QTL Mapping Studies Research Articles

Identification of Quantitative Trait Loci Associated with Plant Adaptation Traits Using Nested Association Mapping Population.

This study evaluated 290 recombinant inbred lines (RILs) of the nested association mapping (NAM) population from the UK. The population derived from 24 families, where a common parent was "Paragon," one of the UK's spring wheat cultivar standards. All genotypes were tested in two regions of Kazakhstan at the Kazakh Research Institute of Agriculture and Plant Industry (KRIAPI, Almaty region, Southeast Kazakhstan, 2019-2022 years) and Alexandr Barayev Scientific-Production Center for Grain Farming (SPCGF, Shortandy, Akmola region, Northern Kazakhstan, 2019-2022 years). The studied traits consisted of plant adaptation-related traits, including heading date (HD, days), seed maturation date (SMD, days), plant height (PH, cm), and peduncle length (PL, cm). In addition, the yield per m2 was analyzed in both regions. Based on a field evaluation of the population in northern and southeastern Kazakhstan and using 10,448 polymorphic SNP (single-nucleotide polymorphism) markers, the genome-wide association study (GWAS) allowed for detecting 74 QTLs in four studied agronomic traits (HD, SMD, PH, and PL). The literature survey suggested that 16 of the 74 QTLs identified in our study had also been detected in previous QTL mapping studies and GWASs for all studied traits. The results will be used for further studies related to the adaptation and productivity of wheat in breeding projects for higher grain productivity.

Identification and expression analysis of genomic regions associated with the traits contributing to lodging tolerance in wheat (Triticum aestivum L.)

Crop lodging, either stem breaking/stem bending or root lodging, is a major concern for farmers worldwide. In the present study, meta-QTLs, ortho-MQTLs and candidate genes related to lodging and its associated traits were identified using 836 of the 1269 known QTLs retrieved from 107 QTL mapping studies published during 1998–2022. The study resulted in the identification of 86 MQTLs with an average confidence interval (CI) of 1.66 cM (4.26-fold reduction) as against a CI of > 7.08 cM in the initial QTLs. Out of 86 MQTLs, a subset of 12 MQTLs demonstrated stability and robustness, earning them the title of breeders’ MQTLs. These selections were made based on criteria such as the number of initial QTLs involved, small CI, high LOD scores, and PVE values. Furthermore, leveraging synteny and collinearity facilitated the identification of 10 ortho-MQTLs shared between wheat and maize. Further, in silico expression analysis allowed the detection of 53 significantly expressed candidate genes encoding different proteins/products including the following: F-box protein, GDSL lipase/esterases, SANT/Myb domain transcription factor, pectin esterase inhibitor domain, glycoside hydrolase family, protein kinase domain, zinc finger domain, cytochrome P450, UDP-glucuronosyl/UDP-glucosyltransferase, glycosyltransferase 61 etc. In addition, 26 lodging tolerance genes from Arabidopsis, rice, and maize were also utilized to identify 34 wheat homologues in wheat MQTL regions. Among these, three genes TraesCS2D02G256600 (TaEREB114-2D), TraesCS7B02G340100 (TaIRX14-7B), and TraesCS1B02G347600 (TaGA2ox4-1B) were prioritized for qRT-PCR-based expression analysis in one lodging-tolerant (i.e., WH-1105) and one lodging-susceptible (i.e., WH-1184) variety. When comparing these two varieties, we found higher relative expression levels of these three genes in the second basal internode at the milky endosperm stage of the lodging-tolerant variety. The MQTLs, ortho-MQTLs, and candidate genes (CGs) identified in this study can be utilized for marker-assisted selection to improve lodging tolerance and enhance our understanding of the molecular basis of lodging tolerance in wheat.

The Ecology of Hybrid Incompatibilities.

