Polymorphic SSR Markers Research Articles

Population Study Reveals Genetic Variation and Introgression of Four Deciduous Oaks at the Junction between Taihang Mountain and Yanshan Mountain

Oaks (Quercus spp.) are considered model plants for studying plant evolution and natural gene introgression. Beijing area is at the junction between Taihang Mountain and Yanshan Mountain, and it is an overlapping distribution area of several deciduous oaks native to China. Interspecific hybridization often occurs in sympatric sibling species, resulting in blurred interspecific boundaries and hindering the development of breeding. To have better improvement and protection of these oaks, it is urgently necessary to evaluate the genetic diversity and population structure of these oak species. In this study, we collected eleven populations of four oak species (Q. variabilis, Q. mongolica, Q. dentata and Q. aliena) in the Beijing area. By using the polymorphic SSR markers, we analyzed the genetic variation of the collected 400 individuals, investigated the population structure, and found gene introgression events. Q. variabilis had a clearer genetic background as compared to the other three species. Q. mongolica had a more frequent gene introgression with Q. dentata and Q. aliena. Our data reveal the introgression and genetic diversity of the four oak species native to the Beijing area, laying the foundation for conducting an oak germplasm nursery with a clear genetic background for protection and further improvement.

Quantitative Trait Locus Mapping for Fusarium Wilt Race 4 Resistance in a Recombinant Inbred Line Population of Pima Cotton (Gossypium Barbadense).

Fusarium oxysporum f. sp. vasinfectum (FOV) race 4 (FOV4) causes seedling death immediately after emergence, in addition to leaf chlorosis and necrosis, vascular discoloration, plant wilting, defoliation, and plant death at late stages. Breeding for FOV4 resistance is the most cost effective management method. In this study, 163 recombinant inbred lines (RILs) of FOV4-resistant Pima S-6 × susceptible 89590, together with the two parents (Gossypium barbadense), were artificially inoculated with FOV4 and assayed for resistance based on foliar disease severity ratings (DSR) at 30 days post inoculation (dpi) in two replicated tests in the greenhouse or controlled conditions. Significant genotypic variations were detected for FOV4 resistance in a combined analysis of variance. Although a significant genotype × test interaction was detected for DSR, the 10 most resistant RILs had significantly and consistently lower DSR than the susceptible parent in both tests. The heritability estimate for DSR was 0.65, indicating that two-thirds of the phenotypic variation for FOV4 resistance in this Pima RIL population was due to genetic factors. Based on 404 polymorphic SSR markers, five and four quantitative trait loci (QTL) on six chromosomes (c14, c17, c19, c21, c24, and c25) were detected in Tests 1 and 2, respectively, and each explained 15 to 29% of the phenotypic variation. Three QTL on c17, c24, and c25 were in common between the two tests, accounting for 60% and 75% of the QTL detected in Tests 1 and 2, respectively. The three QTL were also reported in previous studies and will be useful for marker-assisted selection for FOV4 resistance in Pima cotton.

Microsatellite marker based DNA fingerprinting of cotton (Gossypium spp.) hybrids and their parents

