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

Biofortification of grain iron (Fe) and zinc (Zn) in cereals is a cost-effective method to address micronutrient deficiencies. Six metal homeostasis genes (YSL15, NAS2, FRO7, IREG, ZIP2 and VIT1) were pyramided in the wheat cultivar 'PBW343 LrYr' to enhance the content of Fe and Zn in the grain. The crosses of twenty pre-bred wheat-Aegilops genotypes with varying combinations of these genes resulted in the production of 1245 F1 seeds, out of which 680 were germinated. The selection of 103 F1 plants was achieved through the use of ITAP markers and inductively coupled plasma mass spectrometry (ICPMS) to screen for metal homeostasis genes and grain Fe and Zn content respectively. The 151 plants were selected from 103 F2 progeny and these plants were further whittled down to 83 in F3 and 76 in F4, with a final selection of 12 progeny that exhibited a variety of combinations of the six alleles. It is important to note that derivatives such as 'EU19144-500-477' and 'EU19144-506-503' exhibited high grain Fe and Zn contents without a yield penalty. The genes FRO7, IREG and ZIP2 exhibited the significant increase in grain Fe (140.61%) and Zn (122.75%) in the derivative 'EU19144-506-502'. The number of tillers, grain Fe, grain Zn and flag leaf Zn content were negatively correlated with thousand grain weight, while seeds per spike and plant height were positively correlated. [ABSTRACT FROM AUTHOR]

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

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

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

The growth of bivoltine silk production in eastern and north-eastern india lags behind drastically in comparison to southern states due to non-availability of suitable bivoltine hybrids. The major constraints in bivoltine popularization are adverse climatic conditions. to overcome this limitation and to continuously rear bivoltine hybrids in these harsh climatic conditions throughout the year, the present proposal aims to identify robust and abiotic stress tolerant bivoltine silkworm breeds through integrating conventional breeding (directional selection) for improved productivity and advanced genome technologies such as MAS (marker assisted selection), gene specific markers for high humidity and thermo-tolerant DNA markers (Pyx3, Pyx4, S0803 and S0816) for tolerance to high temperature and high humidity and other abiotic factors. These robust hybrids could be reared throughout the year and would provide opportunities for further popularizing and improving bivoltine raw silk production in the eastern and north-eastern region. the present investigation identified wb1hh bivoltine breed to be having highest survival rate and better shell ratio of 18.81% in abiotic stress condition. MAS selection identified DNA markers in all breeds and among them WB1HH showed all four markers, confirming the genetic ability of the breed for tolerance to high temperature and humidity. [ABSTRACT FROM AUTHOR]

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

Introduction Melon (Cucumis melo L.) is a diploid plant with (2n = 2x = 24) chromosomes, dicotyledonous and annual, which has been receiving lots of attention for its biological characteristics and economic value for a long time. Iran with production of about 1.6 million tons per year ranks third in melon production in the world after China and Turkey. Vascular wilt caused by the soil borne fungus Fusarium oxysporum f. sp. melonis is one of the most important diseases causing damage to the melon plant. Due to the survival of this fungus in the form of chlamydospores in the soil and plant debris its control has been a difficult challenge so that, the only way to deal with this disease is to use resistant cultivars. The present study was conducted to characterize morphologically different melon cultivars with varying levels of resistance against Fusarium vascular wilt. Furthermore, the presence pattern of two MRGH genes belonging to the MRGH21 linkage group was tracked in the genome of the melon line, and their variations were defined. Moreover, the potential for using these genes in gene-assisted selection was investigated. Materials and Methods Five different varieties of melon named Charentais T, Charentais Fom1, Charentais Fom2, BG-5384 and the local cultivar Khatouni were grown under greenhouse conditions. Different characteristics of the plant, including leaf shape, male flowers, female flowers and normal flowers, and after harvesting the fruits, fruit weight, fruit diameter and length, diameter of flesh and middle cavity. The differentiation of resistant and sensitive cultivars was investigated based on the evaluated morphological traits. Additionally, the presence patterns of resistance genes were examined in the genomic data of the aforementioned melon cultivars. The genomic analysis of melons aimed to locate the MRGH21 linkage group, which carries several resistance genes. The sequence of this linkage group was tracked from two gene bank databases in NCBI and MELONOMICS database. Results Based on the obtained results, although it was possible to differentiate melon cultivars based on morphological traits, but since the study of these traits in the evaluation of a large number of samples in selective studies is a very time-consuming and costly task. Therefore, the presence pattern of resistance genes were analyzed in the genomic data of different melon cultivars. The sequence between two genes MRGH12 and MRGH13 including MRGH21 linkage group as one of the linkage groups carrying a number of resistance genes on Ch09 chromosome was retrieved form two gene bank databases in NCBI and MELONOMICS. Due to the presence of multiple point mutations in the genomic data, the MRGH13 gene sequence was selected for investigation in melon cultivars. Specific primers, PSh21-F/R, were designed to track part of this gene's sequence. The tracking results showed that a single specific band, corresponding to the expected size, could be detected in the cultivars Charentais Fom1 and BG-5384. Sequence analysis using the InterPro network tool confirmed the possible role of the protein coded by the MRGH13 gene. It was identified as a member of the protein family carrying leucine-rich repeat sequences, including the TIR, NB-ARC, and LRR domains. Discussion Attaining suitable markers to distinguish melon cultivars resistant to Fusarium wilt disease can support the development of breeding programs with higher accuracy and speed. The results of the present study showed that based on the morphological traits such as leaf shape, the presence of full flowers, and the number of petals, some differences can be observed between different melon cultivars, but the noteworthy point is that in selection programs searching for these morphological traits will be a very time-consuming and expensive task due to the large number of investigated samples. Therefore, if molecular markers related to the resistance trait are available, the efficiency of breeding programs is expected to increase significantly. In the present study MRGH13 gene was selected to be investigated for tracking in melon cultivars and specific primers were designed to track part of the sequence of this gene. The tracking results showed that a single specific band could be detected in the cultivars Charentais Fom1 and BG-5384. Biological processes related to MRGH13 protein in the QuickGO network tool showed its relevance in the signaling pathway that regulates immune responses. In future studies, it is suggested to evaluate the ability to distinguish resistant cultivars based on resistance genes, including the MRGH13 gene, in a larger number of samples. Moreover, considering to the predicted functions of MRGH13 protein, more investigation on its interaction with other resistance proteins as well as proteins of pathogenic agents can be useful for identification of its functional role in resistance.

