Mapping Population Research Articles

Identification and Fine Mapping of Quantitative Trait Loci for Tiller Angle Using Chromosome Segment Substitution Lines in Rice (Oryza Sativa L.)

The tiller angle, which is an important agronomic trait, determines plant architecture and greatly influences the grain yield of rice. In this study, a population of chromosome segment substitution lines derived from a cross between a japonica variety with a compact plant architecture—Koshihikari—and an indica variety with a spread-out plant architecture—Nona Bokra—was used to investigate the genetic basis of the tiller angle. Five quantitative trait loci (qTA1, qTA5, qTA9-1, qTA9-2, and qTA11) for the tiller angle were detected on chromosomes 1, 5, 9, 9, and 11 in two different environments. The phenotypic variation in these QTLs ranged from 3.78% to 8.22%. Two pairs of digenic epistatic QTLs were detected in Lingshui. The epistatic interaction explained 15.19% and 13.60% of the phenotypic variance, respectively. Among the five QTLs, qTA9-2 was detected in both environments. An F2 mapping population containing the qTA9-2 QTL was established. The location of qTA9-2 was narrowed down to a 187 kb region between InDel markers M9 and M10 on chromosome 9. Thirty open reading frames (ORFs), including TAC1, a gene known to regulate the tiller angle, were identified in this region. The gene sequencing results suggested that a base substitution from G to A at position 1557 in the 3′-untranslated region led to a difference in the expression of qTA9-2 in Koshihikari and Nona Bokra. These findings provide a potential gene resource for the improvement of rice plant architecture.

Accelerated breeding strategies for biochemical marker-assisted backcross breeding and mapping population development in bread wheat (Triticum aestivum L.)

In order to rapidly adapt to the evolving climate and sustainably nourish the growing global population, plant breeders are actively investigating more efficient strategies to enhance crop yields. In this study, we present the development of a bread wheat mapping population and backcross breeding program, serving as a valuable genetic resource for mapping the effects of different alleles on trait performance. We employed innovative methodologies to rapidly introgress traits into the bread wheat cultivar. Specifically, we utilized two parents, including Tosunbey x Tahirova2000, in a recombinant inbred line population, in addition, a backcross strategy was applied with line 148 (obtained by crossing Tosunbey x Tahirova2000 with high gluten quality) as the recipient parent of the Nevzatbey cv., known for its awnless feature. The two most important applications of the rapid breeding method are extending the light period and breaking dormancy in early harvested seeds. Both applications were successfully implemented in our study. Our vegetation periods ranging from approximately 50–60 days. Additionally, an early genotype in our developed population was harvested in 40 days. Considering that the genotype underwent a 15-day vernalization period, the generation cycle, including vernalization, drying, and refrigeration, was completed in a total of 64 days. Notably, we employed not only biochemical markers for selection but also incorporated the rapid generation advance technology known as ‘speed breeding’, allowing us to develop BC5F1 within a span of two years. We posit that this approach proves instrumental in swiftly transferring genes for multiple target traits into adapted wheat cultivars or in pyramiding desirable traits within elite breeding material.

Examining the Influence of Historical Redlining on Firearm Injuries in Current Day Baltimore, Maryland.

Firearm injuries are a common and major public health problem in Baltimore, Maryland. The city is also one of the first U.S. cities in which the 1930s discriminatory practice of redlining first emerged. This study examines the association between current day firearm injuries and residence in these historically redlined areas at a neighborhood level using zip codes. Firearm injury outcomes in patients who presented to a hospital in Maryland from 2015 to 2020 were measured from the Health Services Cost Review Commission (HSCRC) in conjunction with both geospatial data from Richmond's Digital Scholarship Lab's Mapping Inequality project and population data from the U.S. Census. A redlining score was calculated to represent the extent of redlining in each zip code. Negative binomial regression models were utilized to measure the association between neighborhood zip codes and rate of firearm injuries. Our adjusted regression model shows that for every one-unit increase of the Home Owners' Loan Corporation (HOLC) redlining score, there is a 2.24-fold increase in the rate of firearm injuries (RR 2.24; 95% CI: 0.31, 1.31, p < 0.001). These findings suggest a strongassociation between historically redlined areas and population risk of firearm injury today. Further research is needed to investigate the underlying mechanisms that may contribute to this relationship, such as access to firearms or social and economic factors. Overall, our study highlights the potential impact of historical redlining policies on contemporary health outcomes in Baltimore.

