP Markers for Marker-Assisted Selection of Health-Promoting Varieties.

This study evaluated alkylresorcinol concentration (ARC) in recombinant inbred lines (RILs) from the cross of Zhongmai 578 and Jimai 22 in three environments. ARC exhibited a continuous distribution ranging from 337.4 to 758.0, 495.4-768.0, and 456.3-764.7 µg/g, respectively, in three environments. Analysis of variance (ANOVA) indicated significant (P < 0.001) impacts of genotypes, environments, and their interactions. The broad-sense heritability of ARC was 0.76. Genome-wide linkage mapping analysis identified four stable quantitative trait loci (QTL) for ARC on chromosomes 2A, 3A, 4D, and 7A. Kompetitive allele-specific PCR (KASP) marker of each QTL was developed and validated in 206 representative wheat varieties. Wheat varieties harboring 0, 1, 2, 3, and 4 favorable alleles had ARC of 499.1, 587.8, 644.7, 668.5, and 711.1 µg/g, respectively. This study suggests that combining multiple minor-effect QTL through KASP markers can serve as an effective strategy for breeding high-ARC wheat, thereby enhancing innovations in functional food production.

Molecular selection of soybean towards adaptation to Central European agroclimatic conditions.

Europe is highly dependent on soybean meal imports and anticipates an increase of domestic plant protein production. Ongoing climate change resulted in northward shift of plant hardiness zones, enabling spring-sowing of freezing-sensitive crops, including soybean. However, it requires efficient reselection of germplasm adapted to relatively short growing season and long-day photoperiod. In the present study, a PCR array has been implemented, targeting early maturity (E1-E4, E7, E9, and E10), pod shattering (qPHD1), and growth determination (Dt1) genes. This array was optimized for routine screening of soybean diversity panel (204 accessions), subjected to the 2018-2020 survey of phenology, morphology, and yield-related traits in a potential cultivation region in Poland. High broad-sense heritability (0.84-0.88) was observed for plant height, thousand grain weight, maturity date, and the first pod height. Significant positive correlations were identified between the number of seeds and pods per plant, between these two traits and seed yield per plant as well as between flowering, maturity, plant height, and first pod height. PCR array genotyping revealed high genetic diversity, yielding 98 allelic combinations. The most remarkable correlations were identified between flowering and E7 or E1, between maturity and E4 or E7 and between plant height and Dt1 or E4. The study demonstrated high applicability of this PCR array for molecular selection of soybean towards adaptation to Central Europe, designating recessive qPHD1 and dominant Dt1, E3, and E4 alleles as major targets to align soybean growth season requirements with the length of the frost-free period, improve plant performance, and increase yield.

Pyramiding of triple Clubroot resistance loci conferred superior resistance without negative effects on agronomic traits in Brassica napus.

Clubroot disease caused by Plasmodiophora brassicae is becoming a serious threat to rapeseed (Brassica napus) production worldwide. Breeding resistant varieties using CR (clubroot resistance) loci is the most promising solution. Using marker-assisted selection and speed-breeding technologies, we generated Brassica napus materials in homozygous or heterozygous states using CRA3.7, CRA08.1, and CRA3.2 loci in the elite parental line of the Zhongshuang11 background. We developed three elite lines with two CR loci in different combinations and one line with three CR loci at the homozygous state. In our study, we used six different clubroot strains (Xinmin, Lincang, Yuxi, Chengdu, Chongqing, and Jixi) which are categorized into three groups based on our screening results. The newly pyramided lines with two or more CR loci displayed better disease resistance than the parental lines carrying single CR loci. There is an obvious gene dosage effect between CR loci and disease resistance levels. For example, pyramided lines with triple CR loci in the homozygous state showed superior resistance for all pathogens tested. Moreover, CR loci in the homozygous state are better on disease resistance than the heterozygous state. More importantly, no negative effect was observed on agronomic traits for the presence of multiple CR loci in the same background. Overall, these data suggest that the pyramiding of triple clubroot resistance loci conferred superior resistance with no negative effects on agronomic traits in Brassica napus.

Relationship between Indel Variants within the JAK2 Gene and Growth Traits in Goats.

Janus kinase 2 (JAK2) plays a critical role in myoblast proliferation and fat deposition in animals. Our previous RNA-Seq analyses identified a close association between the JAK2 gene and muscle development. To date, research delving into the relationship between the JAK2 gene and growth traits has been sparse. In this study, we sought to investigate the relationship between novel mutations within the JAK2 gene and goat growth traits. Herein, two novel InDel (Insertion/Deletion) polymorphisms within the JAK2 gene were detected in 548 goats, and only two genotypes were designated as ID (Insertion/Deletion) and DD (Deletion/Deletion). The results indicate that the two InDels, the del19008 locus in intron 2 and del72416 InDel in intron 6, showed significant associations with growth traits (p < 0.05). Compared to Nubian and Jianzhou Daer goats, the del72416 locus displayed a more pronounced effect in the Fuqing breed group. In the Nubian breed (NB) group, both InDels showed a marked influence on body height (BH). There were strong linkages observed for these two InDels between the Fuqing (FQ) and Jianzhou (JZ) populations. The DD-ID diplotype was associated with inferior growth traits in chest width (ChW) and cannon circumference (CaC) in the FQ goats compared to the other diplotypes. In the NB population, the DD-DD diplotype exhibited a marked negative impact on BH and HuWI (hucklebone width index), in contrast to the other diplotypes. In summary, our findings suggest that the two InDel polymorphisms within the JAK2 gene could serve as valuable molecular markers for enhancing goat growth traits in breeding programs.

