Simple Sequence Repeat Markers Research Articles

Assessing the genetic diversity of taro germplasm collection in Vietnam using simple sequence repeat markers

ABSTRACT This study evaluated the genetic diversity of 253 taro (Colocasia esculenta (L.) Schott) germplasm accessions collected in Vietnam at the molecular level using 20 Simple Sequence Repeat (SSR) markers. High genetic diversity in the taro germplasm accessions were detected with 100% polymorphic SSR loci, and 89 alleles were obtained at the 20 SSR loci with an average of 4.45 alleles per locus, of which 14 markers had high polymorphism (3 alleles/locus). Polymorphic Information Content (PIC) values obtained at 20 SSR loci ranged from 0.31 (Ce0078) to 0.85 (HK34), with an average of 0.65. The genetic similarity coefficient within the accessions ranged from 0.39 to 1.00. All 253 accessions were classified into 2 groups at a genetic similarity level of 0.60; one of the groups (group 2) was divided into 8 sub-groups at a genetic similarity level of 0.64. Some accessions (such as 28279 and SP-19-009; SP-19-061 and SP-19-023; 28278 and SP-19-006) with a high genetic similarity coefficient (1.00) showed a very close genetic relationship, while others (such as 10063 and 11544) with a low genetic similarity coefficient (0.39) showed a fairly distant genetic relationship. The study’s results provide a foundation for preserving and breeding taro in Vietnam. Five taro accessions (28211, SP-19-017, T.3578, T.3515, and 10098) carrying specific alleles that could be identified by 6 SSR markers (uq55–112, uq73–164, HK35, Ce0078, HK22, and HK31) were detected. Furthermore, the SSR marker approach showed the potential application in identifying genetic relationships and distinguishing different taro cultivars.

Molecular markers for genetic analysis of Indian tropical tasar ecoraces and hybrid populations (Antheraea mylitta.d)

The tropical tasar silkworm Antheraea mylitta D., a wild sericigenous and polyphagous insect is cultivated in the dense, humid, tropical forests of eastern, central and southern India. Its primary food plants are Terminalia arjuna, Terminalia tomentosa and Shorea robusta. The improved varieties of these silkworms can be evolved by hybridization through backcross method, to improve the traits in the upcoming generation by selective parental selection. The present studies of genetic relations between Andhra local and Daba TV ecoraces is identified by DNA markers viz., simple sequence repeats (SSRs), most of which have produced polymorphic bands and based on phylogeny of tasar ecoraces using SSR markers, which further provides molecular evidence of the fact that climatic factors, the changes at DNA level and its wide range of distribution in varied geographic conditions would lead to genetic divergence ultimately leading to the formation of new ecorace.. KEYWORDS :Antheraea mylitta, tasar ecorace, microsatellites, phylogeny, genetic diversity, Breeding, Backcross

Genetic diversity in Pima (Gossypium barbadense L.) and advanced interspecific hybrids (Gossypium hirsutum x Gossypium barbadense) of cotton germplasm in Ethiopia

This study was conducted to assess the genetic diversity in Pima (Gossypium barbadense L.) and advanced interspecific hybrids (G. hirsutum L. x G. barbadense L.) of cotton germplasm in Ethiopia. A total of 26 germplasm were genotyped using 26 polymorphic simple sequence repeat (SSR) markers. A total of 165 polymorphic loci, with a range of 3 to 13 alleles and a mean of 6.35 per marker were detected. About 11% of total alleles were unique alleles in 11 germplasm. The gene diversity varied from 0.39 to 0. 89, while the heterozygosity was in the range of 0 to 1.00. Furthermore, the polymorphic information content of the markers varied from 0.37 (BNL1417) to 0.88 (BNL1672) with an average of 0.68. Among the complete panel of cotton germplasm used in this study, the pairwise genetic distance ranged from 0.08 to 0.94, with an overall mean of 0.61. The UPGMA cluster analysis grouped the Pima cotton germplasm into two cluster groups and the advanced interspecific hybrid cotton germplasm makes one cluster. Principal coordinate analysis indicates that the first three most informative principal coordinates explained 68.4% of the genetic variation. The result evidenced very low to high genetic dissimilarity and overall, a considerable genetic diversity among and within germplasm which could be used to further broaden the genetic base and to enlarge the number of available cotton germplasm.

