SSR Primer Pairs Research Articles

Development of polymorphic SSR markers and their applicability in genetic diversity evaluation in Euptelea pleiosperma

Euptelea pleiosperma is a characteristic species of East Asian flora with both ornamental and scientific values. Based on the reduced-representation sequencing (RRS) technology of RAD-Seq, this study conducted high-throughput Illumina paired-end sequencing to find SSR marker information in the genome of E. pleiosperma, and to screen and verify polymorphism of SSR markers. We obtained 5.5G of high-quality data using RAD-Seq. The total number of contigs of the RAD tags was 299,376, with the maximum contig length of 2,062 bp and the average length of 445 bp. From these sequences, we identified 20,718 SSR loci, with a distribution density of one SSR per 6.45 kb (1/6.45 kb). Among all SSRs, dinucleotides (52.00%) were the most detected SSRs, followed by mononucleotides (21.63%). AG/CT was the dominant motif in the SSR loci, accounting for 34.8%. Primers were successfully designed for 14,593 loci, and 100 pairs of these primers were randomly selected for chemical synthesis and validated by SSR-PCR amplification in 20 individuals of E. pleiosperma. Seventy-nine primers were able to amplify the target bands. Cervus 3.0 software was used to analyze the selected 20 SSR loci with good polymorphism. For the 20 SSR markers, the number of alleles ranged from 4 to 9, and the observed heterozygosity and expected heterozygosity were from 0.35 to 0.75 and 0.541 to 0.875, respectively. The information content of polymorphic loci ranged from 0.463 to 0.848, with an average value of 0.638. Among them, there were 18 highly polymorphic loci, and 20 SSR loci did not deviate from the HardyWeinberg equilibrium. Furthermore, the 20 pairs of SSR primers were used to conduct PCoA analysis based on Nei’s genetic distance of 51 individuals from three populations. The results showed that these SSR markers could distinguish genetic differences based on different geographical locations.

Genetic Diversity Analysis of Maize in Baoshan Yunnan by SSR Markers

The genetic diversity of 15 maize and it’s popularization grown in Baoshan city were carried out based on SSR primers recommended by Chinese agricultural industry standard (NY/T1432-2014). The results showed that 17 pairs of SSR primers presented polymorphic, and 72 alleles were detected. The number of alleles detected by each pair of primers was 3 to 6, with an average of 4.3. The effective number of alleles was 1.219 to 1.750, with an average of 1.448. The Nei’s genetic diversity index was 0.176 to 0.418, with an average of 0.283. The Shannon information index was 0.315 to 0.605, with an average of 0.444. The SSR polymorphic information (PIC) distribution ranges from 0.512 to 0.812, with an average of 0.686. The cluster analysis showed that the genetic similarity coefficient ranged from 0.417 to 0.819, with an average of 0.632, when the genetic similarity coefficient was 0.65, 15 varieties were divided into 5 groups. The results can provide theoretical and technical support for breeding and promotion of Baoshan maize varieties in Yunnan province.

Genome-wide development of interspecific microsatellite markers for Saccharum officinarum and Saccharum spontaneum

Sugarcane has a large, complex, polyploid genome that has hindered the progress of genomic research and molecular marker-assisted selection. The user-friendly SSR markers have attracted considerable attention owing to their ideal genetic attributes. However, these markers were not characterized and developed at the genome-wide scale due to the previously lacking high-quality chromosome-level assembled sugarcane genomes. In this present study, 744305 and 361638 candidate SSRs were identified from the genomes of S. officinarum and S. spontaneum, respectively. We verified the reliability of the predicted SSRs by using 1200 interspecific SSR primer pairs to detect polymorphisms among 11 representative accessions of Saccharum, including S. spontaneum, S. officinarum, S. robustum, and modern sugarcane hybrid. The results showed that 660 SSR markers displayed interspecific polymorphisms among these accessions. Furthermore, 100 SSRs were randomly selected to detect the genetic diversity for 39 representative Saccharum accessions. A total of 320 alleles were generated using 100 polymorphic primers, with each marker ranging from two to seven alleles. The genetic diversity analysis revealed that these accessions were distributed in four main groups, including group I (14 S. spontaneum accessions), group II (two S. officinarum accessions), group III (18 modern sugarcane hybrid accessions), and group IV (five S. robustum accessions). Experimental verification supported the reliability of the SSR markers based on genome-wide predictions. The development of a large number of SSR markers based on wet experiments is valuable for genetic studies, including genetic linkage maps, comparative genome analysis, genome-wide association studies, and marker-assisted selection in Saccharum.

