Gene Pyramiding Research Articles

Pyramiding of bacterial blight resistance genes into promising restorer BRRI31R line through marker-assisted backcross breeding and evaluation of agro-morphological and physiochemical characteristics of developed resistant restorer lines.

BRRI31R is one of the Bangladesh's most promising restorer lines due to its abundant pollen producing capacity, strong restoring ability, good combining ability, high outcrossing rate and genetically diverse from cytoplasmic male sterile (CMS) line. But the drawback of this line is that it is highly susceptible to bacterial blight (BB) disease of rice caused by Xanthomonas oryzae pv. oryzae. The present study highlighted the pyramiding of effective BB resistance genes (xa5, xa13 and Xa21) into the background of BRRI31R, through marker-assisted backcrossing (MABC). Backcross progenies were confirmed and advanced based on the foreground selection of target genes. Pyramided lines were used for pathogenicity test against five Bangladeshi Xanthomonas oryzae (BXo) races (BXo93, BXo220, BXo822, BXo826, BXo887) and confirmed the dominant fertility restore genes, Rf3 and Rf4 and further validated against SNP markers for more confirmation of target resistance genes. All pyramided restorer lines consisted of Xa4 (in built), xa5, xa13, Xa21, and Chalk5 with two fertility restorer genes, Rf3, Rf4. and these restorer lines showed intermediate amylose content (<25%). Restorer lines BRRI31R-MASP3 and BRRI31R-MASP4 showed high levels of resistance against five virulent BXo races and SNP genotyping revealed that these lines also contained a blast resistance gene Pita races. Gene pyramided restorer lines, BRRI31R-MASP3 and BRRI31R-MASP4 can directly be used as a male parent for the development of new BB resistant hybrid rice variety or could be used as a replacement of restorer line of BRRI hybrid dhan5 and 7 to enhance the quality of hybrid seeds as well as rice production in Bangladesh.

Association mapping of septoria tritici blotch resistance in bread wheat in Bale and Arsi highlands, Ethiopia

Septoria tritici blotch (STB) caused by the fungal pathogen Zymoseptoria tritici, anamorph Septoria tritici Rob. ex Desm., is an important wheat pathogen worldwide, reported to be major wheat production threating factor, posing considerable yield loss every year. Developing resistant cultivars is an efficient, economical, environmentally friendly and simple approach for managing STB. This study was carried out to evaluate spring bread wheat lines for their reaction to STB disease under field conditions; to associate phenotypic and genotypic data for identification of STB disease resistance; and to identify genomic region(s) associated with resistance to STB in spring bread wheat lines. Two hundred forty (240) spring bread wheat lines were evaluated under field conditions in non-replicated trials, using an augmented design. The trials were conducted at three locations (Kulumsa Agricultural Research Center, Madda Walabu University Research Site and Sinana Agricultural Research Center) in 2017 main cropping season (July to December). Out of these 240 wheat lines, 123 of them were genotyped with 10263 single nucleotide polymorphism (SNPs) markers and population structure and association mapping analysis was done. The wheat lines showed significant variations in percentage disease severity and area under the disease progress curve at all the three locations they were evaluated. The wheat lines were classified as resistant, moderately resistant, moderately susceptible and susceptible based on the percentage disease severity scored. Five wheat lines were found to be resistant to STB in all the three locations and are recommended for direct release by the national program and parentage purposes in wheat breeding programs. The 123 wheat lines were clustered into 3 subpopulations in which the first cluster contained 99 wheat lines; the second 17 and the last one 7. Among the polymorphic 8127 SNPs markers, 26 markers on chromosomes 7B, 1D, 3A, 2B, 6B and 3D were found to be significantly (P < 0.001) associated with STB resistance so that they can be utilized for marker assisted selection and gene pyramiding in resistance breeding programs.