The Uniqueness of Megapodius reinwardt and the Wisdom of the Local Community as Tourism Attraction and Conservation at Moyo Island

The distribution, graduation and conservation of Megapodius reinwardt based on the ecological knowledge of local residents to support ecotourism on moyo island, has been carried out. The objectives are: 1) to obtain an accurate picture of the distribution of the population and its behavior, 2) knowledge of the ecology of the local population, 3) perception and behavior of the local population, 4) to increase the population, and 5) to carry out conservation to prevent its extinction in the Moyo Island. This research consists of two stages of activities, namely first, mapping population distribution, nest analysis, diseases, pathogens, interviews and discussions with local community about their perception and knowledge about M. reinwardt, document study about tourist visits; second, building awareness and participation of local community to support M. reinwardt conservation activities, formulating its conservation design and identifying potential nests as tourist attractions. The perception of the local residents of Moyo Island towards the existence of M. reinwardt is useful in supporting the fulfillment of their life needs directly or indirectly. Locals believe that by keeping M. reinwardt, his life needs can be met. In addition, the locals of Moyo Island think that laboring the bird at the time of laying eggs will be "Mali" or bring bad luck to hunters. The attitude of the local residents of Moyo Island towards the preservation of M. reinwardt is mostly 85% of residents agree with the preservation of M. reinwardt on Moyo Island, 10% are still hesitant and 5% disagree. The efforts to manage M. reinwardt as one of the tourist attractions, must involve and be able to accommodate the needs of local residents, tourists, tourism entrepreneurs and the government. For the success of the bird conservation efforts, six things must be considered, namely: 1) an agreement on the recognition of the minimum rights of group members; 2) the clarity of the boundaries of the scope of control of each active management community group; 3) the suitability between the cost of nest management and the benefits obtained; 4) conflict resolution mechanisms; 5) firmness in the application of sanctions and 6) willingness to receive knowledge/information and technology on the conservation and management of M. reinwardt from outside the moyo island area.

QTL mapping of downy mildew resistance in foxtail millet by SLAF‑seq and BSR-seq analysis.

Key message Three major QTLs for resistance to downy mildew were located within an 0.78 Mb interval on chromosome 8 in foxtail millet. Downy mildew, a disease caused by Sclerospora graminicola, is a serious problem that jeopardizes the yield and quality of foxtail millet. Breeding resistant varieties represents one of the most economical and effective solutions, yet there is a lack of molecular markers related to the resistance. Here, a mapping population comprising of 158 F6:7 recombinant inbred lines (RILs) was constructed from the crossing of G1 and JG21. Based on the specific locus amplified fragment sequencing results, a high-density linkage map of foxtail millet with 1031 bin markers, spanning 1041.66 cM was constructed. Based on the high-density linkage map and the phenotype data in four environments, a total of nine quantitative trait loci (QTL) associated with resistance to downy mildew were identified. Further BSR-seq confirmed the genomic regions containing the potential candidate genes related to downy mildew resistance. Interestingly, a 0.78-Mb interval between C8M257 and C8M268 on chromosome 8 was highlighted because of its presence in three major QTL, qDM8_1, qDM8_2, and qDM8_4, which contains 10 NBS-LRR genes. Haplotype analysis in RILs and natural population suggest that 9 SNP loci on Seita8G.199800, Seita8G.195900, Seita8G.198300, and Seita.8G199300 genes were significantly correlated with disease resistance. Furthermore, we found that those genes were taxon-specific by collinearity analysis of pearl millet and foxtail millet genomes. The identification of these new resistance QTL and the prediction of resistance genes against downy mildew will be useful in breeding for resistant varieties and the study of genetic mechanisms of downy mildew disease resistance in foxtail millet.