The Kirkhouse Trust: Successes and Challenges in Twenty Years of Supporting Independent, Contemporary Grain Legume Breeding Projects in India and African Countries.

This manuscript reviews two decades of projects funded by the Kirkhouse Trust (KT), a charity registered in the UK. KT was established to improve the productivity of legume crops important in African countries and in India. KT's requirements for support are: (1) the research must be conducted by national scientists in their home institution, either a publicly funded agricultural research institute or a university; (2) the projects need to include a molecular biology component, which to date has mostly comprised the use of molecular markers for the selection of one or more target traits in a crop improvement programme; (3) the projects funded are included in consortia, to foster the creation of scientific communities and the sharing of knowledge and breeding resources. This account relates to the key achievements and challenges, reflects on the lessons learned and outlines future research priorities.

Genetic Markers Related to Meat Quality Properties in Fattened HF and HF x Charolaise Steers.

This study involved 45 Holstein and 60 Holstein-Charolaise steers, tailored with specific diets according to breed and rearing systems. DNA genotyping was conducted for DGAT1, LEP, SCD1, SREBF1, and TG genes to investigate their impact on carcass conformation traits, beef quality traits, and sensory quality traits. The results showed associations between the genetic variants and the analyzed traits. Specifically, DGAT1 was found to affect drip loss, meat brightness, and color saturation. The TG gene was associated with marbling and meat color. LEP influenced trim fat and pH levels, while SCD1 was linked to metabolic energy live weight gains, and pH levels. SREBF1 was related to fatness.

Characterization of a Powdery Mildew Resistance Gene in Wheat Breeding Line Jingzi 102 Using Bulk Segregant RNA Sequencing.

Wheat (Triticum aestivum L.) is one of the most important crops worldwide. Powdery mildew caused by Blumeria graminis f. sp. tritici is a destructive disease threatening wheat yield and quality. The utilization of resistant genes and cultivars is considered the most economical, environmentally friendly, and effective method to control powdery mildew. Wheat breeding line Jingzi 102 was highly resistant to powdery mildew at both seedling and adult plant stages. Genetic analysis of F1, F2, and F2:3 populations of "Jingzi 102 × Shixin 828" showed that the resistance of Jingzi 102 against powdery mildew isolate E09 at the seedling stage was controlled by a single dominant gene, temporarily designated PmJZ. Using bulked segregant RNA sequencing combined with molecular markers analysis, PmJZ was located on the long arm of chromosome 2B and flanked by markers BJK695-1 and CIT02g-20 with the genetic distances of 1.2 and 0.5 centimorgan, respectively, corresponding to the bread wheat genome of Chinese Spring (International Wheat Genome Sequencing Consortium RefSeq v2.1) 703.8 to 707.6 Mb. PmJZ is most likely different from the documented Pm genes on chromosome 2BL based on their physical positions, molecular markers analysis, and resistance spectrum. Based on the gene annotation information, five genes related to disease resistance could be considered as the candidate genes of PmJZ. To accelerate the application of PmJZ, the flanking markers BJK695-1 and CIT02g-20 can serve for marker-assisted selection of PmJZ in wheat disease-resistance breeding.

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

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

QTL analysis on a lemon population provides novel insights on the genetic regulation of the tolerance to the two-spotted spider mite attack.

BACKGROUND: Among the Citrus species, lemon (Citrus limon Burm f.) is one of the most affected by the two-spotted spider mite (Tetranychus urticae Koch). Moreover, chemical control is hampered by the mite's ability to develop genetic resistance against acaricides. In this context, the identification of the genetic basis of the host resistance could represent a sustainable strategy for spider mite control. In the present study, a marker-trait association analysis was performed on a lemon population employing an association mapping approach. An inter-specific full-sib population composed of 109 accessions was phenotyped through a detached-leaf assays performed in modified Huffaker cells. Those individuals, complemented with two inter-specific segregating populations, were genotyped using a target-sequencing approach called SPET (Single Primer Enrichment Technology), the resulting SNPs were employed for the generation of an integrated genetic map. RESULTS: The percentage of damaged area in the full-sib population showed a quantitative distribution with values ranging from 0.36 to 9.67%. A total of 47,298 SNPs were selected for an association mapping study and a significant marker linked with resistance to spider mite was detected on linkage group 5. In silico gene annotation of the QTL interval enabled the detection of 13 genes involved in immune response to biotic and abiotic stress. Gene expression analysis showed an over expression of the gene encoding for the ethylene-responsive transcription factor ERF098-like, already characterized in Arabidopsis and in rice for its involvement in defense response. CONCLUSION: The identification of a molecular marker linked to the resistance to spider mite attack can pave the way for the development of marker-assisted breeding plan for the development of novel selection coupling favorable agronomical traits (e.g. fruit quality, yield) with a higher resistance toward the mite.