Ecologically mediated selection against hybrids, caused by hybrid phenotypes fitting poorly into available niches, is typically viewed as distinct from selection caused by epistatic Dobzhansky-Muller hybrid incompatibilities. Here, we show how selection against transgressive phenotypes in hybrids manifests as incompatibility. After outlining our logic, we summarize current approaches for studying ecology-based selection on hybrids. We then quantitatively review QTL-mapping studies and find traits differing between parent taxa are typically polygenic. Next, we describe how verbal models of selection on hybrids translate to phenotypic and genetic fitness landscapes, highlighting emerging approaches for detecting polygenic incompatibilities. Finally, in a synthesis of published data, we report that trait transgression-and thus possibly extrinsic hybrid incompatibility in hybrids-escalates with the phenotypic divergence between parents. We discuss conceptual implications and conclude that studying the ecological basis of hybrid incompatibility will facilitate new discoveries about mechanisms of speciation.

Impacts of salinity stress on crop plants: improving salt tolerance through genetic and molecular dissection.

Improper use of water resources in irrigation that contain a significant amount of salts, faulty agronomic practices such as improper fertilization, climate change etc. are gradually increasing soil salinity of arable lands across the globe. It is one of the major abiotic factors that inhibits overall plant growth through ionic imbalance, osmotic stress, oxidative stress, and reduced nutrient uptake. Plants have evolved with several adaptation strategies at morphological and molecular levels to withstand salinity stress. Among various approaches, harnessing the crop genetic variability across different genepools and developing salinity tolerant crop plants offer the most sustainable way of salt stress mitigation. Some important major genetic determinants controlling salinity tolerance have been uncovered using classical genetic approaches. However, its complex inheritance pattern makes breeding for salinity tolerance challenging. Subsequently, advances in sequence based breeding approaches and functional genomics have greatly assisted in underpinning novel genetic variants controlling salinity tolerance in plants at the whole genome level. This current review aims to shed light on physiological, biochemical, and molecular responses under salt stress, defense mechanisms of plants, underlying genetics of salt tolerance through bi-parental QTL mapping and Genome Wide Association Studies, and implication of Genomic Selection to breed salt tolerant lines.

Candidate genes associated with heat stress and breeding strategies to relieve its effects in dairy cattle: a deeper insight into the genetic architecture and immune response to heat stress.

The need for food products of animal origin is increasing worldwide. Satisfying these needs in a way that has minimal impact on the environment requires cutting-edge technologies and techniques to enhance the genetic quality of cattle. Heat stress (HS), in particular, is affecting dairy cattle with increasing frequency and severity. As future climatic challenges become more evident, identifying dairy cows that are more tolerant to HS will be important for breeding dairy herds that are better adapted to future environmental conditions and for supporting the sustainability of dairy farming. While research into the genetics of HS in the context of the effect of global warming on dairy cattle is gaining momentum, the specific genomic regions involved in heat tolerance are still not well documented. Advances in omics information, QTL mapping, transcriptome profiling and genome-wide association studies (GWAS) have identified genomic regions and variants associated with tolerance to HS. Such studies could provide deeper insights into the genetic basis for response to HS and make an important contribution to future breeding for heat tolerance, which will help to offset the adverse effects of HS in dairy cattle. Overall, there is a great interest in identifying candidate genes and the proportion of genetic variation associated with heat tolerance in dairy cattle, and this area of research is currently very active worldwide. This review provides comprehensive information pertaining to some of the notable recent studies on the genetic architecture of HS in dairy cattle, with particular emphasis on the identified candidate genes associated with heat tolerance in dairy cattle. Since effective breeding programs require optimal knowledge of the impaired immunity and associated health complications caused by HS, the underlying mechanisms by which HS modulates the immune response and renders animals susceptible to various health disorders are explained. In addition, future breeding strategies to relieve HS in dairy cattle and improve their welfare while maintaining milk production are discussed.

Mapping of quantitative trait loci for growth traits around the first overwintering period in Songpu mirror carp (Cyprinus carpio L.) cultured in Northeast China