Anthracnose caused by Colletotrichum lindemuthianum is one of the most prevalent and severe disease of beans. Anthracnose resistance to most of the prevalent races in the state is provided by Co-5 gene. Therefore, deployment of this gene is more relevant as the lines developed under this study harboring Co-5 gene have potential to impart resistance against prevalent races. Hybridisation between a resistant genotype, TU having bean anthracnose resistance gene Co-5 and elite cultivar Arka Komal was done and further advanced to generate F1, BC1F1, BC2F1 and BC2F2 plants. Co-5 gene linked SCAR marker SAB3 was used for screening of hybridity of F1, BC1F1, BC2F1 and BC2F2 plants/pods. The results of the foreground selection in these plants revealed that out of a population of 50 BC2F2 plants, 36 plants portrayed Co-5 gene. Further foreground selection with SAB3 SCAR marker, revealed lack of segregation in 12 progenies. Screening of these progenies by detached pod and germinated seed dip methods using race 3 of C. lindemuthianum, validated Co-5 resistance in all 12 BC2F3 progenies. All 12 Co-5 gene-positive BC2F4 progenies were evaluated for 17 agronomic traits including 8 qualitative and 9 quantitative traits. Evaluation identified AKTU 19 and AKTU 33 lines that possessed better elite background. These progenies can further be advanced to isolate variety/(ies) directly or as prebred donor of anthracnose resistance gene Co-5 in the future breeding programmes. [ABSTRACT FROM AUTHOR]

Background: SnRK2 plays vital role in responding to adverse abiotic stimuli. The applicability of TaSnRK2.4 and TaSnRK2.9 was investigated to leverage the potential of these genes in indigenous wheat breeding programs. Methods: Genetic diversity was assessed using pre-existing markers for TaSnRK2.4 and TaSnRK2.9. Furthermore, new markers were also developed to enhance their broader applicability. KASP markers were designed for TaSnRK2.4, while CAPS-based markers were tailored for TaSnRK2.9. Results: Analysis revealed lack of polymorphism in TaSnRK2.4 among Pakistani wheat germplasm under study. To validate this finding, available gel-based markers for TaSnRK2.4 were employed, producing consistent results and offering limited potential for application in marker-assisted wheat breeding with Pakistani wheat material. For TaSnRK2.9-5A, CAPS2.9-5A-1 and CAPS2.9-5A-2 markers were designed to target SNP positions at 308 nt and 1700 nt revealing four distinct haplotypes. Association analysis highlighted the significance of Hap-5A-1 of TaSnRK2.9-5A, which exhibited association with an increased number of productive tillers (NPT), grains per spike (GPS), and reduced plant height (PH) under well-watered (WW) conditions. Moreover, it showed positive influence on NPT under WW conditions, GPS under water-limited (WL) conditions, and PH under both WW and WL conditions. High selection intensity observed for Hap-5A-1 underscores the valuable role it has played in Pakistani wheat breeding programs. Gene expression studies of TaSnRK2.9-5A revealed the involvement of this gene in response to PEG, NaCl, low temperature and ABA treatments. Conclusion: These findings propose that TaSnRK2.9 can be effectively employed for improving wheat through marker-assisted selection in wheat breeding efforts. [ABSTRACT FROM AUTHOR]