Genetic diversity of oat accessions revealed by SSR markers

Oat is an important cereal crop for the food and feed industries. Genetic resources of oat are the basic materials for sustainable breeding programs. Microsatellites (SSR) are a useful tool for understanding the genetic background of oat germplasm resources. We used 83 SSR primer pairs to assess the genetic diversity of 286 oat accessions from five countries. The results indicated the presence of considerable variation among accessions. The number of alleles per SSR locus ranged from 2 to 8, with an average of 3.49; allelic frequencies ranged from 0.002 to 0.709; Nei’s genediversity was 0.67, ranging from 0.44 to 0.85; and polymorphism information content (PIC) values ranged from 0.37 to 0.83. Genetic distance estimated by the Jaccard model was compared between accession groups as well as among all accessions using all marker alleles. The principle coordinates analysis based on genetic dissimilarity also revealed distinct groups of accessions. We concluded that SSR markers are effective for identification of oat germplasm resources and use of germplasm from North America and Asia should lead to significant progress in Mongolian oat breeding programs.

A novel twisted bud mutant from Ziziphus jujubaMill. ‘Dongzao’

The twisted growth of organs is a distinctive and attractive trait for woody plants. A bud mutant with twisted branches was discovered from ‘Dongzao’, the most popular and tasty table cultivar of Chinese jujube (Ziziphus jujuba Mill.). This study explored the morphological and nutritional characteristics and SSR marker changes of the novel variant. Compared to its mother plant and an external control ‘Dongzao’, the variant had shorter fruit (oblate rather than round) and shorter bearing shoots with smaller internode length. Although the sugar/acid ratio increased in the variant fruit, the soluble sugar, titrated acid and ascorbic acid contents of the fruit were not significantly different between the variant and its mother. No differences in the DNA fingerprint were observed between the variant and its mother using 50 pairs of SSR primers. The novel twisted variant of ‘Dongzao’ could be a valuable germplasm for jujube breeding because it has high-quality fruit and good yield. It also has great potential for direct economic utilization and could be used as a desirable material for research on the mechanism of twisted growth.

Tissue-specific transcriptome for Rheum tanguticum reveals candidate genes related to the anthraquinones biosynthesis.

The online version contains supplementary material available at 10.1007/s12298-021-01099-8.

Virulence and SSR Diversity of Brown Planthopper (Nilaparvata lugens) Adapted on Differential Rice Host Varieties

Brown planthopper biotype 1, 2, 3 and a representative field population are required for resistance screening of promising rice lines in Indonesia, but the current biotype stocks has shown deviation in virulence patterns. The objectives of this study were to develop a set of brown planthopper populations with differential virulence and to investigate their genetic variability using SSR marker. Females originated from two field populations were selected on variety Mudgo (carries Bph1 gene) or ASD7 (bph2 gene) using honeydew excretion as the virulence parameter. Selection cycles resulted in population T, M, A, and R, which was raised and adapted on variety TN1 (carries no Bph gene), Mudgo, ASD7, and Rathu Heenathi (Bph3, Bph17), respectively. Population R was the most virulent as expected and can be used to represent a field population, but the remaining populations still showed high virulence level. AMOVA and PCoA results based on analysis with 38 SSR primer pairs revealed partial genetic separation among populations, with population R was the most genetically distant from the remaining populations. The desired virulence character of the remaining populations is expected could be achieved after further selection and prolonged adaptation on their respective hosts.

Development of genome-wide SSR markers in rapeseed by next generation sequencing.