QTL mapping studies of growth traits based on high-density linkage maps in Northeast China has great significance for local enterprises in achieving MAS and improving the selection accuracy of parent fish. Here, we constructed a high-density genetic linkage map with 11,445 single nucleotide polymorphism (SNP) markers in a full-sib F1 family consisting of 120 progenies in Songpu mirror carp (Cyprinus carpio) reared in Northeast China. The consensus map covered 5471.93 centimorgans (cM) across the 50 linkage groups with an average resolution of 0.54 cM. Around the first overwintering period, a total of 15 QTLs for growth traits were identified on five LGs (LG7, LG8, LG14, LG30, and LG41). All of them were responsible for body weight (BW) at both 150 (before overwintering) and 350 (after overwintering) days, explaining 9.8–17.9 % of the phenotypic variation (PV). Two major-effect QTLs were detected on LG30, which explained 16.5 % and 16.4 % (qTL9–30), and 15.8 % and 17.9 % (qTL10–30) of the PV at 150 and 350 days, respectively. In addition, 15 loci were identified for 4 growth traits other than BW at both time points, including 6 loci for body length (BL), 7 loci for body height (BH), 3 loci for body thickness (BT) and 5 loci for head length (HL). These loci explained PV ranging from 15.9 % to 21.2 % for BL, 9.3–19.6 % for BH, 9.6–15.5 % for BT, and 10.6–18.1 % for HL. Nine candidate genes (IGF1b, LEPb, PACAP1a, GHSR1a, PPSS2, IRS1, APOAIb, IRS2b and ADSS1) were identified, five of which were directly related to growth hormone (GH), including IGF1b, PACAP1a, GHSR1a, PPSS2 and IRS1. Notably, three genes (GHSR1a, PPSS2 and IRS1) were derived from two major-effect QTLs (qTL9–30 and qTL10–30). In conclusion, these novel findings may shed light on early selection of growth traits of common carp cultured in Northeast China and other relatively high-latitude regions.

Parental Polymorphism between Samba Mahsuri and False Smut Tolerant Landraces using SSR and InDel Markers

In the present study, 868 SSR and 475 InDel markers were selected to study parental polymorphism of two different crosses between recipient parent Samba Mahsuri and false smut donor linesIC379047 and IC334233 at ICAR-Indian Institute of Rice Research, Rajendranagar, Hyderabad. Out of 1343 markers used for parental polymorphism, 100 markers were polymorphic between parental lines Samba Mahsuri and landrace IC379047 and the total polymorphism percentage recorded was 7.44%. Ninety-nine markers exhibited polymorphism between parental lines Samba Mahsuri and IC334233 and 7.37% of total polymorphism percentage was recorded between the parents. The identified polymorphic markers could be further used for QTL mapping studies in false smut resistance.

High-resolution structural variants catalogue in a large-scale whole genome sequenced bovine family cohort data

BackgroundStructural variants (SVs) are chromosomal segments that differ between genomes, such as deletions, duplications, insertions, inversions and translocations. The genomics revolution enabled the discovery of sub-microscopic SVs via array and whole-genome sequencing (WGS) data, paving the way to unravel the functional impact of SVs. Recent human expression QTL mapping studies demonstrated that SVs play a disproportionally large role in altering gene expression, underlining the importance of including SVs in genetic analyses. Therefore, this study aimed to generate and explore a high-quality bovine SV catalogue exploiting a unique cattle family cohort data (total 266 samples, forming 127 trios).ResultsWe curated 13,731 SVs segregating in the population, consisting of 12,201 deletions, 1,509 duplications, and 21 multi-allelic CNVs (> 50-bp). Of these, we validated a subset of copy number variants (CNVs) utilising a direct genotyping approach in an independent cohort, indicating that at least 62% of the CNVs are true variants, segregating in the population. Among gene-disrupting SVs, we prioritised two likely high impact duplications, encompassing ORM1 and POPDC3 genes, respectively. Liver expression QTL mapping results revealed that these duplications are likely causing altered gene expression, confirming the functional importance of SVs. Although most of the accurately genotyped CNVs are tagged by single nucleotide polymorphisms (SNPs) ascertained in WGS data, most CNVs were not captured by individual SNPs obtained from a 50K genotyping array.ConclusionWe generated a high-quality SV catalogue exploiting unique whole genome sequenced bovine family cohort data. Two high impact duplications upregulating the ORM1 and POPDC3 are putative candidates for postpartum feed intake and hoof health traits, thus warranting further investigation. Generally, CNVs were in low LD with SNPs on the 50K array. Hence, it remains crucial to incorporate CNVs via means other than tagging SNPs, such as investigation of tagging haplotypes, direct imputation of CNVs, or direct genotyping as done in the current study. The SV catalogue and the custom genotyping array generated in the current study will serve as valuable resources accelerating utilisation of full spectrum of genetic variants in bovine genomes.