Pyramiding aphid resistance genes into the elite cowpea variety, Zaayura, using marker-assisted backcrossing

The cowpea aphid (Aphis cracivora) is a cosmopolitan insect pest that causes economic damage on cowpea. Although the pest persists at all the growth stages of the crop, in West Africa, aphids are the only major insect pests that farmers regularly control at the vegetative stage. Thus, deploying aphid-resistant crop varieties can reduce farmers' expenditure on insecticide. The availability of different biotypes of the pest and reports of resistance breakdown necessitates pyramiding of sources of aphid resistance to develop a more robust genotype for durable resistance. Two aphid-resistance genes, sourced from SARC-1-57-2 and IT97K-556-6, were introgressed through gene pyramiding technique into a farmers’ preferred cowpea variety, Zaayura, using marker-assisted backcrossing. A simple sequence repeat (SSR) marker, CP 171F/172R, and an allele-specific single nucleotide polymorphism (SNP) marker, 1_0912, were used for foreground selection of the SARC-1-57-2 and IT97K-556-6 aphid resistance genes, respectively. A stepwise backcross approach was used to introgress the major aphid resistance QTL (QAc-vu7.1) from IT97K-556-6 into Zaayura using the marker 1_0912 coupled with intermittent screening under artificial aphid infestation. After the fourth backcross generation, three heterozygous BC4F1 of Zaayura/TT97K-556-6 were intercrossed to Zaayura Pali to develop intercross F1 (ICF1). Three true ICF1 hybrids allowed to self to produce ICF2. Five (5) out of 48 ICF2 plants which were genotyped with the two foreground markers had the two aphid resistance genes fixed in the double homozygous dominant state. For background selection, out of 192 allele-specific markers screened, only 47 polymorphic markers were identified and used for the background analysis of the pyramided lines. The recurrent parent genome recovery ranged from 72 to 93.8 %. ICF2_Zaa/556/SARC-P6 had the highest recurrent parent genome and the least heterozygosity among the five improved lines. The five pyramided lines showed superior resistance under artificial aphid infestation as compared to the two donor parents with damage scores ranging from 2.0 to 2.3. On the field, however, there were no significant differences between the pyramided lines and their recurrent parent for all the agronomic traits measured except for grain yield. The pyramided lines do not only stand the chance of being released as new varieties but are also valuable genetic resources for other breeding programs that seek to improve cowpea for aphid resistance.

Identification and expression of gene loci underlying the quantitative trait loci of starch content in cassava

ABSTRACT In this study, a genetic linkage map was developed based on simple sequence repeat (SSR) markers to aid in the identification and expression analysis of gene loci underlying the quantitative trait loci (QTL) of starch content (SC) in cassava (Manihot esculenta). A total of 912 polymorphic loci from 4,515 tested SSRs were mapped into 18 linkage groups. QTL analysis revealed four loci with highly significant associations with starch. Gene annotation was performed, and potential genes related to starch synthesis were identified. Of these, expression of four genes related to starch synthesis (Raffinose synthase [RS], Phosphoenolpyruvate kinase [PK], Glucose-6-phosphate [G6P], and Glycogen synthase kinase 3 [GSK-3]) was investigated by real-time PCR assays. The results found a statistically significant difference (p < 0.05) at 3 months after planting (MAP) in all the tested genes, whereas a higher expression was detected in the low-SC group with specific genotypes of linked markers. A higher level of expression was observed in the RS, PK, and G6P genes at six and nine MAP, indicating that starch accumulation mainly occurs after 3 MAP, during which the root system begins to form. The potential genes identified in this study could provide a better understanding of the starch biosynthesis mechanism, and could be useful for applications in marker-assisted selection to facilitate cassava breeding programs in the future.