Rapeseed (Brassica napus L.) is an important oil crop with a huge genome. This study used next generation sequencing technology to develop SSR markers in rapeseed. A total of 213,876 sequence reads were obtained in 58.8Mb. For these reads, 21,523 SSRs were recovered from 18,575 microsatellites sequences and 8,964 SSR primer pairs were identified. Di- and mono-nucleotides were the most abundant, accounting for 47.5% and 30.7% of all SSRs, respectively. A total of 8,776 SSRs were designed from contigs and 100 SSR primers were tested for validation of SSR locus amplification. Nearly all (94%) of the markers were found to produce clear amplicons and to be reproducible. For these markers, forty-three SSRs showed polymorphic bands in eight rapeseed accessions. Thirty-four SSRs were then applied to 78 rapeseed accessions from China to evaluate the genetic diversity. Result showed that the allele number varied from two to seven, with a mean value of 3.59. The effective allele number of ranged from 1.14 to 3.25, with an average of 2.09. The average values of observed heterozygosity and expected heterozygosity were 0.54 and 0.49, respectively. The Nei's gene diversity varied from 0.12 to 0.69, with a mean value of 0.48. Resulting of the markers testing showed that the identified genome-wide SSRs were useful in rapeseed genetic studies, including genetic diversity, QTL mapping and marker-assisted selection for breeding.

Genetic diversity of sugar palm (Arenga pinnata) derived from nine regions in Indonesia based on SSR markers

Abstract. Rinawati DY, Reflinur, Dinarti D, Sudarsono. 2021. Genetic diversity of sugar palm (Arenga pinnata) derived from nine regions in Indonesia based on SSR markers. Biodiversitas 22: 3749-3755. Sugar palm (Arenga pinnata (Wurmb) Merr.) has an important economic and conservation value. Indonesia has genetic diversity potential of sugar palm, considering the widespread distribution of sugar palm in Indonesia which has variations in geographical type. This study aims to determine the diversity and relationship of sugar palm from nine regions in Indonesia based on SSR markers. The genetic material consists of 141 sugar palm accessions derived from Bangka, Lampung, Lebak, Bogor, Tasikmalaya, Brebes, Gowa, Bombana, and Muna. Nine pairs of SSR primers were used for genotyping. The highest and lowest genetic diversity was found in the Bangka and Muna populations, respectively. The genetic diversity within a population (79%) was higher than the genetic diversity between populations (21%). The genetic distance between Bangka and Lebak is the closest (0.033), while between Lampung and Muna is the farthest (0.283). The accession relationship is divided into three major clusters. Clusters 1 consisted of Bangka, Lampung, Bogor, Tasikmalaya, Brebes, Gowa, Bombana and Muna accessions. Cluster 2 consisted of Bangka, Lampung, Lebak, Bogor, Tasikmalaya, Brebes, and Gowa accessions. Cluster 3 consisted of Bangka, Lebak, Brebes, Tasikmalaya, and Gowa accessions. Accession clustering does not show a typical relationship pattern based on geographic location.

Virulence and molecular diversity among Puccinia striiformis f. sp. tritici pathotypes identified in India between 2015 and 2019

Yellow rust, caused by Puccinia striiformis f. sp. tritici (Pst), is economically one of the most important diseases of wheat in India and worldwide. During four wheat-growing seasons (2015-19), a total of 951 yellow rust samples collected from farmers’ fields (n = 602) and trap plot nurseries (n = 349) were analyzed for virulence on 30 differentials. From this analysis, 11 distinct Pst pathotypes were identified. The virulence pattern of these pathotypes was also tested on 14 Avocet near-isogenic lines (NILs) and Avocet S. None of the pathotypes were virulent to Yr5, Yr10, Yr15, Yr16, Yr24, Yr32, and YrSP. Pathotype 46S119 (46E159) was most prevalent and widely distributed in all the areas and its overall frequency was maximum (56.2%) followed by 110S119 (110E159, 31.9%). However, the frequency of 46S119 has decreased gradually from 62.0% (2015-16) to 48.4% (2018-19). Pathotype 238S119 (238E159) being the most virulent among the identified pathotypes, was detected in 6.8% of samples. Each of the remaining pathotypes was identified in <5% of the samples. Genetic diversity among eleven pathotypes was assessed using novel 89 SSR primer-pairs out of which 24 primers showed polymorphism. Finally, 69 alleles were detected across the loci with an average of 2.87 alleles per locus. Polymorphic information content (PIC) value was in the range from 0.28 to 0.68, with a mean of 0.47. Expected heterozygosity was in the 0.34 to 0.73 range, with a mean of 0.56. Cluster analysis based on both avirulence/virulence pattern and SSR profile categorized the identified pathotypes into two major clades. Generated information will potentially be helpful in rust resistance breeding and deployment of resistant cultivars in yellow rust-prone areas.