Linkage Mapping and Genome-Wide Association Study Identified Two Peanut Late Leaf Spot Resistance Loci, PLLSR-1 and PLLSR-2, Using Nested Association Mapping.

Identification of candidate genes and molecular markers for late leaf spot (LLS) disease resistance in peanut (Arachis hypogaea) has been a focus of molecular breeding for the U.S. industry-funded peanut genome project. Efforts have been hindered by limited mapping resolution due to low levels of genetic recombination and marker density available in traditional biparental mapping populations. To address this, a multi-parental nested association mapping population has been genotyped with the peanut 58K single-nucleotide polymorphism (SNP) array and phenotyped for LLS severity in the field for 3 years. Joint linkage-based quantitative trait locus (QTL) mapping identified nine QTLs for LLS resistance with significant phenotypic variance explained up to 47.7%. A genome-wide association study identified 13 SNPs consistently associated with LLS resistance. Two genomic regions harboring the consistent QTLs and SNPs were identified from 1,336 to 1,520 kb (184 kb) on chromosome B02 and from 1,026.9 to 1,793.2 kb (767 kb) on chromosome B03, designated as peanut LLS resistance loci, PLLSR-1 and PLLSR-2, respectively. PLLSR-1 contains 10 nucleotide-binding site leucine-rich repeat disease resistance genes. A nucleotide-binding site leucine-rich repeat disease resistance gene, Arahy.VKVT6A, was also identified on homoeologous chromosome A02. PLLSR-2 contains five significant SNPs associated with five different genes encoding callose synthase, pollen defective in guidance protein, pentatricopeptide repeat, acyl-activating enzyme, and C2 GRAM domains-containing protein. This study highlights the power of multi-parent populations such as nested association mapping for genetic mapping and marker-trait association studies in peanuts. Validation of these two LLS resistance loci will be needed for marker-assisted breeding.

Fine mapping a QTL for BYDV-PAV resistance in maize

Barley yellow dwarf (BYD) is one of the economically most important virus diseases of cereals worldwide, causing yield losses up to 80%. The means to control BYD are limited, and the use of genetically resistant cultivars is the most economical and environmentally friendly approach. The objectives of this study were i) to identify the causative gene for BYD virus (BYDV)-PAV resistance in maize, ii) to identify single nucleotide polymorphisms and/or structural variations in the gene sequences, which may cause differing susceptibilities to BYDV-PAV of maize inbreds, and iii) to characterize the effect of BYDV-PAV infection on gene expression of susceptible, tolerant, and resistant maize inbreds. Using two biparental mapping populations, we could reduce a previously published quantitative trait locus for BYDV-PAV resistance in maize to ~ 0.3 Mbp, comprising nine genes. Association mapping and gene expression analysis further reduced the number of candidate genes for BYDV-PAV resistance in maize to two: Zm00001eb428010 and Zm00001eb428020. The predicted functions of these genes suggest that they confer BYDV-PAV resistance either via interfering with virus replication or by inducing reactive oxygen species signaling. The gene sequence of Zm00001eb428010 is affected by a 54 bp deletion in the 5`-UTR and a protein altering variant in BYDV-PAV-resistant maize inbreds but not in BYDV-PAV-susceptible and -tolerant inbreds. This finding suggests that altered abundance and/or properties of the proteins encoded by Zm00001eb428010 may lead to BYDV-PAV resistance.

Variability in Chromosome 1 of Select Moroccan Pyrenophora teres f. teres Isolates Overcomes a Highly Effective Barley Chromosome 6H Source of Resistance.