Molecular Diversity and Combining Ability in Newly Developed Maize Inbred Lines under Low-Nitrogen Conditions.

Nitrogen is an essential element for maize growth, but excessive application can lead to various environmental and ecological issues, including water pollution, air pollution, greenhouse gas emissions, and biodiversity loss. Hence, developing maize hybrids resilient to low-N conditions is vital for sustainable agriculture, particularly in nitrogen-deficient soils. Combining ability and genetic relationships among parental lines is crucial for breeding superior hybrids under diverse nitrogen levels. This study aimed to assess the genetic diversity of maize inbred lines using simple sequence repeat (SSR) markers and evaluate their combining ability to identify superior hybrids under low-N and recommended conditions. Local and exotic inbred lines were genotyped using SSR markers, revealing substantial genetic variation with high gene diversity (He = 0.60), moderate polymorphism information content (PIC = 0.54), and an average of 3.64 alleles per locus. Twenty-one F1 hybrids were generated through a diallel mating design using these diverse lines. These hybrids and a high yielding commercial check (SC-131) were field-tested under low-N and recommended N conditions. Significant variations (p < 0.01) were observed among nitrogen levels, hybrids, and their interaction for all recorded traits. Additive genetic variances predominated over non-additive genetic variances for grain yield and most traits. Inbred IL3 emerged as an effective combiner for developing early maturing genotypes with lower ear placement. Additionally, inbreds IL1, IL2, and IL3 showed promise as superior combiners for enhancing grain yield and related traits under both low-N and recommended conditions. Notably, hybrids IL1×IL4, IL2×IL5, IL2×IL6, and IL5×IL7 exhibited specific combining abilities for increasing grain yield and associated traits under low-N stress conditions. Furthermore, strong positive associations were identified between grain yield and specific traits like plant height, ear length, number of rows per ear, and number of kernels per row. Due to their straightforward measurability, these relationships underscore the potential of using these traits as proxies for indirect selection in early breeding generations, particularly under low-N stress. This research contributes to breeding nitrogen-efficient maize hybrids and advances our understanding of the genetic foundations for tolerance to nitrogen limitations.

Molecular Identification of Genetic Diversity and Population Structure in Moroccan Male Date Palm (Phoenix dactylifera L.) Using Inter-Simple Sequence Repeat, Direct Amplification of Minisatellite DNA, and Simple Sequence Repeat Markers

Understanding genetic diversity and population structure plays a vital role in the efficient use of available material in plant-breeding programs and in germplasm conservation strategies. In the present study, we aim to evaluate the genetic variations and population structure of male date palms from Morocco. The genetic diversity of 100 date palm (Phoenix dactylifera L.) genotypes was investigated using the performance of three types of molecular markers: inter-simple sequence repeats (ISSRs), direct amplification of minisatellite DNA (DAMD), and simple sequence repeats (SSRs). On the basis of their polymorphic information content (PIC) (ISSRs = 0.38; DAMD = 0.4; SSRs = 0.33), effective multiplex ratio (EMR) (ISSRs = 27.34; DAMD = 52.31; SSRs = 22.20), Resolving power Rp (ISSR = 13.81; DAMD = 28.73; SSR = 14.6), and marker index (MI) (ISSRs = 9.22; DAMD = 20.23; SSRs = 7.54) values, all markers used in our study are considered informative markers. Among them, DAMD markers demonstrated slightly higher informativeness compared to ISSR and SSR markers. A total of 216, 438, and 248 bands were, respectively, detected using ISSRs, DAMD, and SSRs, with 95%, 98% and 94% of polymorphism, respectively. The AMOVA results revealed considerable diversity within date palms. The PCOa results showed that males of Tinghir and Errachidia were regrouped into the same cluster, while males of Goulmima were separated into another group. A cluster and structure analysis separated the studied genotypes into three groups. One group comprises genotypes of males from Zagora with some female varieties scattered in this group. The second group includes male genotypes from Goulmima along with accessions of female and male varieties. The third group contains males of Errachidia, Tata and Tinghir populations. The cluster and structure analysis separated the studied genotypes according to their origin.