ZbAGL11, a class D MADS-box transcription factor of Zanthoxylum bungeanum, is involved in sporophytic apomixis

Apomixis is a reproductive model that bypasses sexual reproduction, so it does not require the combination of paternal and maternal gametes but instead results in the production of offspring directly from maternal tissues. This reproductive mode results in the same genetic material in the mother and the offspring and has significant applications in agricultural breeding. Molecular and cytological methods were used to identify the reproductive type of Zanthoxylum bungeanum (ZB). Fluorescence detection of the amplified products of 12 pairs of polymorphic SSR primers showed consistent fluorescence signals for mother and offspring, indicating that no trait separation occurred during reproduction. In addition, the cytological observation results showed differentiation of ZB embryos (2n) from nucellar cells (2n) to form indefinite embryonic primordia and then form adventitious embryos (2n), indicating that the apomictic type of ZB is sporophytic apomixis. The MADS-box transcription factor ZbAGL11 was highly expressed during the critical period of nucellar embryo development in ZB. Unpollinated ZbAGL11-OE Arabidopsis produced fertile offspring and exhibited an apomictic phenotype. The overexpression of ZbAGL11 increased the callus induction rate of ZB tissue. In addition, the results of the yeast two-hybrid experiment showed that ZbAGL11 could interact with the ZbCYP450 and ZbCAD11 proteins. Our results demonstrate that ZbAGL11 can cause developmental disorders of Arabidopsis flower organs and result in apomixis-like phenotypes.

An assessment on intraspecific transferability of SSR markers on fennel (Foeniculum vulgare Mill.) varieties.

The amplification potential of 27 SSR primer pairs originally reported on exotic fennel (Foeniculum vulgare Mill.) was studied on Indian fennel. Only 13 primer pairs developed amplicons (only one amplicon per primer pair) of sizes ranging from 100 to 450 bp. To determine their polymorphic potential, a set of 20 diverse fennel germplasm lines was used. Four primers exhibiting polymorphism, did segregate the 20 diverse lines in 9 clusters. However, these primer pairs did not differentiate between 17 improved varieties of fennel.

Cross-genera amplification of Cajanus spp. specific SSR markers in Clitoria ternatea (L.) and their application in genetic diversity studies

Clitoria ternatea (L.) is a medicinal leguminous plant and is cultivated to cater the need of herbal industries and asthetic purposes. The unavailability of steady molecular marker impedes the genetic improvement of C. ternatea. In the present study, transferability of 98 pairs of Cajanus spp. specific SSR primers were assessed among 14 genotypes of C. ternatea, varied for their flower color, floral architecture and bio-metabolite (taraxerol and delphinidin) content, and out of them 43 had successfully amplified the fragments. Among them, 36 pairs of primers showed 100% transferability, whereas rest seven varied from 42.86 to 92.85% transferability. The transferable 43 pairs ofSSR primers generated 196 alleles across the 14 genotypes and the AMOVA analysis showed moderate genetic variation (55.1%) among the genotypes of C. ternatea, which was also reinforced by Nei's genetic distance and gene identity estimates derived haplotype matrix. Similarly, both the principal coordinate analysis and dendrogram grouped these 14 genotypes of C. ternatea into two major clusters based on SSR allele distribution and frequency, and the clustering pattern is in accordance with petal color but in contrast to floral architecture. MCheza based outlier analysis revealed 16 alleles for balancing selection, which are putatively involved in the maintenance of genetic polymorphism in C. ternatea. Moreover, the estimates of molecular diversity and bio-metabolite content revealed the possible use of these genotypes in future breeding programme of this species.