Pyramiding aphid resistance genes into the elite cowpea variety, Zaayura, using marker-assisted backcrossing

The cowpea aphid (Aphis cracivora) is a cosmopolitan insect pest that causes economic damage on cowpea. Although the pest persists at all the growth stages of the crop, in West Africa, aphids are the only major insect pests that farmers regularly control at the vegetative stage. Thus, deploying aphid-resistant crop varieties can reduce farmers' expenditure on insecticide. The availability of different biotypes of the pest and reports of resistance breakdown necessitates pyramiding of sources of aphid resistance to develop a more robust genotype for durable resistance. Two aphid-resistance genes, sourced from SARC-1-57-2 and IT97K-556-6, were introgressed through gene pyramiding technique into a farmers’ preferred cowpea variety, Zaayura, using marker-assisted backcrossing. A simple sequence repeat (SSR) marker, CP 171F/172R, and an allele-specific single nucleotide polymorphism (SNP) marker, 1_0912, were used for foreground selection of the SARC-1-57-2 and IT97K-556-6 aphid resistance genes, respectively. A stepwise backcross approach was used to introgress the major aphid resistance QTL (QAc-vu7.1) from IT97K-556-6 into Zaayura using the marker 1_0912 coupled with intermittent screening under artificial aphid infestation. After the fourth backcross generation, three heterozygous BC4F1 of Zaayura/TT97K-556-6 were intercrossed to Zaayura Pali to develop intercross F1 (ICF1). Three true ICF1 hybrids allowed to self to produce ICF2. Five (5) out of 48 ICF2 plants which were genotyped with the two foreground markers had the two aphid resistance genes fixed in the double homozygous dominant state. For background selection, out of 192 allele-specific markers screened, only 47 polymorphic markers were identified and used for the background analysis of the pyramided lines. The recurrent parent genome recovery ranged from 72 to 93.8 %. ICF2_Zaa/556/SARC-P6 had the highest recurrent parent genome and the least heterozygosity among the five improved lines. The five pyramided lines showed superior resistance under artificial aphid infestation as compared to the two donor parents with damage scores ranging from 2.0 to 2.3. On the field, however, there were no significant differences between the pyramided lines and their recurrent parent for all the agronomic traits measured except for grain yield. The pyramided lines do not only stand the chance of being released as new varieties but are also valuable genetic resources for other breeding programs that seek to improve cowpea for aphid resistance.

Marker-Assisted Gene Pyramiding for Powdery Mildew Resistance in Thai Mungbean Variety SUT1 by Backcross Breeding

Marker-Assisted Gene Pyramiding for Powdery Mildew Resistance in Thai Mungbean Variety SUT1 by Backcross Breeding

Development and Validation of a Resistance Management Model for the Soybean Cyst Nematode, Heterodera glycines.

Plant-parasitic nematodes are a key yield-limiting pest of crops around the world. Deployment of plant resistance genes are an important management tactic for many economically important plant-parasitic nematodes. The selection for virulence in nematode populations is a major threat to the effectiveness of resistance gene-based management. Little research has gone into resistance management modelling despite the importance of both plant-parasitic nematodes and resistance genes for their management. In this paper, we report on a cyst nematode resistance management model created to explore the factors which are most important for determining the durability of resistance genes to this important family of plant-parasitic nematodes. The relative dominance of virulence expression, the level of inbreeding, and the number of generations per cropping season were the most important factors in predicting resistance gene durability. Aspects of cyst nematode biology that reduce the number of generations per season for a portion of the population had a much smaller effect on the durability of resistance genes. These factors included delayed hatching within a season and early dormancy. The accuracy and utility of the model was tested using the soybean cyst nematode (SCN) rhg1-mediated resistance system. The model accurately predicted the rate at which virulence to the rhg1b resistance gene developed in Iowa over a two-decade period. The model suggested resistance gene pyramids as the most durable management solution for SCN with multiple possible avenues to obtain acceptable efficacy and durability.

Comparative Analysis of Virulence and Molecular Diversity of Puccinia striiformis f. sp. tritici Isolates Collected in 2016 and 2023 in the Western Region of China.