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

Landraces and indigenous varieties comprise valuable sources of crop species diversity. Their utilization in plant breeding may lead to increased yield and enhanced quality traits, as well as resilience to various abiotic and biotic stresses. Recently, new approaches based on the rapid advancement of genomic technologies such as deciphering of pangenomes, multi-omics tools, marker-assisted selection (MAS), genome-wide association studies (GWAS), and CRISPR/Cas9 gene editing greatly facilitated the exploitation of landraces in modern plant breeding. In this paper, we present a comprehensive overview of the implementation of new genomic technologies and highlight their importance in pinpointing the genetic basis of desirable traits in landraces and indigenous varieties of annual, perennial herbaceous, and woody crop species cultivated in the Mediterranean region. The need for further employment of advanced -omic technologies to unravel the full potential of landraces and indigenous varieties underutilized genetic diversity is also indicated. Ultimately, the large amount of genomic data emerging from the investigation of landraces and indigenous varieties reveals their potential as a source of valuable genes and traits for breeding. The role of landraces and indigenous varieties in mitigating the ongoing risks posed by climate change in agriculture and food security is also highlighted. [ABSTRACT FROM AUTHOR]

Ascochyta blight (AB), caused by a fungal pathogen Ascochyta rabiei is a serious threat to chickpea cultivation. It becomes, thus, imperative to evaluate the existing germplasm against this disease as a foundational step toward crop enhancement. We prepared a potent inoculum of the prevalent local races of the pathogen and assessed the disease resistance of eighty chickpea genotypes containing approved varieties, advance lines etc., against AB. Out of total eighty genotypes, six, fifty six and eleven genotypes correspondingly, were found resistant, tolerant and susceptible. Using the tool of association mapping, we were able to detect 43 marker trait associations (MTAs) for disease severity while 36 MTAs for disease score and many genes related to stress tolerance in both growing seasons. The six resistant genotypes identified in our germplasm can be an excellent source for breeding AB resistant chickpea cultivars. In addition, the significant MTAs linked with AB may assist in the molecular breeding program to develop high yielding disease resistant cultivars of chickpea. [ABSTRACT FROM AUTHOR]

Biotic stress factors cause massive damage to crops and account for major economic losses globally. With the global temperature on the rise, a great threat looms on the global economy and food security as sustainable agriculture is expected to be devastated by larger outbreaks of diseases worldwide. Plants have developed versatile counter-strategies to overcome these stressors. These strategies rely on preformed defense or induced defense responses which, in turn, entail a complex crosstalk among different signaling pathways. Once the presence of a pathogen is detected, the plant host switches on its defense response. Very specific recognition of the invading pathogen is mediated via the detection of their Avr effector proteins by the cognate elements in the plant host, i.e., the R proteins, encoded by R genes. Successful recognition of Avr by the cognate host R proteins sets distinct signaling cascade(s) into motion to activate defense responses. The nucleotide-binding leucine-rich repeat proteins (NB-LRRs or NLRs) represent the major class of R proteins and insights gained regarding their structural complexity and underlying signal transduction has enabled researchers to exploit them for competent introgression of disease resistance in plants against a single or a broad range of pathogens. In addition to conventional breeding, more recent biotechnological interventions have also been employed to develop plants with improved disease resistance with the use of R genes. The domain of R gene-mediated disease resistance has gained much attention from plant breeders and through experimental interventions, many promising opportunities for conferring resistance for effective management of diseases have come forth. This review attempts to summarize the progress made hitherto and focuses on how the knowledge base so created has been used to find out solutions to the major biotic problems occurring throughout the world. [ABSTRACT FROM AUTHOR]