Chloroplast Haplotype Diversity in the White Oak Populations of the Italian Peninsula, Sicily, and Sardinia

A phylogeographic study on the chloroplast DNA of natural white oak forests (Quercus subgen. Quercus, sect. Quercus) was carried out to identify possible haplotype-structured distribution within the Italian Peninsula, Sicily, and Sardinia. Sixty white oak populations belonging to Q. frainetto, Q. robur and the collective groups Q. petraea and Q. pubescens were considered and analyzed by combining five Chloroplast Simple Sequence Repeat (cpSSR) markers. A total of 28 haplotypes were detected. Central and southern Italy displayed the highest variability (14 and 10 haplotypes, respectively), followed by northern Italy (7), Sardinia (7), and Sicily (5). A complex geographical structure of the haplotype distribution emerged, highlighting (i) a high number of low-frequency haplotypes; (ii) the marked isolation of Sardinia; (iii) the occurrence of haplotypes widely distributed throughout the Italian Peninsula; (iv) the idiosyncrasy of Sicily, which exhibits exclusive haplotypes, and haplotypes shared with Sardinia and the rest of the Italian Peninsula. The haplotype distribution was also found to be partially related to the taxonomic identity of the specimens, with the following features emerging: a geographic separation between the central Italy and southern Italy Q. frainetto populations, an unexpected discontinuity between the Calabrian and Sicilian Q. petraea subsp. austrotyrrhenica populations, and the absence of the most common haplotype among the Q. pubescens populations of central and southern Italy.

Machine Learning-Based Identification of Mating Type and Metalaxyl Response in Phytophthora infestans Using SSR Markers.

Phytophthora infestans is the causal agent of late blight in potato. The occurrence of P. infestans with both A1 and A2 mating types in the field may result in sexual reproduction and the generation of recombinant strains. Such strains with new combinations of traits can be highly aggressive, resistant to fungicides, and can make the disease difficult to control in the field. Metalaxyl-resistant isolates are now more prevalent in potato fields. Understanding the genetic structure and rapid identification of mating types and metalaxyl response of P. infestans in the field is a prerequisite for effective late blight disease monitoring and management. Molecular and phenotypic assays involving molecular and phenotypic markers such as mating types and metalaxyl response are typically conducted separately in the studies of the genotypic and phenotypic diversity of P. infestans. As a result, there is a pressing need to reduce the experimental workload and more efficiently assess the aggressiveness of different strains. We think that employing genetic markers to not only estimate genotypic diversity but also to identify the mating type and fungicide response using machine learning techniques can guide and speed up the decision-making process in late blight disease management, especially when the mating type and metalaxyl resistance data are not available. This technique can also be applied to determine these phenotypic traits for dead isolates. In this study, over 600 P. infestans isolates from different populations-Estonia, Pskov region, and Poland-were classified for mating types and metalaxyl response using machine learning techniques based on simple sequence repeat (SSR) markers. For both traits, random forest and the support vector machine demonstrated good accuracy of over 70%, compared to the decision tree and artificial neural network models whose accuracy was lower. There were also associations (p < 0.05) between the traits and some of the alleles detected, but machine learning prediction techniques based on multilocus SSR genotypes offered better prediction accuracy.