Puccinia striiformis f. sp. tritici (Pst) is adept at overcoming resistance in wheat cultivars, through variations in virulence in the western provinces of China. To apply disease management strategies, it is essential to understand the temporal and spatial dynamics of Pst populations. This study aimed to evaluate the virulence and molecular diversity of 84 old Pst isolates, in comparison to 59 newer ones. By using 19 Chinese wheat differentials, we identified 98 pathotypes, showing virulence complexity ranging from 0 to 16. Associations between 23 Yr gene pairs showed linkage disequilibrium and have the potential for gene pyramiding. The new Pst isolates had a higher number of polymorphic alleles (1.97), while the older isolates had a slightly higher number of effective alleles, Shannon's information, and diversity. The Gansu Pst population had the highest diversity (uh = 0.35), while the Guizhou population was the least diverse. Analysis of molecular variance revealed that 94% of the observed variation occurred within Pst populations across the four provinces, while 6% was attributed to differences among populations. Overall, Pst populations displayed a higher pathotypic diversity of H > 2.5 and a genotypic diversity of 96%. This underscores the need to develop gene-pyramided cultivars to enhance the durability of resistance.

Physio-Biochemical, Anatomical, and Molecular Analysis of Resistant and Susceptible Wheat Cultivars Infected with TTKSK, TTKST, and TTTSK Novel Puccinia graminis Races.

Stem rust, caused by Puccinia graminis f.sp. tritici, is one of the most dangerous rust diseases on wheat. Through physiological, biochemical, and molecular analysis, the relationship between the change in resistance of 15 wheat cultivars to stem rust disease and the response of 41 stem rust resistance genes (Sr,s) as well as TTKSK, TTKST, and TTTSK races was explained. Some cultivars and Sr genes, such as Gemmeiza-9, Gemmeiza-11, Sids-13, Sakha-94, Misr-1, Misr-2, Sr31, and Sr38, became susceptible to infection. Other new cultivars include Mir-3 and Sakha-95, and Sr genes 13, 37, 40, GT, and FR*2/SRTT3-SRTT3-SR10 remain resistant. Some resistance genes have been identified in these resistant cultivars: Sr2, Sr13, Sr24, Sr36, and Sr40. Sr31 was not detected in any cultivars. Reactive oxygen species such as hydrogen peroxide and superoxide, enzymes activities (catalase, peroxidase, and polyphenoloxidase), and electrolyte leakage were increased in the highly susceptible cultivars, while they decreased in the resistant ones. Anatomical characteristics such as the thickness of the epidermis, ground tissue, phloem tissue and vascular bundle diameter in the midrib were decreased in susceptible cultivars compared with resistant cultivars. Our results indicated that some races (TTKSK, TTKST, and TTTSK) appeared for the first time in Egypt and many other countries, which broke the resistant cultivars. The wheat rust breeding program must rely on land races and pyramiding genes in order to develop new resistance genes that will survive for a very long time.

Breeding new seedless table grapevines for a more sustainable viticulture in Mediterranean climate.

The growing demand for sustainable and environmentally friendly viticulture is leading to a multiplication of breeding programs aimed at obtaining vines that are resistant to powdery mildew (PM) and downy mildew (DM), the two most damaging vine diseases. In Puglia, the most important Italian region for the production of table grapes, an extensive crossing program was launched in 2015 with 113 crosses, including elite table varieties, seedless varieties, and resistant varieties. The main seedling production parameters were measured for each cross. In particular, berries harvested as well as the number of seeds and seedlings obtained were considered. Approximately 103,119 seedlings were obtained and subjected to marker-assisted selection for seedlessness using the marker VvAGL11 and for resistance to PM and DM with appropriate markers. Approximately one third (32,638) of the progenies were selected as putative seedless and seventeen thousand five hundred-nine (17,509) were transferred to the field for phenotypic evaluation, including 527 seedless individuals putatively resistant, of which 208 confirmed to be resistant to DM, 22 resistant to PM, and 20 individuals that combined resistance and seedlessness traits. The work discusses the effects of parental combinations and other variables in obtaining surviving progeny and pyramiding genes in table grapes and provides useful information for selecting genotypes and increasing the efficiency of breeding programs for seedless disease-resistant grapes.