Cotton production in India by the vast majority comes from cotton hybrids whose genetic purity is of great significance in the seed production chain and trade. Therefore, there is a need to develop a rapid, reliable and reproducible technique to assess the genetic purity of cotton hybrids as the traditional, morphological traits-based ‘Grow-Out Test’ is resource intensive, time consuming, tedious and not an infallible procedure. In this regard, a study was planned to understand the genetic diversity among the hybrids and their parents and also to identify SSR markers for confirmation of genetic purity or hybridity. One intra-arboreum hybrid, CICR2 (DS 5 GMS × LD 327 Sel.), four intra-hirsutum hybrids viz., CSHH198 (CSH 19 × CSH 8), CSHH238 (SH 2379 9Y × PIL 8 Sel.), CSHH243 (CSH 2013 × CSH 43), CSHH1862 (GMS 16A × CB 33) and one hirsutum × barbadense hybrid, Phule 388 (RHC-006 × RHCb-001) along with their respective parental lines were selected for molecular characterization. Of the total 215 SSR markers surveyed, 60 markers conveyed polymorphism. The information conveyed by the polymorphic SSR markers was utilized to assess the molecular divergence among the study material. Maximum genetic dissimilarity of 0.66 was noted between Phule 388 and LD 327 (Sel.), and between RHC-006 and DS 5 (GMS). Minimum genetic dissimilarity of 0.07 was observed between CSHH1862 and CB 33, followed by 0.11 between CICR2 and DS 5 (GMS). SSR markers were highly efficient in capturing both intra-species and inter-species level diversity. The clustering and factorial analysis were  in congruence with the species of Gossypium. The diploid species genotypes were clustered separately and distinctly from the rest of the genotypes. All the hirsutum hybrids and their respective parents were found closely clustered. The inter-specific hybrid, Phule 388 along with its parents was found grouped closely. The genetic purity of the hybrids was confirmed using identified SSR markers [GH486, BNL1421, BNL3594, JESPR151 for G. hirsutum hybrids, CSHH198; GH486, BNL2449, JESPR151, TMB0436 for G. hirsutum hybrids, CSHH238; BNL2449, JESPR151, JESPR152 for G. hirsutum hybrid, CSHH243 and GH527, BNL3812, TMB1484, TMB1645, NAU1190, BNL3816 for inter-specific G. hirsutum × G. barbadense hybrid Phule 388]. The SSR markers were efficient in the analysis of hybrid seed purity. The information generated in the present study about genetic diversity and genetic purity testing will greatly facilitate quality seed production of these cotton hybrids and thus, better cotton production. Keywords: Cotton, DNA fingerprinting, Hybrids, Microsatellites, SSR markers, Diversity

GENETIC VARIABILITY IN WEEDY RICE BIOTYPES FOUND IN DIRECT-SEEDED RICE AREAS IN THE PHILIPPINES

Weedy rice can severely impact rice production through yield reduction because of its competitive ability to reduce growth resources for cultivated rice. The characteristic weedy traits have made weedy rice very challenging to manage as they have the same agro-morphological characteristics with cultivated rice. The study examined the relationships between selected cultivated rice (Oryza sativa L.) cultivars, weedy rice biotypes, and wild rice collected from different locations in the Philippines, using simple sequence repeat markers. Cluster analysis, using UPGMA, enabled the genetic differentiation and relationships examination of the test materials. Subgroups of 13 with at least two biotypes formed 100% similarity based on post-harvest data, with the cultivated rice cultivars forming one subgroup. With polymorphic SSR markers, five major clusters range from three (group I) to 62 biotypes (group III). There was 100% similarity observed for 15 subgroups ranging from two to 10 biotypes. The wild rice cultivars formed species-specific groupings. Subgroups with 100% similarity came from the same province; likewise, one with 100% similarity came from both Iloilo and Batangas; and still another from cultivated rice cultivar and weedy rice biotype from Pangasinan. The possible relationships of weedy rice biotypes with wild rice relatives (>65% similarity) include two biotypes related to Oryza minuta, one for O. meyeriana, and 22 biotypes for O. rufipogon. Concerning cultivated rice cultivars, high similarity (>80%) was observed in 22 biotypes closely related to PSB Rc 82, 13 biotypes to NSIC Rc 222, six to NSIC Rc 160, three biotypes each to NSIC Rc 215, NSIC Rc 152, NSIC Rc 64, NSIC Rc 18, and NSIC Rc 10, and one biotype each to IR64 and NSIC Rc 14.

Marker - trait association analysis for yield related traits in rice (Oryza sativa L.)

This study was undertaken to identify marker-trait associations for twelve yield related traits with a set of 48 rice genotypes. A total of 38 polymorphic SSR markers across the 12 chromosomes of rice were used for the association analysis. Marker-trait associations were performed using mixed linear model approach. A total of 84 significant marker-trait associations were detected at Pd £ 0.05 with the R2 values ranging from 6.71 to 27.24%. The most significant marker associations for days to 50% flowering on chromosome 12 with RM17, plant height on chromosome 4 with RM7051, panicle length on chromosome 7 with RM125, flag leaf length on chromosome 9 with RM219, flag leaf breadth on chromosome 10 with RM216, effective tiller per plant on chromosome 5 with RM164, total grains per panicle on chromosome 12 with RM28305, hundred grain weight on chromosome 1 with RM6324, grain yield per plant and grain length on chromosome 8 with RM8264, grain breadth on chromosome 7 with RM320 and grain length-breadth ratio on chromosome 1 with RM6324. The present study has revealed that the twenty-three markers showed association with more than one trait and correlated traits such as panicle length, total grains per panicle, hundred grain weight, grain yield per plant, grain length, grain breadth and grain length-breadth ratio were located in the same chromosome regions. These traits may be controlled by genes which have pleotropic effect. The result suggest that marker-trait association analysis is a fascinating tool to identify marker-trait association for complex traits using diverse rice genotypes. The SSR markers identified in this study would be useful in marker assisted selection for the improvement of yield related traits in rice.