Morphological and molecular characterization of ‘Saragolla’ wheats (Triticum turgidum subsp. durum from Abruzzo, Italy)

A morphological and genetic characterization of autochthonous ‘Saragolla’ wheats, currently cultivated in Abruzzo Region (Italy), was carried out. Using 15 simple sequence repeat (SSR) markers and 24 UPOV morphological traits we compared: (a) 13 ‘Saragolla’ genotypes with traits of the italicum/apulicum botanical varieties (Saragolla (Sar.) italicum), (b) 26 ‘Saragolla’ genotypes with traits of leucurum/affine botanical varieties (Sar. leucurum), (c) 8 breeding varieties (pure lines), and (d) 5 Italian autochthonous wheats and 1 turanicum line (old wheats). One hundred twenty-six (126) alleles were identified. The number of alleles per locus spanned from 4 to 15 and the number of alleles per genotype varied between 12 and 21. Values of gene diversity (Nei) across the 53 genotypes was 0.17. The groups of Sar. leucurum and Sar. italicum genotypes were morphologically distinguishable from the groups of old wheats and pure lines. Likewise, the analysis of molecular data using the discriminant analysis revealed that genotypes with the Sar. italicum phenotype displayed distinct genetic differences from Sar. leucurum, pure lines and old wheats. These results make Sar. italicum genotypes distinguishable and eligible as a conservation variety. Ward's clustering analysis of the 53-genotype pool showed that the ‘Saragolla’ landrace is a valuable repository of genetic diversity.

Utilizing SSR markers to examine the population structure and molecular genetic diversity of walnut (Juglans regia L.) genotypes in the Northwestern Himalayan region of Jammu and Kashmir

By using 16 simple sequence repeat (SSR) markers, the genetic relatedness of 21 exceptional walnut genotypes was assessed. A significant degree of genetic diversity was observed within a given population, as indicated by the number of alleles per locus ranging from 2 to 4. WGA-1, WGA-4, and WGA-79 contained the greatest number of alleles (4), followed by WGA-118, WGA-202, and WGA-42. Conversely, WGA-27, WGA-69, and WGA-32 contained the fewest alleles. The range of the PIC value was 0.11 to 0.38. Using model-based cluster analysis, all genotypes were categorized into two primary clusters according to the UPGMA dendrogram, with varying degrees of sub-clustering. All the genotypes were categorized into six genetically distant subpopulations. The genotypes were genetically distinct but had variable degrees of admixture. The anticipated heterozygosity at a specific locus ranged from 0.563 to 0.741. Additionally, population differentiation (Fst) ranged between 0.176 and 0.261. These findings highlight the importance of considering germplasm diversity in walnut breeding programs and conservation efforts aimed at enhancing walnut cultivation in the region. Overall, this study contributes to our understanding of walnut genetic diversity in the Northwestern Himalayan region of Jammu and Kashmir and informs future breeding and conservation strategies.

Genetic diversity studies between Ipomoea wild species and cultivated sweet potato (Ipomoea batatas (L.) Lam.) using SSR markers

Sweet potato (Ipomoea batatas (L.) Lam) is one of the major tuber crops in Asian countries, including India, yet the interrelationship and genetic variability among the cultivar and its crop wild relatives remain obscure. The wild relatives of sweet potato represent a vital source of untapped genetic diversity in the breeding programs. In this study, a set of 12 Simple Sequence Repeats (SSR) markers were utilized to understand the extent of genetic diversity and relationship within and between 20 sweet potato accessions, 23 wild Ipomoea species and two Merremia species for utilization in breeding programmes. The SSR primers produced 84 polymorphic alleles within the range of 105–393 bp, collectively showing an average polymorphism of 94.5 %. The average Polymorphic Information Content (PIC) value of 0.67 showed that all the primers were polymorphic in nature. Similarity coefficient based dendrogram and Principal Component Analysis (PCA) scatter plot clearly differentiated all the cultivars and wild species. The cluster dendrogram analysis revealed the close relationship of cultivars with I. triloba and I. trifida at a similarity index of 0.75. Our analysis showed a high degree of genetic variability within and between hexaploid sweet potato and diploid wild species, whereas lower within the cultivars, which shows that there is a high level of genetic diversity exists within the Ipomoea species for its utilization in breeding programs. Thus, the two wild species, I. trifida and I. triloba could be used in hybridization for improvement of sweet potato through ploidy manipulation.