Strong culm: a crucial trait for developing next-generation climate-resilient rice lines.

Lodging, a phenomenon characterized by the bending or breaking of rice plants, poses substantial constraints on productivity, particularly during the harvesting phase in regions susceptible to strong winds. The rice strong culm trait is influenced by the intricate interplay of genetic, physiological, epigenetic, and environmental factors. Stem architecture, encompassing morphological and anatomical attributes, alongside the composition of both structural and non-structural carbohydrates, emerges as a critical determinant of lodging resistance. The adaptive response of the rice culm to various biotic and abiotic environmental factors further modulates the propensity for lodging. Advancements in next-generation sequencing technologies have expedited the genetic dissection of lodging resistance, enabling the identification of pertinent genes, quantitative trait loci, and novel alleles. Concurrently, contemporary breeding strategies, ranging from biparental approaches to more sophisticated methods such as multi-parent-based breeding, gene pyramiding, genomic selection, genome-wide association studies, and haplotype-based breeding, offer perspectives on the genetic underpinnings of culm strength. This review comprehensively delves into physiological attributes, culm histology, epigenetic determinants, and gene expression profiles associated with lodging resistance, with a specialized focus on leveraging next-generation sequencing for candidate gene discovery.

Gene pyramiding of ZmGLK36 and ZmGDIα-hel for rough dwarf disease resistance in maize.

The online version contains supplementary material available at 10.1007/s11032-024-01466-9.

Genome wide association study and genomic prediction for stripe rust resistance at the seedling stage in advanced spring bread wheat genotypes of ICARDA Morocco

One of the most devastating diseases impacting wheat (Triticum aestivum L.) worldwide is stripe rust, which is propagated by Puccinia striiformis f. Sp. Tritici (Pst). The development and utilization of resistant cultivars offer an effective and eco-friendly approach to manage this disease. However, the emergence of new virulent strains of Pst, driven by continuous mutations within the pathogen, rapidly undermines the effectiveness of existing resistance genes. This necessitates the ongoing identification and incorporation of new resistance genes to breed wheat varieties that can maintain resistance against evolving strains of the pathogen. A genome-wide association study (GWAS) and genomic prediction (GP) were conducted using yellow rust data from the seedling stage under controlled conditions, involving 200 elite bread wheat genotypes and 13,151 SNP markers. GWAS analysis identified fourteen SNP markers significantly associated with yellow rust resistance, using a general linear model (GLM). The markers (wsnp Ex c1085 2078944, wsnp Ku c3682 6,786,230) on chromosome 1D and (wsnp Ex c8240 13,914,674) on chromosome 3A were notably correlated with seedling-level resistance to yellow rust. Additionally, the marker 'AX-94703603′ on chromosome 3A, which recorded the highest -Log10(p) value, was linked to the gene 'TraesCS3A02G335300' encoding the protein kinase domain. These markers, after validation, could be utilized for gene pyramiding in wheat breeding programs to enhance rust resistance through marker-assisted selection.

Screening of Apple Cultivars for Scab Resistance in Kazakhstan

Scab, caused by Venturia inaequalis, is the most destructive fungal disease of apple worldwide. Apple scab incidence was studied in apple orchards in the south and southeast of Kazakhstan, including the Almaty, Zhambyl, and Turkestan regions, during 2022 and 2023. Disease incidence was higher in the Zhambyl region than in the Turkestan and Almaty regions in both years. The field evaluation suggested that 19 genotypes showed resistance to apple scab. Molecular screening was carried out using eight gene-specific molecular markers (AM19, CH05e03, OPL19, Hi07f02, AL07, K08, HB09, and CH02f06). The results of the molecular screening revealed that in 38 of the 45 studied cultivars, which included 11 Kazakh cultivars and 34 foreign cultivars, the Rvi (Rvi2, Rvi4, Rvi5, Rvi6, Rvi8, Rvi9, Rvi11, Rvi14, and Rvi15) resistance genes were amplified. Resistance genes such as Rvi2, Rvi4, Rvi6, and Rvi9 are still useful for breeding, but their use is recommended only in extended pyramids of multiple resistance genes. Several cultivars will be strong candidates for further breeding programs against apple scab and for the pyramiding of scab resistance genes in new cultivars.