3D-GBS: a universal genotyping-by-sequencing approach for genomic selection and other high-throughput low-cost applications in species with small to medium-sized genomes

Despite the increased efficiency of sequencing technologies and the development of reduced-representation sequencing (RRS) approaches allowing high-throughput sequencing (HTS) of multiplexed samples, the per-sample genotyping cost remains the most limiting factor in the context of large-scale studies. For example, in the context of genomic selection (GS), breeders need genome-wide markers to predict the breeding value of large cohorts of progenies, requiring the genotyping of thousands candidates. Here, we introduce 3D-GBS, an optimized GBS procedure, to provide an ultra-high-throughput and ultra-low-cost genotyping solution for species with small to medium-sized genome and illustrate its use in soybean. Using a combination of three restriction enzymes (PstI/NsiI/MspI), the portion of the genome that is captured was reduced fourfold (compared to a “standard” ApeKI-based protocol) while reducing the number of markers by only 40%. By better focusing the sequencing effort on limited set of restriction fragments, fourfold more samples can be genotyped at the same minimal depth of coverage. This GBS protocol also resulted in a lower proportion of missing data and provided a more uniform distribution of SNPs across the genome. Moreover, we investigated the optimal number of reads per sample needed to obtain an adequate number of markers for GS and QTL mapping (500–1000 markers per biparental cross). This optimization allows sequencing costs to be decreased by ~ 92% and ~ 86% for GS and QTL mapping studies, respectively, compared to previously published work. Overall, 3D-GBS represents a unique and affordable solution for applications requiring extremely high-throughput genotyping where cost remains the most limiting factor.

A polygenic basis for birth weight in a wild population of red deer (Cervus elaphus).

The genetic architecture of traits under selection has important consequences for the response to selection and potentially for population viability. Early QTL mapping studies in wild populations have reported loci with large effect on trait variation. However, these results are contradicted by more recent genome-wide association analyses, which strongly support the idea that most quantitative traits have a polygenic basis. This study aims to re-evaluate the genetic architecture of a key morphological trait, birth weight, in a wild population of red deer (Cervus elaphus), using genomic approaches. A previous study using 93 microsatellite and allozyme markers and linkage mapping on a kindred of 364 deer detected a pronounced QTL on chromosome 21 explaining 29% of the variance in birth weight, suggesting that this trait is partly controlled by genes with large effects. Here, we used data for more than 2,300 calves genotyped at >39,000 SNP markers and two approaches to characterise the genetic architecture of birth weight. First, we performed a genome-wide association (GWA) analysis, using a genomic relatedness matrix to account for population structure. We found no SNPs significantly associated with birth weight. Second, we used genomic prediction to estimate the proportion of variance explained by each SNP and chromosome. This analysis confirmed that most genetic variance in birth weight was explained by loci with very small effect sizes. Third, we found that the proportion of variance explained by each chromosome was slightly positively correlated with its size. These three findings highlight a highly polygenic architecture for birth weight, which contradicts the previous QTL study. These results are probably explained by the differences in how associations are modelled between QTL mapping and GWA. Our study suggests that models of polygenic adaptation are the most appropriate to study the evolutionary trajectory of this trait.

High-Throughput Association Mapping in Brassica napus L.: Methods and Applications.

Oil seed rape (Braasica napus L.) is ranked second among oil seed crops cultivated globally for edible oil for human, and seed cake for animal consumption. Recent genetic and genomics advancements highlighted the diversity that exists within B. napus, which is largely discovered using the most promising genetic markers called single nucleotide polymorphism (SNP). Their calling rate is also enhanced to ~100 folds after the continuous advancements in the next generation sequencing (NGS) technologies. As the high throughput of NGS resulted in multi-Giga bases data, the detailed quality control (QC) prior to downstream analyses is a pre-requisite. It mainly involved the removal of false positives, missing proportions, filtering of low-quality SNPs, and adjustments of minor-allele frequency and heterozygosity. After marker-trait association, for conformation of target SNPs, validations of SNPs can be performed using various methods, especially allele-specific PCR assay-based methods have been utilized for SNP genotyping of genes targeting agronomic traits and somaclonal variations occurred during transgenic studies. In the present study, the authors mainly argue on the genotypic progress, and pipelines/methods that are being used for detection, calling, filtering, and validation of SNPs. Also, insight is provided into the application of SNPs in linkage and association mapping, including QTL mapping and genome-wide association studies targeting mainly developmental traits related to the root system and plant architecture, flowering time, silique, and oil quality. Briefly, the present study provides the recent information and recommendations on the SNP genotyping methods and its applications, which can be useful for marker-assisted breeding in B. napus and other crops.