Quantitative trait loci (QTL) mapping is used for the precise localization of genomic regions regulating various traits in plants. Two major QTLs regulating Soil Plant Analysis Development (SPAD) value (qSPAD-7-1) and trichome density (qTric-7-2) in mungbean were identified using recombinant inbred line (RIL) populations (PMR-1-Pusa Baisakhi) on chromosome 7. Functional analysis of QTL region identified 35 candidate genes for SPAD value (16 No) and trichome (19 No) traits. The candidate genes regulating trichome density on the dorsal leaf surface of the mungbean include VRADI07G24840, VRADI07G17780, and VRADI07G15650, which encodes for ZFP6, TFs bHLH DNA-binding superfamily protein, and MYB102, respectively. Also, candidate genes having vital roles in chlorophyll biosynthesis are VRADIO7G29860, VRADIO7G29450, and VRADIO7G28520, which encodes for s-adenosyl-L-methionine, FTSHI1 protein, and CRS2-associated factor, respectively. The findings unfolded the opportunity for the development of customized genotypes having high SPAD value and high trichome density having a possible role in yield and mungbean yellow vein mosaic India virus (MYMIV) resistance in mungbean. [ABSTRACT FROM AUTHOR]

Fusarium wilt is one of the most destructive chickpea diseases worldwide. Race 5 (Foc5) is the most harmful in the Mediterranean basin. The primary objective of this study is to validate a block of six SNP markers previously mapped in Ca2 in a diverse panel of cultivars, advanced and inbred lines phenotyped for resistance to fusarium wilt. Additionally, we aim to assess the effectiveness of using these markers in the selection of resistant Foc5 lines in an ongoing breeding program. The results showed a 100% coincidence between phenotype and expected haplotype in plant material evaluated for Foc5. We also analyzed 67 inbred lines previously phenotyped by different authors for fusarium wilt reaction, though the specific race was not specified. In these accessions, 65.8% of the analyzed lines exhibited complete correspondence between the phenotype and haplotype. Our results suggest that in early generations it is possible to select resistant materials with reliability, leading to the removal of a significant number of lines, thereby reducing costs and facilitating the handling of materials for additional trait evaluations. Functional annotation of genes delimited by the SNP block revealed several genes in the "response to stimulus" category with potential roles in the resistance reaction. [ABSTRACT FROM AUTHOR]

Background: Oil palm (Elaeis guineensis Jacq.) is one of the major oil-producing crops. Improving the quality and increasing the production yield of oil palm have been the primary focuses of both conventional and modern breeding approaches. However, the conventional breeding approach for oil palm is very challenging due to its longevity, which results in a long breeding cycle. Thus, the establishment of marker assisted selection (MAS) for oil palm breeding programs would speed up the breeding pipeline by generating new oil palm varieties that possess high commercial traits. With the decreasing cost of sequencing, Genotyping-by-sequencing (GBS) is currently feasible to many researchers and it provides a platform to accelerate the discovery of single nucleotide polymorphism (SNP) as well as insertion and deletion (InDel) markers for the construction of a genetic linkage map. A genetic linkage map facilitates the identification of significant DNA regions associated with the trait of interest via quantitative trait loci (QTL) analysis. Methods: A mapping population of 112 F1 individuals from a cross of Deli dura and Serdang pisifera was used in this study. GBS libraries were constructed using the double digestion method with HindIII and TaqI enzymes. Reduced representation libraries (RRL) of 112 F1 progeny and their parents were sequenced and the reads were mapped against the E. guineensis reference genome. To construct the oil palm genetic linkage map, informative SNP and InDel markers were used to discover significant DNA regions associated with the traits of interest. The nine traits of interest in this study were fresh fruit bunch (FFB) yield, oil yield (OY), oil to bunch ratio (O/B), oil to dry mesocarp ratio (O/DM) ratio, oil to wet mesocarp ratio (O/WM), mesocarp to fruit ratio (M/F), kernel to fruit ratio (K/F), shell to fruit ratio (S/F), and fruit to bunch ratio (F/B). Results: A total of 2.5 million SNP and 153,547 InDel markers were identified. However, only a subset of 5,278 markers comprising of 4,838 SNPs and 440 InDels were informative for the construction of a genetic linkage map. Sixteen linkage groups were produced, spanning 2,737.6 cM for the maternal map and 4,571.6 cM for the paternal map, with average marker densities of one marker per 2.9 cM and one per 2.0 cM respectively, were produced. A QTL analysis was performed on nine traits; however, only QTL regions linked to M/F, K/F and S/F were declared to be significant. Of those QTLs were detected: two for M/F, four for K/F and one for S/F. These QTLs explained 18.1–25.6% of the phenotypic variance and were located near putative genes, such as casein kinase II and the zinc finger CCCH domain, which are involved in seed germination and growth. The identified QTL regions for M/F, K/F and S/F from this study could be applied in an oil palm breeding program and used to screen palms with desired traits via marker assisted selection (MAS). [ABSTRACT FROM AUTHOR]