Single nucleotide polymorphism SNP19140160 A > C is a potential breeding locus for fast-growth largemouth bass (Micropterus salmoides).

Largemouth bass (Micropterus salmoides) has significant economic value as a high-yielding fish species in China's freshwater aquaculture industry. Determining the major genes related to growth traits and identifying molecular markers associated with these traits serve as the foundation for breeding strategies involving gene pyramiding. In this study, we screened restriction-site associated DNA sequencing (RAD-seq) data to identify single nucleotide polymorphism (SNP) loci potentially associated with extreme growth differences between fast-growth and slow-growth groups in the F1 generation of a largemouth bass population. We subsequently identified associations between these loci and specific candidate genes related to four key growth traits (body weight, body length, body height, and body thickness) based on SNP genotyping. In total, 4,196,486 high-quality SNPs were distributed across 23 chromosomes. Using a population-specific genotype frequency threshold of 0.7, we identified 30 potential SNPs associated with growth traits. Among the 30 SNPs, SNP19140160, SNP9639603, SNP9639605, and SNP23355498 showed significant associations; three of them (SNP9639603, SNP9639605, and SNP23355498) were significantly associated with one trait, body length, in the F1 generation, and one (SNP19140160) was significantly linked with four traits (body weight, height, length, and thickness) in the F1 generation. The markers SNP19140160 and SNP23355498 were located near two growth candidate genes, fam174b and ppip5k1b, respectively, and these candidate genes were closely linked with growth, development, and feeding. The average body weight of the group with four dominant genotypes at these SNP loci in the F1 generation population (703.86g) was 19.63% higher than that of the group without dominant genotypes at these loci (588.36g). Thus, these four markers could be used to construct a population with dominant genotypes at loci related to fast growth. These findings demonstrate how markers can be used to identify genes related to fast growth, and will be useful for molecular marker-assisted selection in the breeding of high-quality largemouth bass.

Confirmations on gene introgression events and hybridity for BLB resistance and yield in rice

A superior variety of rice with high yield and resistance to diseases is expected to meet the increasing demand for this one of the most important carbohydrate sources worldwide. Bacterial leaf blight (BLB) caused by Xanthomonas oryzae pv. oryzae (Xoo) is one of the major biotic stresses limiting rice production. Combining BLB resistance and high-yield traits is possible through gene pyramiding. Introgression of targeted traits in the parental genotypes and hybridity confirmation in the F1 generation are important initial steps in gene pyramiding. This study aimed to confirm the presence of targeted genes in parent genotypes using specific molecular markers and to confirm the hybridity of F1 plants generated from three crosses combinations of Inpari 32 (as the female parent) and three Code-qTSN4 lines (as the male parents) using SSR markers. This study successfully confirmed the introgression of BLB-resistance genes in Inpari 32 (Xa4, Xa7, and Xa21) and in Code-qTSN4 (Xa4, Xa7). The introgression of yield-related QTL, qTSN4, was confirmed in the three Code-qTSN4 lines (A10-1, B12-2, and A16-5) by RM17483 marker. Five SSR markers (RM5, RM55, RM105, RM223, and RM561) successfully confirmed the hybridity of F1 derived from Inpari 32xA10-1 (five individuals), Inpari 32xB12-2 (one individual), Inpari 32xA16-5 (two individuals). These confirmed hybrids can be further evaluated in the F2 generation.&#x0D; Keywords: Gene pyramiding; molecular marker; SSR; qTSN4; Xoo.

Metabolic Pathway Engineering Improves Dendrobine Production in Dendrobium catenatum.