Barley net form net blotch (NFNB) is a destructive foliar disease caused by Pyrenophora teres f. teres. Barley line CIho5791, which harbors the broadly effective chromosome 6H resistance gene Rpt5, displays dominant resistance to P. teres f. teres. To genetically characterize P. teres f. teres avirulence/virulence on the barley line CIho5791, we generated a P. teres f. teres mapping population using a cross between the Moroccan CIho5791-virulent isolate MorSM40-3 and the avirulent reference isolate 0-1. Full genome sequences were generated for 103 progenies. Saturated chromosome-level genetic maps were generated, and quantitative trait locus (QTL) mapping identified two major QTL associated with P. teres f. teres avirulence/virulence on CIho5791. The most significant QTL mapped to chromosome (Ch) 1, where the virulent allele was contributed by MorSM40-3. A second QTL mapped to Ch8; however, this virulent allele was contributed by the avirulent parent 0-1. The Ch1 and Ch8 loci accounted for 27 and 15% of the disease variation, respectively, and the avirulent allele at the Ch1 locus was epistatic over the virulent allele at the Ch8 locus. As a validation, we used a natural P. teres f. teres population in a genome-wide association study that identified the same Ch1 and Ch8 loci. We then generated a new reference quality genome assembly of parental isolate MorSM40-3 with annotation supported by deep transcriptome sequencing of infection time points. The annotation identified candidate genes predicted to encode small, secreted proteins, one or more of which are likely responsible for overcoming the CIho5791 resistance. [Formula: see text] The author(s) have dedicated the work to the public domain under the Creative Commons CC0 "No Rights Reserved" license by waiving all of his or her rights to the work worldwide under copyright law, including all related and neighboring rights, to the extent allowed by law, 2024.

Genetic mapping of regions associated with root system architecture in rice using MutMap QTL-seq

The root system architecture is an important complex trait in rice. With changing climatic conditions and soil nutrient deficiencies, there is an immediate need to breed nutrient-use-efficient rice varieties with robust root system architectural (RSA) traits. To map the genomic regions associated with crucial component traits of RSA viz. root length and root volume, a biparental F2 mapping population was developed using TI-128, an Ethyl Methane Sulphonate (EMS) mutant of a mega variety BPT-5204 having high root length (RL) and root volume (RV) with wild type BPT-5204. Extreme bulks having high RL and RV and low RL and RV were the whole genome re-sequenced along with parents. Genetic mapping using the MutMap QTL-Seq approach elucidated two genomic intervals on Chr.12 (3.14–3.74 Mb, 18.11–20.85 Mb), and on Chr.2 (23.18–23.68 Mb) as potential regions associated with both RL and RV. The Kompetitive Allele Specific PCR (KASP) assays for SNPs with delta SNP index near 1 were associated with higher RL and RV in the panel of sixty-two genotypes varying in root length and volume. The KASP_SNPs viz. Chr12_S4 (C→T; Chr12:3243938), located in the 3’ UTR region of LOC_Os12g06670 encoding a protein kinase domain-containing protein and Chr2_S6 (C→T; Chr2:23181622) present upstream in the regulator of chromosomal condensation protein LOC_Os2g38350. Validation of these genes using qRT-PCR and in-silico studies using various online tools and databases revealed higher expression in TI-128 as compared to BPT- 5204 at the seedling and panicle initiation stages implying the functional role in enhancing RL and RV.

Research on Photovoltaic Maximum Power Point Tracking Control Based on Improved Tuna Swarm Algorithm and Adaptive Perturbation Observation Method

In situations where photovoltaic (PV) systems are exposed to varying light intensities, the conventional maximum power point tracking (MPPT) control algorithm may become trapped in a local optimal state. In order to address this issue, a two-step MPPT control strategy is suggested utilizing an improved tuna swarm optimization (ITSO) algorithm along with an adaptive perturbation and observation (AP&amp;O) technique. For the sake of enhancing population diversity, the ITSO algorithm is initialized by the SPM chaos mapping population. In addition, it also uses the parameters of the spiral feeding strategy of nonlinear processing and the Levy flight strategy adjustment of the weight coefficient to enhance global search ability. In the two-stage MPPT algorithm, the ITSO is applied first to track the vicinity of the global maximum power point (MPP), and then it switches to the AP&amp;O method. The AP&amp;O method’s exceptional local search capability enables the global MPP to be tracked with remarkable speed and precision. To confirm the effectiveness of the suggested algorithm, it is evaluated against fuzzy logic control (FLC), standard tuna swarm optimization (TSO), grey wolf optimization (GWO), particle swarm optimization (PSO), and AP&amp;O. Finally, the proposed MPPT strategy is verified by the MATLAB R2022b and RT-LAB experimental platform. The findings indicate that the suggested method exhibits improved precision and velocity in tracking, efficiently following the global MPP under different shading conditions.