Development of KASP and SSR Markers for PmQ, a Recessive Gene Conferring Powdery Mildew Resistance in Wheat Landrace Qingxinmai

A recessive gene PmQ conferring powdery mildew resistance was previously localized on the long arm of chromosome 2B in winter wheat landrace Qingxinmai. Breeder-friendly molecular markers are necessary for introgressing this gene into adapted wheat backgrounds for developing disease-resistant wheat cultivars. Three Kompetitive allele-specific PCR (KASP) markers were developed and validated based on SNP variants detected by Bulked segregant analysis-RNA-Seq (BSR-Seq) analysis using a recombinant inbred population derived from cross Qingxinmai × 041133. Two polymorphic SSR markers were also developed from the motifs in the Chinese Spring reference genome sequences of the target genomic region. Those markers were incorporated into a more saturated genetic linkage map for PmQ. The two flanking markers, Xicsq405 and Xicsk18, are 1.1 and 0.9 cM from PmQ, respectively. The KASP marker Xicsk19 produced unique amplification pattern in 158 out of 160 wheat cultivars or breeding lines. This marker with the gene-linked SSR markers Xicsqc, Xicsqd and Xicsq405 provides an efficient means in molecular marker-assisted selection for PmQ in wheat breeding. The corresponding genomic region of PmQ in the Chinese Spring reference genome has a conserved synteny with the genomes of sequenced wheat cultivars and Triticum durum, T. diccocoides, T. uratu, and barley. The annotation of the two genes, TraesCS2B01G517400.1 and TraesCS2B01G517700.1, associated with plant defense against pathogens placed a start for cloning PmQ.

DRR Dhan 58, a Seedling Stage Salinity Tolerant NIL of Improved Samba Mahsuri Shows Superior Performance in Multi-location Trials

BackgroundImproved Samba Mahsuri (ISM) is an elite, high-yielding, bacterial blight resistant, fine-grained rice variety with low glycaemic index. It is highly sensitive to salt stress, particularly at seedling stage, which significantly reduces its yield potential in coastal areas. A salinity tolerant QTL, Saltol, associated with seedling stage tolerance was previously mapped on chromosome 1 (10.6–11.5 Mb) from the Indian landrace, Pokkali and is effective in different genetic backgrounds. The objective of this study was to enhance salinity tolerance of ISM by incorporating the Saltol QTL through marker-assisted backcross breeding using the breeding line, FL478 (Pokkali/IR29).ResultsForeground selection was carried out at each generation using five Saltol-specific markers and three bacterial blight resistance genes, Xa21, xa13 and xa5. Background selection was conducted using 66 well distributed polymorphic SSR markers and at the BC3F2 generation, a single plant with maximum recurrent parent genome recovery (95.3%) was identified and advanced to the BC3F4 generation. Based on bacterial blight resistance, seedling stage salinity tolerance and resemblance to ISM, four advanced breeding lines were selected for testing in replicated experiments near Hyderabad, India. A promising near-isogenic line, DRR Dhan 58, was evaluated in multi-location trials-coastal salinity and it showed significant salinity tolerance, resistance to bacterial blight disease, high yield and excellent grain quality during the 2019 and 2020 trials. DRR Dhan 58 was 95.1% similar to ISM based on genotyping with the 90 K SNP chip. Whole genome resequencing analysis of Pokkali and FL478 which were salinity tolerant checks, ISM and DRR Dhan 58 showed a high degree of relatedness with respect to the candidate gene loci for Saltol and OsSKC1 (Shoot K+Concentration 1).ConclusionDRR Dhan 58, possessing Saltol and three bacterial blight resistance genes (Xa21, xa13 and xa5) in the genetic background of the Indian mega-variety of rice, Samba Mahsuri, was developed for potential cultivation in areas prone to seedling stage salinity, as well as areas with endemic bacterial blight disease. This entry had a 24% yield advantage over the recurrent parent ISM under coastal saline conditions in multi-location trials and was recently released for commercial cultivation in India.