The sesquiterpene alkaloid dendrobine, widely recognized as the main active compound and a quality control standard of medicinal orchids in the Chinese Pharmacopoeia, demonstrates diverse biological functions. In this study, we engineered Dendrobium catenatum as a chassis plant for the production of dendrobine through the screening and pyramiding of key biosynthesis genes. Initially, previously predicted upstream key genes in the methyl-D-erythritol 4-phosphate (MEP) pathway for dendrobine synthesis, including 4-(Cytidine 5'-Diphospho)-2-C-Methyl-d-Erythritol Kinase (CMK), 1-Deoxy-d-Xylulose 5-Phosphate Reductoisomerase (DXR), 2-C-Methyl-d-Erythritol 4-Phosphate Cytidylyltransferase (MCT), and Strictosidine Synthase 1 (STR1), and a few downstream post-modification genes, including Cytochrome P450 94C1 (CYP94C1), Branched-Chain-Amino-Acid Aminotransferase 2 (BCAT2), and Methyltransferase-like Protein 23 (METTL23), were chosen due to their deduced roles in enhancing dendrobine production. The seven genes (SG) were then stacked and transiently expressed in the leaves of D. catenatum, resulting in a dendrobine yield that was two-fold higher compared to that of the empty vector control (EV). Further, RNA-seq analysis identified Copper Methylamine Oxidase (CMEAO) as a strong candidate with predicted functions in the post-modification processes of alkaloid biosynthesis. Overexpression of CMEAO increased dendrobine content by two-fold. Additionally, co-expression analysis of the differentially expressed genes (DEGs) by weighted gene co-expression network analysis (WGCNA) retrieved one regulatory transcription factor gene MYB61. Overexpression of MYB61 increased dendrobine levels by more than two-fold in D. catenatum. In short, this work provides an efficient strategy and prospective candidates for the genetic engineering of D. catenatum to produce dendrobine, thereby improving its medicinal value.

Pyramiding of blast and bacterial blight resistance genes in premium quality rice variety, BRRI dhan63 through marker-assisted breeding approach

Pyramiding of blast and bacterial blight resistance genes in premium quality rice variety, BRRI dhan63 through marker-assisted breeding approach

Understanding and improving resistance to Hessian fly (Mayetiola destructor) in US wheat using genetic mapping and molecular techniques

AbstractHessian fly (Mayetiola destructor) is a worldwide pest of wheat (Triticum spp.) causing significant yield losses. Utilizing resistant varieties of wheat is the most effective method of control, particularly in mild climates. The effectiveness of resistance genes is lost over time due to genetic diversity within fly populations, and most cultivars have only one resistance gene making them vulnerable to this loss of resistance. Thirty‐seven resistance genes have been mapped along with four Hessian fly response genes and 11 novel quantitative trait loci (QTL). The majority of these exhibit antibiotic resistance, but new research suggests two or more novel QTL are associated with a valuable tolerant response. Studies suggest that fitness costs associated with resistance can be overcome after the initial infestation, but this may not hold true with repeated fly attacks and should be considered when pyramiding genes. Several of these genes do show temperature sensitivity, which should also be considered during breeding. Resistance mechanisms include increased levels of salicylic acid, upregulation of oxo‐phytodienoic acid reductase genes and genes responsible for lipid and protein mobilization, and increased synthesis of polyphenols, among others. These mechanisms are part of an effector‐triggered response. Resistant genes and QTL with KASP markers for use in creating gene pyramids include QHf.hwwg‐6BS, Qhara.icd‐6B, h4, H7, H32, H33, H34, H35, and H36. GWAS has been used to screen large numbers of elite breeding lines for resistance to Hessian fly. Marker trait associations discovered through GWAS can potentially be used in creating gene pyramids with multiple pest and pathogen resistance genes.

Identification of QTLs and allelic effect controlling lignan content in sesame (Sesamum indicum L.) using QTL-seq approach.