Genome Survey Sequence and the Development of Simple Sequence Repeat (SSR) Markers in Erianthus arundinaceus

Erianthus arundinaceus possesses high biomass, vigor, ratoonability and resistance to biotic and abiotic stresses and is considered to be an ideal species for improving sugarcane. In this study, a genome survey sequence was performed in E. arundinaceus, and SSR markers were developed based on a genome survey sequence. A total of 167.36 Gb raw data were obtained and were assembled into 3161 Mb genome sequences, including 15,238,738 scaffolds. The genome size was estimated to be approximately 3.23 Gp based on kmer analysis. In total, 36,616 SSR motifs were identified and characterized, including 60.69% dinucleotide, 34.27% trinucleotide, 3.34% tetranucleotide, 0.98% pentanucleotide and 0.71% hexanucleotide repeats. AG/CT repeat motifs were the most abundant, and GC/CG repeat motifs were somewhat rare, accounting for 54.16% and 2.69% of dinucleotide repeat motifs, respectively. A total of 365 SSR loci were obtained by 20 SSR primer pairs amplified in 20 clones of E. arundinaceus and its related species, and 188 SSR loci were specific to E. arundinaceus. Genetic similarity coefficient analysis by UPMGA methods clustered 20 clones of E. arundinaceus and its related species into two groups. Five clones of E. arundinaceus clustered separately with the remaining clones. These results may establish a foundation for further research investigating the E. arundinaceus genome and identifying genuine hybrids between sugarcane and E. arundinaceus.

ANALYSIS OF GENETIC STABILITY OF MICROPROPAGATED SUGARCANE IN DIFFERENT SUBCULTURE FREQUENCIES USING SSR MARKER / Analisis Kestabilan Genetik Tebu Hasil Mikropropagasi pada Beberapa Frekuensi Subkultur Menggunakan Marka SSR

In vitro technique is an effective method to produce high quality and uniform sugarcane seedlings. This study was aimed to determine genetic stability based on SSR marker analysis of six varieties of sugarcane subcultured in regeneration media. It was conducted at the ICABIOGRAD Molecular Biology Laboratory, Bogor, from May 2015 to October 2016. Six sugarcane varieties (PS 862, PS 865, PS 881, PSJK 922, TK 386, and GMP 3) derived from apical shoot explants were subcultured on MS regeneration media enriched with 0.3 mg/l BAP; 0.5 mg/l IBA; and 100 mg/l PVP, for 3, 6 and 9 times. Sugarcane DNA was extracted using the CTAB method; then, the genetic stability was analyzed using 20 pairs of SSR primers. Data were analyzed in groups using the UPGMA method in the SAHN subprogram available on NTSYS software. The results showed that five sugarcane varieties (PS 865, PS 881, PSJK 922, TK 386, and GMP 3) subcultured up to nine times on the regeneration media remained genetically stable with similarity coefficient to their mother plants value more than 0.94. However, PS 862 variety had genetically unstable after the sixth and the ninth subcultures, the similarity coefficient value to its mother plant was only 0.64, indicated that it experienced somaclonal variations. The study concluded that the in vitro shoots of the other varieties were more genetically stable during subcultures compared to PS 862 sugarcane variety based on SSR marker analysis. Further study is needed to find out the cause of genetic changes in PS 862. Keywords: Saccharum officinarum, apical shoots, in vitro propagation.

Genetic analysis of twenty two selected genotypes of Jatropha curcas L. (physic nut) from Africa, Asia and America, using SSR and AFLP markers

Twenty two genotypes of J. curcas L. from Africa (Senegal, Burkina Faso, Mali, Congo and Madagascar Island), Asia (Cambodia, China and India) and America (Ecuador, Dominican Republic and Brazil) selected for their vigor and their productivity were analyzed with ten SSR primer pairs and six AFLP primer combinations. The two marker approaches showed their ability to effectively reveal polymorphism among the selected genotypes: 94.02 and 56% of polymorphism for AFLPs and SSRs respectively. Among the three groups of selected genotypes, the Asian group was the least diverse while the genetic diversities found in African and American groups were slightly comparable. The Nei’s genetic diversity (He) of all twenty-two selected genotypes was 0.2029 based on combined SSR+AFLP data. The Gst value and the AMOVA analysis indicated that more than 80% of the genetic diversity resided within the groups. The analysis of the genetic relationships between the genotypes using the Nei’s standard dissimilarity matrix gave dissimilarity coefficients ranging from 0.14397 to 0.73943 with an average of 0.3540. The most distant genotypes were found between a genotype from Africa (Congo) and one from America (Ecuador). The clustering of genotypes obtained with the neighbor-joining dendrogram and the PCoA analysis revealed the existence of a certain level of diversity that can be used by breeders. Key words: Biodiesel, genetic diversity, jatropha, molecular markers, AFLP, SSR, plant breeding.