Genome Survey Sequencing and Genetic Background Characterization of Ilex chinensis Sims (Aquifoliaceae) Based on Next-Generation Sequencing

Ilex chinensis Sims. is an evergreen arbor species with high ornamental and medicinal value that is widely distributed in China. However, there is a lack of molecular and genomic data for this plant, which severely restricts the development of its relevant research. To obtain the whole reference genome, we first conducted a genome survey of I. chinensis by next-generation sequencing (NGS) to perform de novo whole-genome sequencing. As a result, our estimates using k-mer and flow cytometric analysis suggested the genome size of I. chinensis to be around 618-655 Mb, with the GC content, heterozygous rate, and repeat sequence rate of 37.52%, 1.1%, and 38%, respectively. A total of 334,649 microsatellite motifs were detected from the I. chinensis genome data, which will provide basic molecular markers for germplasm characterization, genetic diversity, and QTL mapping studies for I. chinensis. In summary, the I. chinensis genome is complex with high heterozygosity and few repeated sequences. Overall, this is the first report on the genome features of I. chinensis, and the information may lay a strong groundwork for future whole-genome sequencing and molecular breeding studies of this species.

Genome-Wide SNP Markers Accelerate Perennial Forest Tree Breeding Rate for Disease Resistance through Marker-Assisted and Genome-Wide Selection.

The ecological and economic importance of forest trees is evident and their survival is necessary to provide the raw materials needed for wood and paper industries, to preserve the diversity of associated animal and plant species, to protect water and soil, and to regulate climate. Forest trees are threatened by anthropogenic factors and biotic and abiotic stresses. Various diseases, including those caused by fungal pathogens, are one of the main threats to forest trees that lead to their dieback. Genomics and transcriptomics studies using next-generation sequencing (NGS) methods can help reveal the architecture of resistance to various diseases and exploit natural genetic diversity to select elite genotypes with high resistance to diseases. In the last two decades, QTL mapping studies led to the identification of QTLs related to disease resistance traits and gene families and transcription factors involved in them, including NB-LRR, WRKY, bZIP and MYB. On the other hand, due to the limitation of recombination events in traditional QTL mapping in families derived from bi-parental crosses, genome-wide association studies (GWAS) that are based on linkage disequilibrium (LD) in unstructured populations overcame these limitations and were able to narrow down QTLs to single genes through genotyping of many individuals using high-throughput markers. Association and QTL mapping studies, by identifying markers closely linked to the target trait, are the prerequisite for marker-assisted selection (MAS) and reduce the breeding period in perennial forest trees. The genomic selection (GS) method uses the information on all markers across the whole genome, regardless of their significance for development of a predictive model for the performance of individuals in relation to a specific trait. GS studies also increase gain per unit of time and dramatically increase the speed of breeding programs. This review article is focused on the progress achieved in the field of dissecting forest tree disease resistance architecture through GWAS and QTL mapping studies. Finally, the merit of methods such as GS in accelerating forest tree breeding programs is also discussed.

Consensus genomic regions associated with grain protein content in hexaploid and tetraploid wheat.