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The leaf curl disease (ToLCD), late blight (LB) and root knot nematode (RKN) are the major obstacles for rainy season tomato production all over the world. Several tactics are being considered for the management of these diseases. Reportedly, the most efficient way to manage these multiple diseases is to adopt resistant cultivars. Though, work on development of resistant cultivars against multiple diseases are very confined due to non-availability of the resistant sources. In the present study, BC2F6 population comprising 132 elite tomato lines were evaluated using different screening techniques including marker assisted selection (MAS) during 2019–2020 and 2020–2021. Punjab Chuhhara (check) was used as susceptible for all three diseases, while PVB-4, LBR-10 and NR-14 were the resistant checks for ToLCD, LB and RKN, respectively. The lines which showed resistance and moderately resistance responses under field and artificial conditions were exposed for MAS of major resistant genes (Ty-1, Ty-2, Ty-3, Ph-2, Ph-3 and Mi-1.2). PDRT-104, PDRT-118, PDRT-122, PDRT-124 and PDRT-125 were found to provide multiple disease resistant. There was significant correlation between the phenotypic and genotypic based screening. The resistant lines identified in the present evaluation can be utilized to develop cultivars for potential durable resistance to multiple diseases. [ABSTRACT FROM AUTHOR]

The substitution and insertion mutation in the fatty acid desaturase gene is responsible for increased oleic acid in groundnut. It can be identified by various genotyping assays with allele specific primers. Present study compares the efficiency of three earlier reported genotyping assays to identify the effective and accurate method. A high yielding groundnut variety GJG 33 was crossed with high oleic acid content variety Girnar 4. Both parents and 23 BC2F2 plants were used for genotyping. Allele specific primers assay proposed by Chen et al. (2010), the CAPS marker assay proposed by Chu et al. (2007 and 2009) and the primers assay proposed by Yu et al. (2013) were used for comparisons. The primer pairs reported by Yu et al. (2013) was found to be efficient in terms of time and cost. Hence these primers may be recommended for utilization in marker assisted breeding to evolve high oleic acid content groundnut genotypes.

Quantitative trait loci (QTL) mapping is used for the precise localization of genomic regions regulating various traits in plants. Two major QTLs regulating Soil Plant Analysis Development (SPAD) value (qSPAD-7-1) and trichome density (qTric-7-2) in mungbean were identified using recombinant inbred line (RIL) populations (PMR-1×Pusa Baisakhi) on chromosome 7. Functional analysis of QTL region identified 35 candidate genes for SPAD value (16 No) and trichome (19 No) traits. The candidate genes regulating trichome density on the dorsal leaf surface of the mungbean include VRADI07G24840, VRADI07G17780, and VRADI07G15650, which encodes for ZFP6, TFs bHLH DNA-binding superfamily protein, and MYB102, respectively. Also, candidate genes having vital roles in chlorophyll biosynthesis are VRADIO7G29860, VRADIO7G29450, and VRADIO7G28520, which encodes for s-adenosyl-L-methionine, FTSHI1 protein, and CRS2-associated factor, respectively. The findings unfolded the opportunity for the development of customized genotypes having high SPAD value and high trichome density having a possible role in yield and mungbean yellow vein mosaic India virus (MYMIV) resistance in mungbean.

Background Oil palm (Elaeis guineensis Jacq.) is one of the major oil-producing crops. Improving the quality and increasing the production yield of oil palm have been the primary focuses of both conventional and modern breeding approaches. However, the conventional breeding approach for oil palm is very challenging due to its longevity, which results in a long breeding cycle. Thus, the establishment of marker assisted selection (MAS) for oil palm breeding programs would speed up the breeding pipeline by generating new oil palm varieties that possess high commercial traits. With the decreasing cost of sequencing, Genotyping-by-sequencing (GBS) is currently feasible to many researchers and it provides a platform to accelerate the discovery of single nucleotide polymorphism (SNP) as well as insertion and deletion (InDel) markers for the construction of a genetic linkage map. A genetic linkage map facilitates the identification of significant DNA regions associated with the trait of interest via quantitative trait loci (QTL) analysis. Methods A mapping population of 112 F1 individuals from a cross of Deli dura and Serdang pisifera was used in this study. GBS libraries were constructed using the double digestion method with HindIII and TaqI enzymes. Reduced representation libraries (RRL) of 112 F1 progeny and their parents were sequenced and the reads were mapped against the E. guineensis reference genome. To construct the oil palm genetic linkage map, informative SNP and InDel markers were used to discover significant DNA regions associated with the traits of interest. The nine traits of interest in this study were fresh fruit bunch (FFB) yield, oil yield (OY), oil to bunch ratio (O/B), oil to dry mesocarp ratio (O/DM) ratio, oil to wet mesocarp ratio (O/WM), mesocarp to fruit ratio (M/F), kernel to fruit ratio (K/F), shell to fruit ratio (S/F), and fruit to bunch ratio (F/B). Results A total of 2.5 million SNP and 153,547 InDel markers were identified. However, only a subset of 5,278 markers comprising of 4,838 SNPs and 440 InDels were informative for the construction of a genetic linkage map. Sixteen linkage groups were produced, spanning 2,737.6 cM for the maternal map and 4,571.6 cM for the paternal map, with average marker densities of one marker per 2.9 cM and one per 2.0 cM respectively, were produced. A QTL analysis was performed on nine traits; however, only QTL regions linked to M/F, K/F and S/F were declared to be significant. Of those QTLs were detected: two for M/F, four for K/F and one for S/F. These QTLs explained 18.1–25.6% of the phenotypic variance and were located near putative genes, such as casein kinase II and the zinc finger CCCH domain, which are involved in seed germination and growth. The identified QTL regions for M/F, K/F and S/F from this study could be applied in an oil palm breeding program and used to screen palms with desired traits via marker assisted selection (MAS).