Confirmation of Alleles Inheritance in F1 Progenies Derived from a Cross of Calcutta-4 [Musa acuminata ssp. burmannicoides] and Musa acuminata ssp. microcarpa Based on SSR Markers

&lt;p&gt;Banana breeding to produce improved varieties with disease resistance haracters and other desired traits could sustain its yield. Alleles harbored by parents could be passed on to the offsprings through hybridization, but need to be confirmed using molecular markers. This study aimed to confirm allele inheritance in F1 progenies derived from a cross of Calcutta-4 (Musa acuminata ssp. burmannicoides) and M. acuminata ssp. microcarpa based on SSR markers. Eleven pairs of SSR primers were used to amplify DNA of 44 progenies using the PCR technique. The results showed that six SSR markers (MaSSR 1.1, MaSSR&lt;br /&gt;5.1, MaSSR 6.1, MaSSR 7.1, MaSSR 8.1, and MaSSR 11.1) were polymorphic in both parents. Four markers (MaSSR 1.1, MaSSR 5.1, MaSSR 6.1, and MaSSR 8.1) had PIC &amp;gt;0.7, indicating their informativeness to distinguish these progenies and other genetic studies of banana germplasms. A total of 44 F1 individuals were confirmed to harbor alleles inherited from their parents,&lt;br /&gt;suggesting as true progenies from the cross of Calcutta-4 and M. acuminata ssp. microcarpa. This population demonstrated 100% success of hybridization performed. Chi-Square analysis revealed that segregation of all markers did not match to Mendelian ratio 1:2:1, except for MaSSR 1.1 (x2 = 5,62) and MaSSR 6.1 (x2 = 3,77) markers. The genetic traceability of banana F1 progenies demonstrating the usefulness and feasibility of SSR markers in this study provided information on selection of true progenies which may be valuable for breeders to assist selection process in future banana breeding program in Indonesia.&lt;/p&gt;

Genetic diversity in oil palm (Elaeis guineensis and Elaeis oleifera) germplasm as revealed by microsatellite (SSR) markers

Genetic variability and relationship of 29 germplasm accessions of two species, viz. Elaeis guineensis Jacq (25 accessions) and Elaeis oleifera (4 accessions) along with two Palode teneras were evaluated at ICAR-Indian Institute of Oil Palm Research, Regional Station, Palode, India during 2014-2016 with an objective to assess the germplasm diversity.Nine oil palms specific SSR primer pairs were used to assess the genetic diversity. All the nine primer pairs produced reproducible unambiguous markers. The total number of alleles per primer pair varied from six (sMo00129, sMo00128, mEgCIR3890, sMo00130, mEgCIR0268, mEgCIR0905, sMo00020, sMo00154,) to seventeen (mEgCIR3399). It produced a total of 107 alleles from the selected two oil palm species and all the makers were polymorphic. Cluster analysis, based on UPGMA was performed in order to realize the extent of similarity/ dissimilarity among the germplasm accessions. The dendrogram showed two major clusters at 0.09 similarity coefficient one with E. oleifera and other with E. guineensis. Among E. oleifera, Chithara (Oleifera palms identified in the commercial plantation owned by OPIL, Kerala) accessions were grouped separately indicating confirmation of distinctness. Among E. guineensis accessions, G1(Nigerian dwarf tenera) and G55 (Tanzanian dura) showed maximum diversity. Evaluation data obtained in this study on the ‘extent of genetic distance’ among accessions can be explored carefully for planning hybridization programme so as to accelerate palm oil yield by maximizing the hybrid vigour. The significant genetic diversity observed among the germplasm accessions indicated the scope of introgression into the current breeding programme.