Morpho-histology of co-occurrence of somatic embryos, shoots, and inflorescences within a callus of Limonium 'Misty Blue'.

This is the first attempt to report the co-occurrence of somatic embryos, shoots, and inflorescences and their sequential development from stem cell niches of an individual callus mass through morpho-histological study of any angiosperm. In the presence of a proper auxin/cytokinin combination, precambial stem cells from the middle layer of a compact callus, which was derived from the thin cell layer of the inflorescence rachis of Limonium, expressed the highest level of totipotency and pluripotency and simultaneously developed somatic embryos, shoots, and inflorescences. This study also proposed the concept of programmed cell death during bipolar somatic embryo and unipolar shoot bud pattern formation. The unique feature of this research was the stepwise histological description of in vitro racemose inflorescence development. Remarkably, during the initiation of inflorescence development, either a unipolar structure with open vascular elements or an independent bipolar structure with closed vascular elements were observed. The protocol predicted the production of 6.6 ± 0.24 and 7.4 ± 0.24 somatic embryos and shoots, respectively, from 400 mg of callus, which again multiplied, rooted, and acclimatised. The plants' ploidy level and genetic fidelity were assessed randomly before acclimatisation by flow cytometry and inter simple sequence repeats (ISSR) marker analysis. Finally, the survivability and flower quality of the regenerated plants were evaluated in the field.

Construction of a DNA Fingerprint Map and a Core Collection of Platycladus orientalis

Platycladus orientalis is one of the main species used in afforestation projects in the arid mountains of north and northwest China, meaning that the species has high ecological and economic value. Studying its genetic diversity and obtaining a core germplasm base and genetic fingerprint data are important for the screening, development, and utilization of the species. This can provide the core materials for the preservation and evaluation and mining of germplasm resources and can provide superior gene resources for breeding programs. In this study, the genetic diversity among 104 P. orientalis germplasm resources was examined using simple sequence repeat (SSR) markers, and a core germplasm containing 31 accessions was constructed that represents the most genetic diversity of P. orientalis accessions. Each of 20 pairs of primers showed polymorphism, and 117 alleles were identified. The average number of alleles at each locus was six, and the mean effective allele number was 2.607. The average Shannon’s information index was 0.983, and the average polymorphism information content was 0.445. There is thus a significant amount of genetic variation within P. orientalis germplasm, yielding a rich genetic diversity. The constructed core germplasm accounted for 30% of the original germplasm. There was no significant difference in genetic diversity between the core germplasm and the original germplasm resources, indicating that the obtained core germplasm resources could fully represent the original germplasm. Using 17 SSR primers with high polymorphism, the DNA fingerprints of 104 P. orientalis germplasm resources were constructed. The results showed that 98 had specific DNA fingerprints. The results of this study provide a valuable basis for the collection, preservation, and utilization of P. orientalis germplasm resources, and the methods adopted in this study have important reference value for the construction of core germplasm of other perennial woody plants.

Molecular characterization of some currants (Ribes species) from Türkiye using inter-primer binding site (iPBS) and simple sequence repeat (SSR) markers

AbstractThis study was carried out to determine the genetic relationships and variation levels among currant genotypes and cultivars in Türkiye. Ten currant cultivars and one hybrid Jostaberry cultivar, which are breeding products of Europe but are best known and have high commercial value in Türkiye, were used. One black-fruited currant cultivar from Türkiye was included. In addition, 14 currant genotypes naturally grown in Türkiye were used. In this study, 14 retrotransposon-based inter-primer binding site (iPBS) and 10 microsatellite-based simple sequence repeat (SSR) markers were used for a total of 26 currant samples. By evaluating the allele profiles obtained from PCR and capillary electrophoresis with iPBS and SSR primers, the size range, average number of alleles, total number of alleles, number of polymorphic alleles, polymorphism rate, heterozygosity, polymorphism information content, marker index and discriminating power were determined successfully. In addition, unweighted pair group method with arithmetic mean (UPGMA) dendrograms and principal coordinate analysis (PCoA) were constructed and performed. The amounts of amplification product produced using iPBS and SSR markers for currant species with different fruit colours were also compared. In this study, it was proven that the level of genetic relatedness among currant cultivars and genotypes can be determined with high accuracy by iPBS markers. Moreover, the use of iPBS markers in currants was performed for the first time in this study. On the other hand, with the preferred SSR markers, the level of genetic relatedness among currants was successfully determined.