This study investigated the associations between the c.189G > T polymorphism of the insulin receptor substrate-1 (IRS-1) gene and the growth and litter size-related traits in the Native rabbit in Middle Egypt (NMER). One hundred sixty-two NMER rabbits were genotyped by RFLP-PCR using Sau3AI restriction enzyme and the associations of the reported genotypes with body weights at 5th, 6th, 8th, 10th, and 12th week old, body gain, and daily gain plus, the litter size-related traits were determined. Additionally, the genotypic and allelic frequencies, the effective (Ne) and observed (NA) numbers of alleles, observed (Ho) and expected (He) heterozygosity, Hardy-Weinberg equilibrium (HWE), and the decrease in heterozygosity because of inbreeding (FIS) were calculated. Three genotypes; GG, GT, and TT with 0.65, 0.33, and 0.02 frequencies, respectively which fit HWE were reported. These genotypes displayed a marked low FIS value. Significant associations of the genotypes with the body weights, and gains, except at the 5th week old determined with superiority of the GT genotype compared with the other genotypes. All reported litter size-related traits significantly varied among different genotypes. In summary, the c.189G > T SNP of the IRS-1 gene is an effective genetic marker to improve growth performance and litter size traits of the NMER rabbits. [ABSTRACT FROM AUTHOR]

Carotenoid biosynthesis and accumulation are important in determining nutritional and commercial value of crop products. Yellow pigmentation of mature kernels caused by carotenoids is considered a vital quality trait in foxtail millet, an ancient and widely cultivated cereal crop across the world. Genomic regions associated with yellow pigment content (YPC), lutein and zeaxanthin in foxtail millet grains were identified by genome-wide association analysis (GWAS), and SiPSY1 (Phytoene synthase 1 which regulates formation of the 40-carbon backbone of carotenoids) was confirmed as the main contributor to all three components by knockout and overexpression analysis. SiPSY1 was expressed in seedlings, leaves, panicles, and mature seeds, and was subcellularly localized to chloroplasts. Transcription of SiPSY1 in 15 DAP immature grains was responsible for YPC in mature seeds. Selection of SiPSY1 combined with increased YPC in mature grains during domestication of foxtail millet was confirmed. Haplotype analysis suggested that expression level of SiPSY1 could be a selection target for future breeding programs, and a KASP marker was developed for selection of favorable SiPSY1 alleles in breeding. The results of this work will benefit nutritional and commercial improvement of foxtail millet varieties, as well as other cereal crops. [ABSTRACT FROM AUTHOR]

A large number of QTLs controlling important traits in different crops have been mapped but their deployment in the marker assisted selection (MAS) is highly limited. The possible reason is lack of availability of stable QTLs over diverse genetic background and environment. QTL meta-analysis provides an opportunity to compile QTLs from different studies and identify consistent QTLs across genetic background and environments. These meta-QTLs can be targeted for further fine mapping and used for MAS after validation. QTL meta-analysis involve library search for reported QTL studies for a particular trait in a crop and subsequently a consensus linkage map is constructed projecting QTLs from different studies using simple scaling rule. The Confidence Interval (CI) of QTL is estimated on the consensus map using the formula as CI (95): ¼ 530/(Nλ), where CI (95) is the confidence interval at 95 percent probability level, N is the size of mapping population and λ is the proportion of phenotypic variance explained by the concerned QTL. Finally, detected QTLs are projected for cluster analysis to determine the exact number and positions of true QTLs. The utility of this approach will help to detect the stable meta-QTLs that will be further helpful to identify candidate genes and their application in MAS program. [ABSTRACT FROM AUTHOR]