Marker-assisted transfer of leaf and stripe rust resistance from Triticum turgidum var. durum cv. Trinakria to wheat variety HD2932.

A marker-assisted backcrossing program initiated to transfer leaf rust resistance gene LrTrk from Triticum turgidum cv. Trinakria to hexaploid wheat variety HD2932 cotransferred a stripe rust resistance gene, YrTrk, along with LrTrk. The cross of hexaploid recurrent parent HD2932 with tetraploid donor parent Trinakria produced pentaploid F1 plants. F1s were backcrossed with recurrent parent HD2932 to produce BC1F1 generation. Foreground and background selection was conducted in each backcross generation to identify plants for backcrossing or selfing. While foreground selection for LrTrk was carried out with linked and validated molecular marker Xgwm234, for background selection, 86 polymorphic SSR markers from the A and B genomes were used. Single selected plants from BC1F1 and BC2F1 generations backcrossed and selfed to produce BC2F1and BC2F2 generations, respectively. Background selection resulted in 83.72%, 91.86%, and 98.25% of RPG recovery in BC1F1, BC2F1, and BC2F2 generations, respectively. A total of 27 plants with LrTrk in homozygous state were identified in BC2F2 generation and selfed to produce 27 BC2F3 NILs. All the NILs were tested for leaf and stripe rust resistance at the seedling stage using seven Puccinia triticina and one Puccinia striiformis f.sp. tritici rust pathotypes. All the 27 NILs were found to be resistant to both leaf and stripe rust pathotypes. So, these NILs are designated to carry leaf and stripe rust resistance genes LrTrk/YrTrk.

SSR marker-based genetic characterization of Turkish oriental tobaccos.

Turkey is one of the traditional oriental tobacco producing countries. Oriental tobaccos produced in Turkey are ecotypes specific to certain regions, local varieties and landraces, and they have unique characteristics. The present study was conducted to reveal the general and interregional genetic diversity levels of tobacco genotypes collected from different regions of Turkey based on DNA markers. A total of 319 ecotypes/lines of Turkish Oriental Tobaccos collected from different regions (Aegean Region, Marmara Region, Karadeniz Region, and East and Southeast Anatolia Regions) of Turkey and cultivars Xanthi 81, Xanthi 2A, Canik Sitmasuyu, Katerini, Canik 190-5 and NC 55 were subjected to SSR marker analysis. Eighty-nine alleles were obtained from 21 markers examined, and the average number of alleles per marker was 4.05. A total of 314 unique tobacco genotypes were found among 319 plants evaluated using 19 polymorphic SSR markers. In the dendrogram constructed using SSR marker data, genotypes were divided into six clades based on geographic regions and levels of genetic diversity. The presence of 314 unique genotypes among 319 tobacco plants evaluated indicated the high level of genetic diversity among Turkish tobaccos. While some of them were N. rustica tobaccos, some others were reminiscent of semi-oriental tobaccos. These genotypes merit further agronomic and technological characterizations, which could allow their utilization in future tobacco breeding.

Mapping of QTLs controlling barley agronomic traits (Hordeum vulgare L.) under normal conditions and drought and salinity stress at reproductive stage

The present study is focused on mapping the genomic regions for controlling some agronomic traits in the reproductive stage of barley under normal, drought and saline conditions. In this regard, a total of 103 samples of F8 families derived from the cross of two cultivars of Badia×Kavir were planted in a completely randomized design in the crop year 2018–2019. The research procedure has been accomplished in the greenhouse of Gonbad Kavous University in three replications. In this case, transgressive segregation was observed for the evaluated traits. This situation indicated the difference between allelic interactions in the parents. Also, linkage maps were prepared using 152 SSR polymorphic markers, 72 ISSR alleles, 7 IRAP alleles, 29 CAAT alleles, 27 SCoT alleles, and 15 iPBS alleles. These markers were assigned to the seven barley chromosomes. Thus, the obtained map covered 999.29 centiMorgans (cM) of the barley genome length, and the average distance between two flanking markers was 3.387 cM. In this study, the most significant QTL under normal conditions have been identified on chromosomes 1, 5, and 6. In the drought conditions, four major QTLs were detected for spike diameter, awn weight, flag leaf weight (qPPT-7, qAWW-7, qFLW-4a and qFLW-5). Under salinity stress conditions, two major QTLs were identified for the number of leaves qLEN-6a and shoot diameter qSHT-6b. In this case, the values of R2 were 18.3 and 17.6, respectively. The major QTLs that control the effect of the desired traits and the markers associated with them can be used in marker-assisted selection programs.