A meta-analysis of QTLs associated with grain protein content (GPC) was conducted in hexaploid and tetraploid wheat to identify robust and stable meta-QTLs (MQTLs). For this purpose, as many as 459 GPC-related QTLs retrieved from 48 linkage-based QTL mapping studies were projected onto the newly developed wheat consensus map. The analysis resulted in the prediction of 57 MQTLs and 7 QTL hotspots located on all wheat chromosomes (except chromosomes 1D and 4D) and the average confidence interval reduced 2.71-fold in the MQTLs and QTL hotspots compared to the initial QTLs. The physical regions occupied by the MQTLs ranged from 140 bp to 224.02 Mb with an average of 15.2 Mb, whereas the physical regions occupied by QTL hotspots ranged from 1.81 Mb to 36.03 Mb with a mean of 8.82 Mb. Nineteen MQTLs and two QTL hotspots were also found to be co-localized with 45 significant SNPs identified in 16 previously published genome-wide association studies in wheat. Candidate gene (CG) investigation within some selected MQTLs led to the identification of 705 gene models which also included 96 high-confidence CGs showing significant expressions in different grain-related tissues and having probable roles in GPC regulation. These significantly expressed CGs mainly involved the genes/gene families encoding for the following proteins: aminotransferases, early nodulin 93, glutamine synthetases, invertase/pectin methylesterase inhibitors, protein BIG GRAIN 1-like, cytochrome P450, glycosyl transferases, hexokinases, small GTPases, UDP-glucuronosyl/UDP-glucosyltransferases, and EamA, SANT/Myb, GNAT, thioredoxin, phytocyanin, and homeobox domains containing proteins. Further, eight genes including GPC-B1, Glu-B1-1b, Glu-1By9, TaBiP1, GSr, TaNAC019-A, TaNAC019-D, and bZIP-TF SPA already known to be associated with GPC were also detected within some of the MQTL regions confirming the efficacy of MQTLs predicted during the current study.

Linkage QTL Mapping and Genome-Wide Association Study on Resistance in Chickpea to Pythium ultimum.

The soilborne oomycete plant pathogen Pythium ultimum causes seed rot and pre-emergence damping-off of chickpea (Cicer arietinum L.). The pathogen has been controlled for several decades using the fungicide metalaxyl as seed treatment but has re-emerged as a severe problem with the detection of metalaxyl-resistant isolates of the pathogen from infested fields in the United States Pacific Northwest. The objective of this study was to identify genetic markers and candidate genes associated with resistance to P. ultimum in an interspecific recombinant inbred line population (CRIL-7) derived from a cross between C. reticulatum (PI 599072) x C. arietinum (FLIP 84-92C) and conduct genome-wide association studies (GWAS) for disease resistance using a chickpea diversity panel consisting of 184 accessions. CRIL-7 was examined using 1029 SNP markers spanning eight linkage groups. A major QTL, “qpsd4-1,” was detected on LG 4 that explained 41.8% of phenotypic variance, and a minor QTL, “qpsd8-1,” was detected on LG8 that explained 4.5% of phenotypic variance. Seven candidate genes were also detected using composite interval mapping including several genes previously associated with disease resistance in other crop species. A total of 302,902 single nucleotide polymorphic (SNP) markers were used to determine population structure and kinship of the diversity panel. Marker–trait associations were established by employing different combinations of principal components (PC) and kinships (K) in the FarmCPU model. Genome-wide association studies detected 11 significant SNPs and seven candidate genes associated with disease resistance. SNP Ca4_1765418, detected by GWAS on chromosome 4, was located within QTL qpsd4-1 that was revealed in the interspecific CRIL-7 population. The present study provides tools to enable MAS for resistance to P. ultimum and identified genomic domains and candidate genes involved in the resistance of chickpea to soilborne diseases.

Identification and Characterization of Resistance Loci to Wheat Leaf Rust and Stripe Rust in Afghan Landrace "KU3067".