Development of SSRs Based on the Whole Genome and Screening of Bolting-Resistant SSR Marker in Brassica oleracea L.

Simple sequence repeats (SSRs), also known as microsatellites, stand out as the most crucial molecular markers in both animals and plants owing to their high polymorphism, extensive information content, ease of detection through polymerase chain reaction (PCR) assays, and widespread distribution across the genome. In this study, a total of 125,443 SSR loci were identified from the whole-genome sequence of B. oleracea, and 82,948 primer pairs for SSR have been designed. Furthermore, each primer pair is designated with a unique identifier (ranging from BolSSR00001 to BolSSR82984). Our findings indicated that certain markers within them could be transferred to other cruciferous crops. In addition, a total of 336 pairs of SSR primers have been used to screen the polymorphism between the bolting-resistant and bolting-easy gene pools. After the test of verification with F2 generation individual plants, we obtained an SSR dominant marker, BolSSR040196, linked with bolting-resistant locus in cabbage, and the genetic distance between this SSR marker and the bolting-resistant locus was 10.69 cM. Moreover, BolSSR040196 is located on the C05 chromosome with a CT motif, characterized by a repeat of 9 in bolting-easy plants and 11 in bolting-resistant plants. Haplotype analysis showed that the correct prediction rate reached 82.35%. The BolSSR040196 marker can be used in marker-assisted selection (MAS) breeding, offering a straightforward and efficient approach for bolting-resistant cabbage breeding in the future.

An aldehyde dehydrogenase gene, GhALDH7B4_A06, positively regulates fiber strength in upland cotton (Gossypium hirsutum L.).

High fiber strength (FS) premium cotton has significant market demand. Consequently, enhancing FS is a major objective in breeding quality cotton. However, there is a notable lack of known functionally applicable genes that can be targeted for breeding. To address this issue, our study used specific length-amplified fragment sequencing combined with bulk segregant analysis to study FS trait in an F2 population. Subsequently, we integrated these results with previous quantitative trait locus mapping results regarding fiber quality, which used simple sequence repeat markers in F2, F2:3, and recombinant inbred line populations. We identified a stable quantitative trait locus qFSA06 associated with FS located on chromosome A06 (90.74-90.83 Mb). Within this interval, we cloned a gene, GhALDH7B4_A06, which harbored a critical mutation site in coding sequences that is distinct in the two parents of the tested cotton line. In the paternal parent Ji228, the gene is normal and referred to as GhALDH7B4_A06O; however, there is a nonsense mutation in the maternal parent Ji567 that results in premature termination of protein translation, and this gene is designated as truncated GhALDH7B4_A06S. Validation using recombinant inbred lines and gene expression analysis revealed that this mutation site is correlated with cotton FS. Virus-induced gene silencing of GhALDH7B4 in cotton caused significant decreases in FS and fiber micronaire. Conversely, GhALDH7B4_A06O overexpression in Arabidopsis boosted cell wall component contents in the stem. The findings of our study provide a candidate gene for improving cotton fiber quality through molecular breeding.