Full-length transcriptome sequencing analysis and characterization, development and validation of microsatellite markers in Kengyilia melanthera.

As a typical psammophyte of the Triticeae, Kengyilia melanthera possesses high feeding potential and great utilization values in desertification control in the Qinghai-Tibet Plateau. However, few gene function and genetic studies have been performed in K. melanthera. In this study, single-molecule real-time sequencing technology was used to obtain the full-length transcriptome sequence of K. melanthera, following the functional annotation of transcripts and prediction of coding sequences (CDSs), transcription factors (TFs), and long noncoding RNA (lncRNA) sequences. Meanwhile, a total of 42,433 SSR loci were detected, with 5′-UTRs having the most SSR loci and trinucleotide being the most abundant type. In total, 108,399 SSR markers were designed, and 300 SSR markers were randomly selected for diversity verification of K. melanthera. A total of 49 polymorphic SSR markers were used to construct the genetic relationships of 56 K. melanthera accessions, among which 21 SSR markers showed good cross-species transferability among the related species. In conclusion, the full-length transcriptome sequence of the K. melanthera will assist gene prediction and promote molecular biology and genomics research, and the polymorphic SSR markers will promote molecular-assisted breeding and related research of K. melanthera and its relatives.

Selection of Sweetpotato Parental Genotypes Using Simple Sequence Repeat Markers.

Knowledge of the genetic diversity and genetic relationship is important in crop improvement. The objective of this study was to determine the genetic diversity of 31 sweetpotato genotypes and furthermore to select distantly related individuals for breeding of superior parental clones. The genotypes (sourced from the Agricultural Research Council, South Africa) originating from Africa and American continent were genotyped using eight highly polymorphic SSR markers. The SSR markers generated a total of 83 putative alleles. The polymorphic information content (PIC) of the tested simple sequence markers varied from 0.73 to 0.91, with a mean of 0.85. At least 11 different alleles were found in 8 loci within the population, with 7 effective alleles per locus. Although high diversity was found among the genotypes, genetic distances among the genotypes were relatively low. Cluster analysis revealed the existence of three distinct genetic groups, and the clustering patterns follow to some extent the geographic origin and pedigree of the genotypes. High gene flow was observed among different sweetpotato accessions. The selected SSR markers were found to be highly polymorphic with high discriminatory power for genetic characterization studies and are useful genomic tool to complement phenotyping of sweetpotato genotypes. Two heterotic groups were found in the study. The heterotic group A was composed of 14 genotypes mainly of South African origin, while the heterotic group B consisted of 17 genotypes of American origin. The two distinct groups were important for the selection of breeding clones that were distantly related to be used as parental clones in the advancement of traits of interest.

Morpho-molecular Diversity Analysis in Rice (Oryza sativa L.) Genotypes using Microsatellite Markers

Background: The insight concerning genetic diversity and relationship among the rice genotypes is a basic contribution to the crop improvement programs. The present field experiment was conducted to study the level of diversity present in 47 rice genotypes using both morphological and molecular analysis. Methods: The experiment was carried out at Agricultural Research Farm, Banaras Hindu University, Varanasi (U.P.), during Kharif-2019 with 47 rice genotypes. Mahalanobis’ D2 analysis was carried out to evaluate the morphological diversity present among the genotypes and 24 polymorphic SSR markers were used for molecular analysis using the NTSYSpc software. Result: Mahalanobis’ D2 grouped 47 rice genotypes into 6 clusters based on the inter-se genetic distance. The highest inter-cluster distance (1134.14) was observed between clusters II and IV indicating the genotypes present in these clusters to be highly divergent. Molecular diversity analysis grouped the 47 rice genotypes into 3 main clusters i.e., cluster I, cluster II and cluster III, which were further divided into sub-clusters. Polymorphic Information Content varied from 0.12 to 0.86, with an average of 0.465. The highest PIC value was observed for locus RM 507 (0.86). All the 24 primers showed polymorphism and the number of alleles was common for all i.e., 2. Together, the morphological and molecular diversity analysis revealed that Desi Dhan and IR 91143-AC 293-1, Desi Dhan and BD 105, IR 85850 and Lal Sundiya, Chauli and Swarna were the most diverse genotypes among the 47 rice genotypes included in the study.