Detection of quantitative genes controlling of chlorophyll content in rice seedling under normal and salinity stress and comparison of different QTL mapping methods

شوری یک محدودیت عمده در توسعه کشت برنج می‌باشد. بهبود بخشیدن به تحمل به شوری در برنج ازنظر ژنتیکی یک مسئله بسیار مهم در برنامه‌های اصلاحی است. به‌منظور مکان یابی ژن های کنترل کننده محتوای کلروفیل، 96 لاین خالص نوترکیب برنج ایرانی حاصل تلاقی ارقام ندا × اهلمی-طارم تحت تنش شوری در مرحله گیاهچه‌ای آزمایشی به‌صورت مرکب در قالب طرح کاملا تصادفی با سه تکرار و دو شرایط کشت نرمال و تنش شوری در دانشگاه گنبد‌کاووس در سال 1395 در شرایط گیاهچه کشت شدند. مکان‌یابی ژن‌های کنترل‌کننده محتوای کلروفیل با استفاده از روش‌های مختلف مکان‌یابی شامل SIM-MEL، SIM، CIM، MIM، PMLE، ICIM و STSIM انجام گرفت و با استفاده از هر کدام از این روش‌ها QTL‌های مشابه و متفاوتی ردیابی شد. 40 نشانگر SSR و 16 نشانگر ISSR (76 آلل تکثیر‌شده چند شکل)، 2 نشانگر IRAP (7 آلل تکثیر‌شده چند شکل) و یک نشانگر iPBS (3 آلل تکثیر‌شده چند شکل) بر روی 12 کروموزوم برنج توزیع شدند. روش ICIM، CIM و SIM در شرایط نرمال و تنش شوری بیشترین تشابه مکان‌های ژنی ردیابی شده را دارا بودند. qCHL-6 در شش روش مکان‌یابی در موقعیت 52 سانتی‌مورگان از کروموزوم 6 شناسایی شد. بنابراین با استفاده از QTL‌های شناسایی شده می‌توان پس از تعیین اعتبار QTLها، ژنوتیپ‌های برتر از نظر محتوای کلروفیل برای برنامه‌های انتخاب به کمک نشانگر را شناسایی کرد.

Assessment of Striga gesnerioides (Willd.) Resistance and Genetic Characterization of Forty-Six Cowpea (Vigna unguiculata (L.) Walp.) Genotypes in Ghana

The parasitic weed, Striga gesnerioides, imposes physiological stress on cowpea (Vigna unguiculata (L.) Walp.) resulting in significant yield loss in the regions of northern Ghana. This warranted identification of resistant cowpeas for sustainable production. The current work aim was to identify Striga-resistant cowpea genotypes and assess their genetic relatedness. Forty-six (46) cowpea genotypes were screened in pots for their reaction to Striga samples obtained from the upper east, upper west, and northern regions of Ghana and validated with C42-2B and 61R-M2 markers involving DNA amplification by PCR assay. Sixteen polymorphic SSR primer pairs were used to assess genetic relatedness among 46 cowpea genotypes. Data were analyzed with PowerMarker V. 3.25 and a dendrogram was generated with MEGA 4. On the whole, 65.2% of the cowpea genotypes had stable resistance to S. gesnerioides from the regions of northern Ghana and 34.8% were susceptible. The C42-2B marker resolved as a single DNA band of 280 bp with segregation efficiency of 80% and 61R-M2 marker as double DNA bands of 320 bp and 380 bp with segregation efficiency of 60% associated with Striga resistance. Sixteen (16) polymorphic SSR primers distinguished all 46 cowpea genotypes into three clusters. Gene diversity ranged from 0.04 to 0.49 with an average of 0.29. The average allele frequency is 0.78, with a mean genetic diversity of 0.29. Polymorphism information content (PIC) varied from 0.08 to 1.00 with an average of 0.55. Therefore, cowpeas with Striga resistance and other desirable traits can be evaluated and released as varieties for farmers to cultivate.