Multi-trait association mapping for phosphorous efficiency reveals flexible root architectures in sorghum

BackgroundOn tropical regions, phosphorus (P) fixation onto aluminum and iron oxides in soil clays restricts P diffusion from the soil to the root surface, limiting crop yields. While increased root surface area favors P uptake under low-P availability, the relationship between the three-dimensional arrangement of the root system and P efficiency remains elusive. Here, we simultaneously assessed allelic effects of loci associated with a variety of root and P efficiency traits, in addition to grain yield under low-P availability, using multi-trait genome-wide association. We also set out to establish the relationship between root architectural traits assessed in hydroponics and in a low-P soil. Our goal was to better understand the influence of root morphology and architecture in sorghum performance under low-P availability.ResultIn general, the same alleles of associated SNPs increased root and P efficiency traits including grain yield in a low-P soil. We found that sorghum P efficiency relies on pleiotropic loci affecting root traits, which enhance grain yield under low-P availability. Root systems with enhanced surface area stemming from lateral root proliferation mostly up to 40 cm soil depth are important for sorghum adaptation to low-P soils, indicating that differences in root morphology leading to enhanced P uptake occur exactly in the soil layer where P is found at the highest concentration.ConclusionIntegrated QTLs detected in different mapping populations now provide a comprehensive molecular genetic framework for P efficiency studies in sorghum. This indicated extensive conservation of P efficiency QTL across populations and emphasized the terminal portion of chromosome 3 as an important region for P efficiency in sorghum. Increases in root surface area via enhancement of lateral root development is a relevant trait for sorghum low-P soil adaptation, impacting the overall architecture of the sorghum root system. In turn, particularly concerning the critical trait for water and nutrient uptake, root surface area, root system development in deeper soil layers does not occur at the expense of shallow rooting, which may be a key reason leading to the distinctive sorghum adaptation to tropical soils with multiple abiotic stresses including low P availability and drought.

A Quantitative Trait Locus with a Major Effect on Root-Lesion Nematode Resistance in Barley.

Although the root-lesion nematode Pratylenchus thornei is known to affect barley (Hordeum vulgare L.), there have been no reports on the genetic control of P. thornei resistance in barley. In this research, P. thornei resistance was assessed for a panel of 46 barley mapping parents and for two mapping populations (Arapiles/Franklin and Denar/Baudin). With both populations, a highly significant quantitative trait locus (QTL) was mapped at the same position on the long arm of chromosome 7H. Single-nucleotide polymorphisms (SNPs) in this region were anchored to an RGT Planet pan-genome assembly and assayed on the mapping parents and other barley varieties. The results indicate that Arapiles, Denar, RGT Planet and several other varieties likely have the same resistance gene on chromosome 7H. Marker assays reported here could be used to select for P. thornei resistance in barley breeding. Analysis of existing barley pan-genomic and pan-transcriptomic data provided a list of candidate genes along with information on the expression and differential expression of some of those genes in barley root tissue. Further research is required to identify a specific barley gene that affects root-lesion nematode resistance.

Characterising Biological and Physiological Drought Signals in Diverse Parents of a Wheat Mapping Population.