Genetic diversity analysis of Camellia fascicularis H. T. Chang based on SSR markers

Camellia fascicularis is a Camellia specie with extremely small populations and unique to Yunnan Province. This study aimed to analyze the genetic diversity of C. fascicularis populations using polymorphic SSR markers. Eighty four samples of eight natural populations were tested for genetic diversity using fourteen SSR markers. The numbers of alleles detected at single polymorphic loci using 14 SSR markers were 2–8, and a total of 68 alleles were identified in this study, with an average allele number of 4.8571 per locus. The average Shannon’s information index I was 1.0925, indicating that C. fascicularis has a high diversity. The percentages of polymorphic loci (PPB) of the eight populations of C. fascicularis were 42.86 %−100 %. There were significant differences in genetic parameters among different populations, and the polymorphisms were all high. The gene flow (Nm) values ranged from 0.0503 to 0.9820, with an average value of 0.5440 < 1. Genetic structure analysis showed that the eight C. fascicularis populations were roughly divided into three groups. Genetic variation occurred mainly within populations, with intra-populations genetic variation accounting for 49.95 % of the total variation. It was found that C. fascicularis has a high genetic diversity, and its rich genetic diversity may be due to the diverse habitat diversity of its distribution area and the long evolutionary history of the species. There was almost no gene exchange among natural populations, and the level of population differentiation was low.

Genetic diversity based on SSR markers of 30 Aeridinae sub-tribe orchid genetic resources of Indonesian Ornamental Crop Research Institute, Cianjur, Indonesia

Abstract. Wegadara M, Dewanti M, Diningsih E, Rachmawati F, Sukma D, Sudarsono. 2022. Genetic diversity based on SSR markers of 30 Aeridinaesub-tribe orchid genetic resources of Indonesian Ornamental Crop Research Institute, Cianjur, Indonesia. Biodiversitas 23: 2943-2956. Advances in molecular biotechnology encourage molecular markers to identify plant diversity to become increasingly common. Using SSR markers, this study will determine the genetic diversity and phylogenetic relationships of 30 accessions from five parental genera of Aeridinaeorchids from the IOCRI genetic resource collection. Molecular characterization of 30 orchid sub-tribes Aeridinaegenetic resources of IOCRI was carried out using 17 polymorphic SSR markers. The resulting binary data was then analyzed using the GenAlEX program to determine Na, Ne, Ho, He, and the PowerMarker V3.25 program to determine the values of MAF, D, and PIC. Molecular characterization using 17 SSR primers generated 240 amplified DNA fragments across 30 accessions, with the fragment sizes ranging from 56-4818 bp. Factorial analysis (PCoA) and phylogenetic tree construction clustered the 30 Aeridinae accessions into three major clusters. Accessions belonging to the Vanda genus are clustered into three clusters (Clusters I, II, and III). The Vascostylisis in Cluster I, along with 12 Vanda accessions. Two accessions of Vanda, two Aranthera, three Arachnis, and one Aerides genera are clustered into Cluster III. This study showed that interspecific hybrids among accessions of Vanda within Cluster I and Cluster II should be possible since they are genetically closely related. Intergeneric hybrids among the accession of Vascostylis and Vanda's genera belonging to Cluster I, should also be possible. Furthermore, intergeneric hybrids among Aerides, Arachnis, Aranthera, and Vanda accessions within Cluster III should also be possible. The generated data from this study should be helpful for future Aeridinae breeding activities intended to generate new hybrid varieties.

Inheritance of Yield Components and Morphological Traits in Avocado cv. Hass From "Criollo" "Elite Trees" via Half-Sib Seedling Rootstocks.