Sesame (Sesamum indicum L.), an oilseed crop, is gaining worldwide recognition for its healthy functional ingredients as consumption increases. The content of lignans, known for their antioxidant and anti-inflammatory effects, is a key agronomic trait that determines the industrialization of sesame. However, the study of the genetics and physiology of lignans in sesame is challenging, as they are influenced by multiple genes and environmental factors, therefore, the understanding of gene function and synthetic pathways related to lignan in sesame is still limited. To address these knowledge gaps, we conducted genetic analyses using F7 recombinant inbred line (RIL) populations derived from Goenbaek and Gomazou as low and high lignin content variants, respectively. Using the QTL-seq approach, we identified three loci, qLignan1-1, qLignan6-1, and qLignan11-1, that control lignan content, specifically sesamin and sesamolin. The allelic effect between loci was evaluated using the RIL population. qLignan6-1 had an additive effect that increased lignan content when combined with the other two loci, suggesting that it could be an important factor in gene pyramiding for the development of high-lignan varieties. This study not only highlights the value of sesame lignan, but also provides valuable insights for the development of high-lignan varieties through the use of DNA markers in breeding strategies. Overall, this research contributes to our understanding of the importance of sesame oil and facilitates progress in sesame breeding for improved lignan content.

Pyramiding BPH genes in rice maintains resistance against the brown planthopper under climate change.

Nilaparvata lugens (brown planthopper; BPH) is a significant rice pest in Asia, causing substantial yield losses. Pyramiding BPH resistance genes with diverse resistance traits into rice cultivars is an effective strategy for pest management. However, the response of pyramiding combinations to environmental changes remains unclear. To address this knowledge gap, we investigated three pyramiding rice lines (BPH2 + 32, BPH9 + 32, and BPH18 + 32) in the context of varying climate change conditions, ensuring sufficient N. lugens-rice interactions. Thus, we set three environmental conditions [30/25 °C (day/night) with 500 ppm CO2 concentration, 32/27 °C (day/night) with 600 ppm CO2 concentration, and 35/30 °C (day/night) with 1000 ppm CO2 concentration]. All three pyramiding rice lines maintained the insect resistant ability under the three environmental settings. In particular, the BPH18 + 32 rice line exhibited stronger antibiotic and antixenosis effects against N. lugens. In addition, BPH18 + 32 rice line had better shoot resilience under N. lugens infestation, whereas the performance of the other two selected pyramiding rice lines varied. Thus, although BPH2, BPH9, and BPH18 represent three alleles at the same locus, their resistance levels against N. lugens may vary under distinct climate change scenarios, as evidenced by the performance of N. lugens on the three pyramiding rice lines. Our findings indicate that all three tested pyramiding rice lines maintained their insect resistance in the face of diverse climate change scenarios. However, these lines exhibited varied repellent responses and resilience capacities in response to climate change. Thus, the combination of pyramiding genes needs to be considered for future breeding programs. © 2023 Society of Chemical Industry.

Combining a Genome-Wide Association Study and Gene-Based Haplotype Analysis to Identify Candidate Genes for Cold Tolerance at the Bud Burst Stage in Rice (Oryza sativa L.)

As a temperature-loving crop, rice is sensitive to low temperatures. With the popularization of direct-seeded rice, cold tolerance (CT) at the bud burst stage has become an important breeding goal. Here, we evaluated CT for 513 rice accessions at the bud burst stage. A total of 13 QTLs were detected by genome-wide association analysis using the severity of damage (SD) and survival rate of seedlings (SR) as indicators of CT. Based on analyses of LD blocks, GO enrichment, gene expression and haplotype, we identified five genes, LOC_Os01g35184, LOC_Os01g56150, LOC_Os01g73410, LOC_Os02g36740, and LOC_Os09g28180, as the most likely candidates for qSD1-1, qSD1-4, qSD1-5, qSD2-1, and qSR9-1, respectively, for CT. The accumulative effects of favorable haplotypes for the above five most likely candidate genes played an important role in the improvement of the CT of rice cultivars. Hence, this study has furnished valuable insights for advancing gene cloning and pyramiding breeding, aiming to enhance cold tolerance during the bud burst stage in rice.