Water deficit affects the growth as well as physiological and biochemical processes in plants. The aim of this study was to determine differences in physiological and biochemical responses to drought stress in two wheat cultivars-Chinese Spring (CS) and SQ1 (which are parents of a mapping population of doubled haploid lines)-and to relate these responses to final yield and agronomic traits. Drought stress was induced by withholding water for 14 days, after which plants were re-watered and maintained until harvest. Instantaneous gas exchange parameters were evaluated on the 3rd, 5th, 10th, and 14th days of seedling growth under drought. After 14 days, water content and levels of chlorophyll a+b, carotenoids, malondialdehyde, soluble carbohydrates, phenolics, salicylic acid, abscisic acid (ABA), and polyamines were measured. At final maturity, yield components (grain number and weight), biomass, straw weight, and harvest index were evaluated. Physiological and biochemical parameters of CS responded more than those of SQ1 to the 14-day drought, reflected in a greater reduction in final biomass and yield in CS. Marked biochemical differences between responses of CS and SQ1 to the drought were found for soluble carbohydrates and polyamines. These would be good candidates for testing in the mapping population for the coincidence of the genetic control of these traits and final biomass and yield.

Identification of a pleiotropic QTL and development KASP markers for HPW, HSW, and SP in peanut

High yield has always been the primary objective of peanut breeding. 100-pod weight (HPW), 100-seed weight (HSW), and shelling percentage (SP), are crucial components of peanut yield. This study aimed to construct a high-density linkage map by resequencing the recombined inbred lines (RILs) derived from a cross between “Silihong” (A. hypogaea var. fastigiate) and “Jinonghei 3” (A. hypogaea var. hypogaea). The map consisted of 4,499 bins spread across 20 chromosomes, totaling 1712.32 cM in length with an average inter-marker distance of 0.38 cM. A total of 46 quantitative trait loci (QTLs) were identified across three environments. The major QTLs, including qHPW5.2, qHPW18.1, qSP7.1, qSP8.1, qSP8.2, qSP18.1, and qSP18.2, exhibited PVE (phenotypic variation explained) of 12.04, 11.41, 16.53, 24.17, 10.49, 10.82, and 29.89%, respectively. Fourteen QTLs identified across multiple environments were considered stable. One QTL (qHPW7, qHSW7.1, qSP7) was associated with all three traits, with the PVE value of 8.91, 9.04, and 16.53% for HPW, HSW, and SP, respectively. The genome-wide association study was conducted using the US mini-core collection to validate the accuracy of QTL mapping. Across two environments, 115 single-nucleotide polymorphisms (SNPs) were significantly associated with HPW, HSW, and SP in the association panel. Six SNPs were associated with two traits, explaining an average phenotypic variation of 13.84%. Combining the two mapping populations, AX-176802178, detected on chromosome 7 in the association panel, which controlled SP, was located within the QTL qSP7 confidence interval defined by the RILs. Moreover, three KASP markers were developed and validated in peanut landraces and varieties. These QTLs might offer valuable insights for understanding the genetic basis of HPW, HSW, and SP and provide useful molecular markers for marker-assisted breeding in peanuts.

Meta-QTL and Candidate Gene Analyses of Agronomic Salt Tolerance and Related Traits in an RIL Population Derived from Solanum pimpinellifolium.

Breeding salt-tolerant crops is necessary to reduce food insecurity. Prebreeding populations are fundamental for uncovering tolerance alleles from wild germplasm. To obtain a physiological interpretation of the agronomic salt tolerance and better criteria to identify candidate genes, quantitative trait loci (QTLs) governing productivity-related traits in a population of recombinant inbred lines (RIL) derived from S. pimpinellifolium were reanalyzed using an SNP-saturated linkage map and clustered using QTL meta-analysis to synthesize QTL information. A total of 60 out of 85 QTLs were grouped into 12 productivity MQTLs. Ten of them were found to overlap with other tomato yield QTLs that were found using various mapping populations and cultivation conditions. The MQTL compositions showed that fruit yield was genetically associated with leaf water content. Additionally, leaf Cl- and K+ contents were related to tomato productivity under control and salinity conditions, respectively. More than one functional candidate was frequently found, explaining most productivity MQTLs, indicating that the co-regulation of more than one gene within those MQTLs might explain the clustering of agronomic and physiological QTLs. Moreover, MQTL1.2, MQTL3 and MQTL6 point to the root as the main organ involved in increasing productivity under salinity through the wild allele, suggesting that adequate rootstock/scion combinations could have a clear agronomic advantage under salinity.