Grafting induces precocity and maintains clonal integrity in fruit tree crops. However, the complex rootstock × scion interaction often precludes understanding how the tree phenotype is shaped, limiting the potential to select optimum rootstocks. Therefore, it is necessary to assess (1) how seedling progenies inherit trait variation from elite ‘plus trees’, and (2) whether such family superiority may be transferred after grafting to the clonal scion. To bridge this gap, we quantified additive genetic parameters (i.e., narrow sense heritability—h2, and genetic-estimated breeding values—GEBVs) across landraces, “criollo”, “plus trees” of the super-food fruit tree crop avocado (Persea americana Mill.), and their open-pollinated (OP) half-sib seedling families. Specifically, we used a genomic best linear unbiased prediction (G-BLUP) model to merge phenotypic characterization of 17 morpho-agronomic traits with genetic screening of 13 highly polymorphic SSR markers in a diverse panel of 104 avocado “criollo” “plus trees.” Estimated additive genetic parameters were validated at a 5-year-old common garden trial (i.e., provenance test), in which 22 OP half-sib seedlings from 82 elite “plus trees” served as rootstocks for the cv. Hass clone. Heritability (h2) scores in the “criollo” “plus trees” ranged from 0.28 to 0.51. The highest h2 values were observed for ribbed petiole and adaxial veins with 0.47 (CI 95%0.2–0.8) and 0.51 (CI 0.2–0.8), respectively. The h2 scores for the agronomic traits ranged from 0.34 (CI 0.2–0.6) to 0.39 (CI 0.2–0.6) for seed weight, fruit weight, and total volume, respectively. When inspecting yield variation across 5-year-old grafted avocado cv. Hass trees with elite OP half-sib seedling rootstocks, the traits total number of fruits and fruits’ weight, respectively, exhibited h2 scores of 0.36 (± 0.23) and 0.11 (± 0.09). Our results indicate that elite “criollo” “plus trees” may serve as promissory donors of seedling rootstocks for avocado cv. Hass orchards due to the inheritance of their outstanding trait values. This reinforces the feasibility to leverage natural variation from “plus trees” via OP half-sib seedling rootstock families. By jointly estimating half-sib family effects and rootstock-mediated heritability, this study promises boosting seedling rootstock breeding programs, while better discerning the consequences of grafting in fruit tree crops.

Inter and intra-specific crossability studies on Mangifera species

Inter-specific and inter-varietal crosses were attempted using Mangifera indica cv. Amrapali as a female parent and M. odorata and M. indica cv. Vanraj as male donor parents (2016–19). Initial fruit set after 7 days of pollination (DAP) was 81.48%, which reduced to 2.48% at harvest. However, in inter-specific crosses, initial fruit set was 79.89%, which reduced to 0.45% at the time of harvesting. Progenies obtained from inter-varietal and inter-specific crosses were subjected to confirmation of parentage using SSR markers. Eight polymorphic SSR markers were used to estimate the paternity, maternity and new alleles in the hybrids. Based on fragment analysis, the paternity, maternity and new alleles of 12 inter-specific and 17 inter-varietal hybrids were estimated by finding a similar number of alleles between the offsprings and parents. Among inter-specific hybrids, AO2, AO7, AO11, and AO12 showed ≥50% of paternal allele inheritance, while AO1, AO2, AO4, AO5, AO7, AO8, AO9, AO10 and AO12 showed ≥50% of maternal allele inheritance. Inter-specific hybrids such as AO1, AO3, AO5, AO9, AO10 and AO11 inherited new alleles. Among inter-varietal hybrids, AV1, AV2, AV4, AV5, AV6, AV10, AV11, AV12, AV13, AV14, AV15 and AV17 possessed ≥50% paternal allele, while, AV1, AV2, AV3, AV5, AV6, AV7, AV8, AV10, AV11 and AV15 had ≥50% maternal allele. Three inter-varietal hybrids, viz. AV8, AV9 and AV16 inherited new alleles. It is concluded that SSRs markers are useful in ascertaining the parentage of hybrids obtained from inter-specific and inter-varietal crosses in mango.

Development of SSR markers and genetic diversity analysis based on RAD-seq technology among Chinese populations of Daphnia magna.