Tomato is one of the worldwide major foods consumed fresh, cooked, or processed. Mineral elements, vitamins, and antioxidant content of tomatoes are of interest because of their nutritional value and beneficial health effects. The present study was performed to evaluate the macro- and micro-elements contents of leaves and fruits of seven wild tomato species, in addition to morphological traits. Wild tomato species had variations for all elements in fruits. Coefficient of variation was calculated for elements as 18.50 to 94.32% for potassium and phosphor, respectively. Most of the wild tomato species had higher content of all mineral elements than cultivated tomato. Resistance genes (Frl, I-2, I-3, Mi-3, Pto Ty-1, Ty-3 and Sw-5) of wild tomato species were screened using molecular markers. LA1971, with six resistant genes, and LA1393 and LA1777, with five resistant genes, were considered the most promising parental candidates for breeding. The results of the analysis of mineral elements of seven wild tomatoes species are useful for future tomato breeding. [ABSTRACT FROM AUTHOR]

Several molecular markers have been used for various purposes since the beginning of contemporary molecular technology: genetic resource characterization, core genetic resource collection, mapping, marker-assisted selection and marker-assisted backcrossing etc. The variety of all plant species, their genetic make-up and the environments in which they dwell are considered to be components of biological diversity. Plant classification and identification can be done most quickly and simply using morphological examination. It has been established that molecular markers are effective instruments for evaluating genetic diversity in groups and individuals as well as germplasm resources. To preserve biodiversity more than just genetic testing and DNA polymorphism detection are needed. It examines significant issues regarding managing plant germplasm both ex-situ and in-situ in order to support decision-making. Significant progress has been made in recent years in mapping, tagging and isolating many important genes for agriculture using molecular markers like (Restriction Fragment Length Polymorphisms, Random Amplified Polymorphic DNAs, Amplified Fragment Length Polymorphisms, Simple Sequence Repeats and Single Nucleotide Polymorphism). Each marking technique has unique benefits, drawbacks and applications. If one was aware of the presence of relevant traits, genes and alleles one might make judgments on the extension of accessions and the preservation of seed stocks to meet an anticipated rise in demand for materials. By including genotypes with well-known and useful genes and alleles in the core collections and then breeders can use them. Utilizing crop plant genetic resources will be simpler as a result increasing their potential. [ABSTRACT FROM AUTHOR]

Enhanced bioavailability of cis-isomers of lycopene, accumulated in orange-fruited tangerine mutant has broadened the scope of nutritional enrichment in tomato. At the same time, advancements in the field of marker assisted selection (MAS) have made the stacking of multiple desirable alleles through molecular breeding to develop superior tomato genotypes possible. Here we report seedling stage MAS from 146 F2 plants, to identify 3 superior performing, root knot disease resistant orange-fruited segregants. In the selected segregants, fruit weight ranged from 39.2 to 54.6 g, pericarp thickness ranged from 4.56 to 6.05 mm and total soluble solid content ranged from 3.65 to 4.87° Brix. Presence of parental diversity allowed identification of the other desirable alleles of the genes governing late blight and mosaic disease resistance, growth habit (determinate and indeterminate) as well as fruit elongation and firmness. Resistance to root knot disease of the selected 3 segregants was also validated through a unique method employing in vitro rooted stem cuttings subjected to artificial inoculation, where the resistant parent and the selected segregants developed no galls in comparison to ~ 24 galls developed in the susceptible parent. The selected segregants form the base for development of multiple disease resistant, nutritionally enriched orange-fruited determinate/indeterminate tomato lines with superior fruit quality. The study also highlights the utility of early generation MAS for detailed characterization of segregants, through which multiple desirable alleles can be precisely targeted and fixed to develop superior tomato genotypes. [ABSTRACT FROM AUTHOR]

The article discusses research which described the development and evaluated cross breed hybrids for Bombyx mori bidensovirus (BmBDV) resistance through molecular marker assisted selection. The study details the screening and selection of silkworm breeds for BmBDV resistance, isolation of genomic DNA, BmBDV resistant marker analysis and BmBDV inoculum preparation. It identifies the economic traits of BmBDV resistant cross breeds, mortality rate and survival rate for BmBDV infection.