Synergizing breeding strategies via combining speed breeding, phenotypic selection, and marker-assisted backcrossing for the introgression of Glu-B1i in wheat.

Wheat is a major food crop that plays a crucial role in the human diet. Various breeding technologies have been developed and refined to meet the increasing global wheat demand. Several studies have suggested breeding strategies that combine generation acceleration systems and molecular breeding methods to maximize breeding efficiency. However, real-world examples demonstrating the effective utilization of these strategies in breeding programs are lacking. In this study, we designed and demonstrated a synergized breeding strategy (SBS) that combines rapid and efficient breeding techniques, including speed breeding, speed vernalization, phenotypic selection, backcrossing, and marker-assisted selection. These breeding techniques were tailored to the specific characteristics of the breeding materials and objectives. Using the SBS approach, from artificial crossing to the initial observed yield trial under field conditions only took 3.5 years, resulting in a 53% reduction in the time required to develop a BC2 near-isogenic line (NIL) and achieving a higher recurrent genome recovery of 91.5% compared to traditional field conditions. We developed a new wheat NIL derived from cv. Jokyoung, a leading cultivar in Korea. Milyang56 exhibited improved protein content, sodium dodecyl sulfate-sedimentation value, and loaf volume compared to Jokyoung, which were attributed to introgression of the Glu-B1i allele from the donor parent, cv. Garnet. SBS represents a flexible breeding model that can be applied by breeders for developing breeding materials and mapping populations, as well as analyzing the environmental effects of specific genes or loci and for trait stacking.

Impairment in a member of AP2/ERF and F-box family protein enhances complete panicle exsertion in rice.

Complete panicle exsertion (CPE) is an economically important quantitative trait that contributes to grain yield in rice. We deployed an integrated approach for understanding the molecular mechanism of CPE using a stable ethyl methanesulfonate mutant line, CPE-109 of the Samba Mahsuri (SM) variety of rice (Oryza sativa), which exhibits CPE. Two consistent genomic regions were identified for CPE through quantitative trait locus (QTL) mapping [qCPE-4 (28.24-31.22 Mb) and qCPE-12 (2.30-3.18 Mb)] and QTL-sequencing [chr 4 (31.21-33.69 Mb) and chr 12 (0.12-3.15 Mb)]. Two non-synonymous single nucleotide polymorphisms, namely KASP 12-12 (T→C; chr12:1269983) in Os12g0126300, encoding an AP2/ERF transcription factor, and KASP 12-16 (G→A; chr12:1515198) in Os12g0131400, encoding an F-box domain-containing protein, explained 81.05% and 59.61% of the phenotypic variance, respectively, and exhibited strong co-segregation with CPE in F2 mapping populations, advanced generation lines, and CPE-exhibiting SM mutants through KASP assays. Down-regulation of these genes in CPE-109 compared with SM (wild type) was observed in transcriptome sequencing of flag leaves, which was validated through qRT-PCR. We propose that the abrogation of Os12g0126300 and Os12g0131400 in CPE-109 combinatorially influences down-regulation of ethylene biosynthetic genes, Os01g0192900 (ACC synthase) and Os05g0497300 (ethylene-responsive factor-2), and up-regulation of a gibberellic acid synthetic gene, Os06g0569900 (ent-kaurene synthase) and the two cytokinin biosynthetic genes Os07g0486700 (cytokinin-O-glucosyltransferase 2) and Os10g0479500 (similar to carboxy-lyase), which results in complete panicle exsertion.

Three Novel er1 Alleles and Their Functional Markers for Breeding Resistance to Powdery Mildew (Erysiphe pisi) in Pea.