Daphnia magna belongs to the Cladocera order and plays an important role in the aquatic ecosystem. With the intensification of water pollution, the wild population of D. magna has declined rapidly in recent years, and insufficient molecular markers have limited effective research and conservation of this species. 26 novel microsatellite (SSR) markers were developed in an artificially domesticated D. magna and 12 wild D. magna populations using restriction site-associated DNA sequencing (RAD-seq). The results showed that the observed heterozygosity (Ho) and expected heterozygosity (He) ranged from 0.083 to 0.999 and 0.085 to 0.862, respectively. The PIC ranged from 0.368 to 0.805. These results indicate that the developed SSR marker is highly polymorphic. Nei's genetic identity (H) ranged from 0.0926 to 0.3462. Shannon's Information index (I) ranged from 0.1333 to 0.4799. Genetic distance and Nei's genetic identity analysis, NJ tree diagram analysis, and PCoA analysis were conducted on populations of D. magna from different regions. The results show that the D. magna genetic relationship between Liaoning and Shanxi, Hunan and Anhui, and Beijing and Hainan are relatively close, while the genetic structure of D. magna in Guangdong, Jiangsu, and Sichuan is quite different from other sampling sites. An analysis of population genetic structure divided the D. magna samples into two major groups. These results indicate that the genetic structure of D. magna differs considerably in different regions. Our research results and the newly developed polymorphic SSR markers for D. magna are of great significance in terms of the genetic breeding of D. magna, identification of wild and artificially domesticated populations and conservation genetics research.

Marker-Assisted Improvement of Bread Wheat Variety HD2967 for Leaf and Stripe Rust Resistance.

The mega wheat variety HD2967 was improved for leaf and stripe rust resistance by marker-assisted backcross breeding. After its release in 2011, HD2967 became susceptible to stripe rust and moderately susceptible to leaf rust. The leaf rust resistance gene LrTrk was transferred into HD2967 from the durum wheat genotype Trinakria. Then, HD2967 was crossed with Trinakria to produce F1 plant foreground selection for LrTrk and background selection for the recurrent parent genotype was carried out in BC1F1, BC2F1 and BC2F2 generations. Foreground selection was carried out with the linked marker Xgwm234, while polymorphic SSR markers between parents were used for background selection. Background selection resulted in the rapid recovery of the recurrent parent genome. A morphological evaluation of 6 near isogenic lines (NILs)—2 resistant to leaf and stripe rust, and 4 resistant to leaf rust only—showed no significant differences in yields among NILs and the recurrent parent HD2967. All of the 6 NILs showed the presence of 2NS/2AS translocation, carrying the linked genes Lr37/Sr38/Yr17 present in HD2967 and the targeted leaf rust resistance gene LrTrk. Two NILs also showed additional resistance to stripe rust. Therefore, these NILs with rust resistance and an at par yielding ability of H2967 can replace the susceptible cultivar HD2967 to reduce yield losses due to disease.

Genome –wide Allelic Variations and Population Structure Analysis of Cotton Genotypes using SSR Markers

The limited genetic base of modern cotton genotypes makes it difficult to improve cotton fibre yield and quality, emphasizing the necessity to study existing cotton germplasm resources. Therefore, this study was conducted to assess the genetic diversity and population structure of different cotton genotypes at DNA level. A total of 105 cotton genotypes were analyzed using 208 polymorphic SSR markers which were distributed on both A and D genomes. The total number of alleles in all genomes are 1382 Out of which 665 and 717 alleles were recorded in A and D genomes, respectively. In A genome, the maximum PIC values; 0.89 was observed for markers M92, M82 and M76 with the 10-total number of alleles exhibiting 100% polymorphism. These markers (M92, M82 and M76) located at the chromosomes 12A, 11A and 10A respectively with the estimation of 0.84 gene diversity. The highest PIC value 0.89 of D genome was detected for M191, M128 and M117 markers on 24D, 16D and 15D chromosomes with the 10 total numbers of alleles having the 0.84 values of gene diversity with 100% polymorphism. The UPGMA cluster DARWIN tree and Model-based Bayesian analysis clustered the studied cotton germplasm into four subpopulations, and the highest molecular variation revealed among subpopulations. Phylogenetic tree constructed for the whole germplasm population identified four major groups including; Group 1, Group 2, Group 3 and Group 4 consisting of 12, 21, 39 and 69 genotypes, respectively. Genetic distances among clusters clearly showed the variations among one another. SSR markers appear to be useful and reliable assets for future genetic and genomic analyses of cotton, such as genetic map construction, comparative genomic analyses, genetic diversity, and molecular marker-assisted breeding to select promising cotton genotypes, according to the current experiment.