Leaf rust and stripe rust are important wheat diseases worldwide causing significant losses where susceptible varieties are grown. Resistant cultivars offer long-term control and reduce the use of hazardous chemicals, which can be detrimental to both human health and the environment. Land races have been a valuable resource for mining new genes for various abiotic and biotic stresses including wheat rusts. Afghan wheat landrace “KU3067” displayed high seedling infection type (IT) for leaf rust and low IT for stripe rust; however, it displayed high levels of field resistance for both rusts when tested for multiple seasons against the Mexican rust isolates. This study focused on identifying loci-conferring seedling resistance to stripe rust, and also loci-conferring adult plant resistance (APR) against the Mexican races of leaf rust and stripe rust. A backcrossed inbred line (BIL) population advanced to the BC1F5 generation derived from the cross of KU3067 and Apav (triple rust susceptible line) was used for both, inheritance and QTL mapping studies. The population and parents were genotyped with Diversity Arrays Technology-genotyping-by-sequencing (DArT-Seq) and phenotyped for leaf rust and stripe rust response at both seedling and adult plant stages during multiple seasons in Mexico with relevant pathotypes. Mapping results identified an all-stage resistance gene for stripe rust, temporarily designated as YrKU, on chromosome 7BL. In total, six QTL-conferring APR to leaf rust on 1AS, 2AL, 4DL, 6BL, 7AL, and 7BL, and four QTL for stripe rust resistance on 1BS, 2AL, 4DL, and 7BL were detected in the analyses. Among these, pleiotropic gene Lr67/Yr46 on 4DL with a significantly large effect is the first report in an Afghan landrace-conferring resistance to both leaf and stripe rusts. QLr.cim-7BL/YrKU showed pleiotropic resistance to both rusts and explained 7.5–17.2 and 12.6–19.3% of the phenotypic variance for leaf and stripe rusts, respectively. QYr.cim-1BS and QYr.cim-2AL detected in all stripe environments with phenotypic variance explained (PVE) 12.9–20.5 and 5.4–12.5%, and QLr.cim-6BL are likely to be new. These QTL and their closely linked markers will be useful for fine mapping and marker-assisted selection (MAS) in breeding for durable resistance to multiple rust diseases.

Meta-QTLs for multiple disease resistance involving three rusts in common wheat (Triticum aestivum L.).

In wheat, multiple disease resistance meta-QTLs (MDR-MQTLs) and underlying candidate genes for the three rusts were identified which may prove useful for development of resistant cultivars. Rust diseases in wheat are a major threat to global food security. Therefore, development of multiple disease-resistant cultivars (resistant to all three rusts) is a major goal in all wheat breeding programs worldwide. In the present study, meta-QTLs and candidate genes for multiple disease resistance (MDR) involving all three rusts were identified using 152 individual QTL mapping studies for resistance to leaf rust (LR), stem rust (SR), and yellow rust (YR). From these 152 studies, a total of 1,146 QTLs for resistance to three rusts were retrieved, which included 368 QTLs for LR, 291 QTLs for SR, and 487 QTLs for YR. Of these 1,146 QTLs, only 718 QTLs could be projected onto the consensus map saturated with 2, 34,619 markers. Meta-analysis of the projected QTLs resulted in the identification of 86 MQTLs, which included 71 MDR-MQTLs. Ten of these MDR-MQTLs were referred to as the 'Breeders' MQTLs'. Seventy-eight of the 86 MQTLs could also be anchored to the physical map of the wheat genome, and 54 MQTLs were validated by marker-trait associations identified during earlier genome-wide association studies. Twenty MQTLs (including 17 MDR-MQTLs) identified in the present study were co-localized with 44 known R genes. In silico expression analysis allowed identification of several differentially expressed candidate genes (DECGs) encoding proteins carrying different domains including the following: NBS-LRR, WRKY domains, F-box domains, sugar transporters, transferases, etc. The introgression of these MDR loci into high-yielding cultivars should prove useful for developing high yielding cultivars with resistance to all the three rusts.

ATP-dependent DNA helicase (TaDHL), a Novel Reduced-Height (Rht) Gene in Wheat.

In wheat, a series of dwarf and semi-dwarf plant varieties have been developed and utilized worldwide since the 1960s and caused the ‘Green Revolution’. To date, 25 reduced-height (Rht) genes have been identified, but only several genes for plant height (PH) have been isolated previously. In this study, we identified a candidate gene, ATP-dependent DNA helicase (TaDHL-7B), for PH via QTL mapping and genome-wide association study (GWAS) methods. We knocked out this gene using the CRISPR/Cas9 system in variety ‘Fielder’. Two homozygous mutant genotypes, AAbbDD (−5 bp) and AAbbDD (−1 bp), were obtained in the T2 generation. The PH values of AAbbDD (−5 bp) and AAbbDD (−1 bp) were significantly reduced compared with the wild-type (WT, ‘Fielder’), indicating that TaDHL-7B is a novel Rht gene that controls the PH. This is the first time that a PH gene of wheat has been isolated with a non-hormone pathway, providing a new insight into the genetic control of PH. The TaDHL gene reduced the PH without a yield penalty. It could be used to improve the lodging resistance and yield in wheat breeding programs.