Genetic background of lily germplasm resources based on SSR markers

To study the genetic background of lily (Lilium spp.) germplasm resources, and accurately evaluate and select excellent germplasm for genetic improvement of lily, we analyzed the genetic background of 62 lily germplasm accessions from 11 provinces of China by using simple sequence repeat (SSR) molecular markers. The results showed that 15 out of 83 pairs of lily SSR primers were polymorphic. A total of 157 allelic loci were amplified, with the number of alleles per locus ranging from 5 to 19 and the average number of effective alleles per locus being 4.162 8. The average observed heterozygosity and expected heterozygosity were 0.228 2 and 0.694 1, respectively. The average polymorphic information content was 0.678 8. The average Nei's diversity index and Shannon's information index were 0.694 1 and 1.594 9, respectively, indicating that the tested lily germplasm had high genetic diversity. The 62 germplasm accessions were classified into 5 groups by the unweighted pair group method with arithmetic mean (UPGMA) and into 3 groups by the principal component analysis. The two analyses revealed a geographic correlation among different groups. The majority of lily germplasm accessions from the same source tended to cluster together. The population structure analysis classified the lily accessions into 4 populations and 1 mixed population. The above results provide a theoretical basis and genetic resources for the precise identification and breeding of lily germplasm resources.

Differences in Albizia odoratissima genetic diversity between Hainan Island and mainland populations in China.

This study aimed at exploring unique population genetic characteristics of Albizia odoratissima (Linn. f) Benth on Hainan Island to provide a scientific basis for its rational utilization and protection. It analyzed the genetic diversity and structure of 280 individuals from 10 subpopulations of A. odoratissima from Hainan Island and Baise City using 16 expression sequence markers - simple sequence repeat markers. The genetic diversity of Hainan population (I = 0.7290, He = 0.4483) was lower than that of the Baise population (I = 0.8722, He = 0.5121). Compared with the Baise population (Nm = 2.0709, FST = 0.1077), the Hainan Island population (Nm = 1.7519, FST = 0.1249) exhibited lower gene flow and higher degree of genetic differentiation. Molecular variance and genetic differentiation analyses showed that the main variation originated from individuals within the subpopulation. There were significant differences in the genetic structure between Hainan and Baise populations. It grouped according to geographical distance, consistent with the Mantel test results (R2 = 0.77, p = 0.001). In conclusion, the genetic diversity of the island A. odoratissima population was lower than that distributed on land, the two populations exhibited obvious genetic structure differences. Both the degrees of inbreeding and genetic differentiation were higher in the island population than in the land population.

Identification and characterization of functionally relevant SSR markers in natural Dalbergia odorifera populations

BackgroundDalbergia odorifera is a rare and precious rosewood specie, which is valued for its amber tones, abstract figural patterns, and impermeability to water and insects. However, the information on genetic diversity and marker-assisted selection breeding of D. odorifera is still limited. Simple sequence repeat (SSR) markers are an ideal tool for genetic diversity analysis and marker-assisted molecular breeding for complex traits.ResultsHere, we have developed SSR markers within candidate genes and used them to explore the genetic diversity among D. odorifera germplasm resources. A total of 635 SSR loci were identified. The proportions of mono-, di- and tri-nucleotide repeat motifs were 52.28%, 22.99% and 21.42%, respectively. From these, a total of 114 SSR primers were synthesized, of which 24 SSR markers displayed polymorphism (polymorphic information content (PIC) > 0.25). Subsequently, these polymorphic markers were used for the genetic diversity analysis of 106 D. odorifera individuals from 11 natural populations. According to the genetic diversity analysis of D. odorifera natural populations, the average observed heterozygosity (Ho) was 0.500, the average expected heterozygosity (He) was 0.524, and the average Shannon’s information index (I) was 0.946. These indicated that the natural populations had moderate genetic diversity. AMOVA analysis showed that 5% of the total variation was within the individuals of a population, whereas 95% of the variation was among the individuals of the populations, indicating a high degree of genetic variation between populations. On the basis of their genetic structures, these populations could be divided into four groups.ConclusionsOur study provides important experimental resources for genetic studies and assists in the program of molecular breeding of D. odorifera wood formation.