Hybrid rice technology offers a great promise to produce 15% to 20% more yield than pure line varieties. The success of hybrid rice hinges on developing superior parental lines. To improve the blast resistance of hybrid rice parental line RP5933‐1‐19‐2R, crosses were made with donors of two major blast resistance genes namely, Pi54 (Tetep) and Pi9 (IR71033–121‐15) and the resulting F1s were confirmed for their hybridity by using Pi54MAS and NMSMPi9‐1 genic markers. The confirmed F1s were intercrossed to obtain ICF1s and selected positive plants by markers were backcrossed to the recurrent parent, as well as selfed for advancing further to BC1F3 and ICF4 generations. The segregating plants were phenotyped for blast resistance at Uniform Blast Nursery. The identified complete restorers namely, RP 6619‐1, RP 6616‐26, RP 6619‐3 and RP 6619‐11 with Pi9 and Pi54 genes would serve as donors for broad spectrum blast resistance. This could ultimately lead to the development of new rice hybrids with improved resistance to blast disease, which is crucial for sustainable rice production and food security. [ABSTRACT FROM AUTHOR]

Globodera rostochiensis resistance has been an important trait in potato (Solanum tuberosum) breeding for decades. Our aim was to complement phenotypic testing with genetic marker analysis. We analysed the re‐ sults of G. rostochiensis resistance greenhouse testing in 4601 tubers of 2918 breeding clones from 11 years. Applicability of H1 gene markers TG689 and 57R was compared. We implemented the latter with the posi‐ tive predictive value of 99.1% and negative predictive value of 60.0% into the breeding scheme. The 57R marker alleles of 22 Estonian cultivars and 470 breeding clones were determined. Two unique 57R alleles, 57R-887 and 57R-1155, were found in Estonian cultivar ‘Anti’. The 887 bp allele has two deletions (14 bp and 490 bp) accompanied by several other indels and SNPs within the 57R marker region. The 1155 bp allele has three deletions (7 bp, 20 bp and 210 bp) accompanied by several other indels and SNPs within the same region. Partial resistance to G. rostochiensis in ‘Anti’ suggests that the newly described alleles could affect the H1-mediated resistance directly or indirectly. [ABSTRACT FROM AUTHOR]

Wheat (Triticum aestivum L.) diseases are major factors responsible for substantial yield losses worldwide, which affect global food security. For a long time, plant breeders have been struggling to improve wheat resistance against major diseases by selection and conventional breeding techniques. Therefore, this review was conducted to shed light on various gaps in the available literature and to reveal the most promising criteria for disease resistance in wheat. However, novel techniques for molecular breeding in the past few decades have been very fruitful for developing broad-spectrum disease resistance and other important traits in wheat. Many types of molecular markers such as SCAR, RAPD, SSR, SSLP, RFLP, SNP, and DArT, etc., have been reported for resistance against wheat pathogens. This article summarizes various insightful molecular markers involved in wheat improvement for resistance to major diseases through diverse breeding programs. Moreover, this review highlights the applications of marker assisted selection (MAS), quantitative trait loci (QTL), genome wide association studies (GWAS) and the CRISPR/Cas-9 system for developing disease resistance against most important wheat diseases. We also reviewed all reported mapped QTLs for bunts, rusts, smuts, and nematode diseases of wheat. Furthermore, we have also proposed how the CRISPR/Cas-9 system and GWAS can assist breeders in the future for the genetic improvement of wheat. If these molecular approaches are used successfully in the future, they can be a significant step toward expanding food production in wheat crops. [ABSTRACT FROM AUTHOR]

The pomegranate (Punica granatum L.) is one of the fruit species with the oldest cultural history. There are many traits to determine the quality of pomegranate fruits. Among them, soft-seeded feature of pomegranate fruit is important trait for the market value of the fruit. For this reason, the demand for pomegranate varieties with soft seeds has been increasing, especially in recent years. In this study, molecular markers associated with seed hardness were developed to distinguish pomegranate cultivars with soft-seeded feature based on genomic DNA at the early stages of the pomegranate breeding process. For this purpose, pomegranate genotypes and/or cultivars from the population involved in reciprocal crosses of hard-seeded Ernar, medium-hard-seeded Hicaznar, and soft-seeded Fellahyemez cultivars were grouped as soft-seeded or hard-seeded. Further, leaf samples were collected from individuals belonging to each group. Then, the genomic DNA was isolated from each plant separately, and equal amount of genomic DNA from individuals with the similar seed hardness were mixed for bulked segregant analysis (BSA). The bulked genomic DNAs of opposite characters were analyzed by polymerase chain reaction (PCR) using random decamer primers to develop random amplified polymorphic DNA (RAPD) markers associated with soft-seeded or hard-seeded pomegranates. A total of three RAPD markers were determined to distinguish the individuals having soft- or hard-seeded pomegranate genotypes and/or cultivars. As a result of the comparison of the DNA sequences of these RAPD markers, insertion-deletions (inDels) primers were designed to developed and validate a PCR assay to distinguish the soft- and hard-seeded pomegranate genotypes/cultivars from each other. The molecular markers developed in this study will enable us to distinguish soft-seeded pomegranate types easily in a short time at the early stages of the pomegranate breeding programs. [ABSTRACT FROM AUTHOR]