Powdery mildew caused by Erysiphe pisi DC is a global notorious disease on peas. Deploying resistance pea cultivars is the most efficient and environmentally friendly method for disease control. This study focuses on revealing the resistance genes in three pea germplasms and developing their functional markers for resistance breeding. The identification of resistance genes involved genetic mapping and the sequencing of the pea mildew resistance locus O homolog PsMLO1 gene. To confirm the heredity of three resistant germplasms, they were crossed with susceptible cultivars to generate F1, F2, and F2:3 populations. The F1 generation exhibited susceptibility to E. pisi, whereas the segregation patterns in subsequent generations adhered to the 3:1 (susceptible: resistant) and 1:2:1 (susceptible homozygotes: heterozygotes: resistant homozygotes) ratios, indicating that powdery mildew resistance was governed by a single recessive gene in each germplasm. Analysis of er1-linked markers and genetic mapping suggested that the resistance genes could be er1 alleles in these germplasms. The multiple clone sequencing results of the three homologous PsMLO1 genes showed they were novel er1 alleles, named er1-15, er1-16, and er1-17. The er1-15 and er1-16 were caused by 1-bp deletion at position 335 (A) and 429 (T) in exon 3, respectively, whereas er1-17 was caused by a 1-bp insertion at position 248 in exon 3, causing a frame-shift mutation and premature termination of PsMLO1 protein translation. Their respective functional markers, kompetitive allele-specific PCR (KASP)-er1-15, KASP-er1-16, and KASP-er1-17, were successfully developed and validated in respective mapping populations and pea germplasms. These results provide valuable tools for pea breeding resistance to E. pisi.

Climate–resilient strategy for shortening the crop cycle in rice and the host influenced rhizosphere microbiome

We present the field rapid generation advancement procedure for shortening the crop cycle in rice. The practical protocol developed by us using different maturity groups of rice showed promising early flower induction. We observed a shortening of crop cycle to about 35–40 days depending on the variety. The spacing between the plants was the major influencer for flower induction compared to other interventions tested viz., clipping, potassium di-hydrogen phosphate and paclobutrazol spray. Our raised bed direct seeding strategy completely avoided the transplantation. The work flow for flower induction can be a reference to increase generations of rice breeding. The rhizosphere bacterial dynamics using 16srRNA gene amplicon sequencing showed the Acinetobacter population abundance as a key mediator and marker for flowering time. The alpha diversity at flowered and unflowered stage showed the species richness as Control < Pusa Sugandh 5 < BPT-5204. The rice rhizosphere of this ecosystem had an abundance of Methylotrophs that utilize methane as a carbon source suggesting that the developed method is a green technique suitable for generation advancement that can be replaced for flooded condition assisted breeding in rice. Selective enrichment of functional abundance between varieties suggested the host - influenced microbiome for early flowering in rice. This protocol is expected to greatly accelerate the process of new variety breeding and the construction of mapping populations.

Identification of Insertion/Deletion Markers for Photoperiod Sensitivity in Rice (Oryza sativa L.).

The current study aims to identify candidate insertion/deletion (INDEL) markers associated with photoperiod sensitivity (PS) in rice landraces from the Vietnamese Mekong Delta. The whole-genome sequencing of 20 accessions was conducted to analyze INDEL variations between two photoperiod-sensitivity groups. A total of 2240 INDELs were identified between the two photoperiod-sensitivity groups. The selection criteria included INDELs with insertions or deletions of at least 20 base pairs within the improved rice group. Six INDELs were discovered on chromosomes 01 (5 INDELs) and 6 (1 INDEL), and two genes were identified: LOC_Os01g23780 and LOC_Os01g36500. The gene LOC_Os01g23780, which may be involved in rice flowering, was identified in a 20 bp deletion on chromosome 01 from the improved rice accession group. A marker was devised for this gene, indicating a polymorphism rate of 20%. Remarkably, 20% of the materials comprised improved rice accessions. This INDEL marker could explain 100% of the observed distinctions. Further analysis of the mapping population demonstrated that an INDEL marker associated with the MADS-box gene on chromosome 01 was linked to photoperiod sensitivity. The F1 population displayed two bands across all hybrid individuals. The marker demonstrates efficacy in distinguishing improved rice accessions within the indica accessions. This study underscores the potential applicability of the INDEL marker in breeding strategies.