Bruchid Resistance Study through Bulked Segregant Analysis: Used as a Preliminary Step for Next-Generation Sequencing

Seed beetles, commonly known as bruchids, are serious insect pests of Indian pulses inflicting high damage during storage. Earlier, a bruchid resistant rice bean landrace (TNAU Red) from Manipur and a susceptible mung bean variety (VRMGg1) from Tamil Nadu were reported and their inter-specific cross was made in Tamil Nadu Agricultural University. In the present study, seeds from the segregating populations (recombinant inbred lines, RILs) of VRM (Gg)1 and TNAU Red were evaluated for bruchid Callosobruchus maculatus Fabricius resistance following standard methods under laboratory conditions. Bulked segregant analysis (BSA) is an efficient method for quick identification of molecular markers linked to any specific gene or genomic region. BSA significantly reduces the scale and cost by simplifying the procedure compared to conventional method of analyzing the entire population. BSA was carried out using 3 marker systems with an attempt to identify markers associated with the present trait of interest. Two DNA bulks namely resistant bulk (RB) and susceptible bulk (SB) were grouped by pooling equal amount of DNA from 5 each of resistant and susceptible RILs based on bruchid responses such as seed damage (%), mean developmental days (MDP) and adult emergence from seeds. Marker analysis carried out with 41 polymorphic SSRs showed skewed segregation distortion towards the susceptible parent. However, out of 9 RAPDs and 10 ISSRs, 2 RAPD (OPB08 and OPX04) and 1 ISSR (UBC810) primers amplified an allele at 200 - 300 and 300 - 400 bp, respectively, in resistant parent and resistant bulk but not in susceptible parent and susceptible bulk. The amplification of resistant parent allele in resistant bulk may indicate the presence of bruchid resistant gene(s) in the resistant RILs. This experiment was aimed at verifying the presence of bruchid resistant lines carrying resistant gene(s) prior to further association mapping or QTL mapping studies. Further, such type of study can be applied as a preliminary step in NGS technology.
 HIGHLIGHTS
 
 Bruchids are the most damaging storage insect in pulses and other legumes causing great economic losses
 Bulk segregant analysis (BSA) conducted using three marker systems in an attempt to identify markers associated with bruchid resistance
 Categorization of RILs based on bruchid responses such as seed damage (%), mean developmental days (MDP), adult emergence from seeds and scoring done
 Marker analysis using BSA useful for verification of the presence of bruchid resistant lines carrying resistant gene(s) prior to further advanced studies such as QTL mapping, NGS, etc.
 
 GRAPHICAL ABSTRACT

Molecular Research Progress on Xishuangbanna Cucumber (Cucumis sativus L. var. Xishuangbannesis Qi et Yuan): Current Status and Future Prospects

The Xishuangbanna (XIS) cucumber is an important botanical variety, accumulating high levels of β-carotene (700 μg/100 g) in the endocarp of mature fruit compared with normal green/white flesh types (25–50 μg/100 g, fresh weight). β-carotene is an essential precursor of provitamin A synthesis required for human health, thus XIS cucumber is an appealing germplasm for vitamin A breeding programs. In this review, we highlighted the molecular research progress of XIS cucumber as well as the bottlenecks undermining its utilization in genetic breeding. The XIS cucumber was first reported in 1983; thereafter, the literature on XIS cucumber was sporadic until 2012 and 2013 following QTL mapping of the Ore gene and subsequent cloning of the CsaBCH1 gene, respectively. Whereas QTL mapping studies underlying its flowering time and fruit quality related traits have been reported, fine mapping of their candidate genes remains unknown. Cucumber fruits are mainly consumed at fresh immature stage; however, XIS cucumber accumulates β-carotene at mature fruit state, thus limiting the utilization of β-carotene derived from it. In our opinion, we believe that the production and commercialization of immature orange-fleshed cucumber would gain wider acceptance among consumers. Additionally, we highlighted a comprehensive breeding strategy, precisely for enhanced β-carotene accumulation based on prior studies of XIS cucumber coupled with those from other crops. In MAS, we proposed schematic molecular backcross breeding strategy using lines possessing both ore and fft1.1 loci. This review, therefore, provides insights of XIS cucumber research and opportunities for further genetic breeding.