Simple Sequence Repeat Marker Alleles Research Articles

Genetic diversity analysis among 123 accessions of castor (Ricinus communis L.) using SSR marker and its association to agronomic traits

Abstract. Anggraeni TDA, Waluyo B, Sugiharto AN, Kuswanto. 2022. Genetic diversity analysis among 123 accessions of castor (Ricinus communisL.) using SSR marker and its association to agronomic traits. Biodiversitas 23: 1211-1221. Castor (Ricinus communis L.) breeding program targets to create dwarf-type plants suitable for mechanical harvesting. Characterization of plantsusing morphological and molecular markers can enhance the successful breeding program. This studyaimed to investigate the diversity of castor accessionsusing Simple Sequence Repeat (SSR) markers and find the SSR markers that are significantly associated with the agronomic traits. The castor germplasm collection consisting of 123 accessions from the islands throughout Indonesia, breeding lines, and introducedaccessions displayed a moderate genetic diversity. The germplasm collection showed high variation in plant height, node length average, number of nodes, 100 seed weight, and oil content. The association analysis using GLM (General Linear Model) and MLM (Mixed Linear Model) could detect six associations between SSR marker alleles and agronomic traits. Among the marker alleles, two marker alleles had an overlap association. RcSSR-12_175 had an association with plant height and flowering day, RcSSR-23_113 had an association with node length average and branch number, and RcSSR-4_125 had an association with seed weight/raceme. This finding could provide information on Indonesia’s castor accession status. The linked-trait SSR markers are useful in marker-assisted selection for breeding high yield dwarf type-castor.

Analysis of European hazelnut (Corylus avellana) reveals loci for cultivar improvement and the effects of domestication and selection on nut and kernel traits.

Turkey is a rich source of European hazelnut (Corylus avellana) germplasm with nearly 400 accessions in the national collection. This genetic material encompasses cultivars, landraces and wild genotypes which were characterized for 12 nut and 13 kernel traits over 2years in the 1990s. Analysis of these attributes revealed both the positive and negative impacts that human selection and breeding have had on hazelnut. Thus, while selection has resulted in larger nuts and kernels, cultivars have fewer nuts per cluster and kernels with larger internal cavities. Breeding has also resulted in a propensity for cultivars to have higher proportions of double kernels and empty nuts, two traits which reduce quality and yield. In addition, it is clear that while selection has successfully increased hazelnut fat content it has not impacted overall flavor, a much more complex trait. The nut and kernel phenotypic data were combined with genotypic data from 406 simple sequence repeat marker alleles for association mapping of the quantitative trait loci (QTL) for the traits. A total of 78 loci were detected in the population with the highest proportions for nut (24%) and kernel (26%) appearance parameters followed by quality (19%), shell thickness (16%) and yield-related (15%) traits. It is hoped that some of the identified QTL will be useful for future breeding of hazelnut for improved nut and kernel yield and quality.

Genetic Variation and Association Analysis of the SSR Markers Linked to the Major Drought-Yield QTLs of Rice.

Drought is one of the major abiotic stresses, which hampers the production of rice worldwide. Informative molecular markers are valuable tools for improving the drought tolerance in various varieties of rice. The present study was conducted to evaluate the informative simple sequence repeat (SSR) markers in a diverse set of rice genotypes. The genetic diversity analyses of the 83 studied rice genotypes were performed using 34 SSR markers closely linked to the major quantitative trait loci (QTLs) of grain yield under drought stress (qDTYs). In general, our results indicated high levels of polymorphism. In addition, we screened these rice genotypes at the reproductive stage under both drought stress and nonstressful conditions. The results of the regression analysis demonstrated a significant relationship between 11 SSR marker alleles and the plant paddy weight under stressful conditions. Under the nonstressful conditions, 16 SSR marker alleles showed a significant correlation with the plant paddy weight. Finally, four markers (RM279, RM231, RM166, and RM231) demonstrated a significant association with the plant paddy weight under both stressful and nonstressful conditions. These informative-associated alleles may be useful for improving the crop yield under both drought stress and nonstressful conditions in breeding programs.

Analysis of rice blast resistance gene Pi-z in rice germplasm using pathogenicity assays and DNA markers

The Pi-z gene in rice confers resistance to a wide range of races of the rice blast fungus, Magnaporthe oryzae. The objective of this study was to characterize Pi-z in 111 rice germplasm accessions using DNA markers and pathogenicity assays. The existence of Pi-z in rice germplasm was detected by using four simple sequence repeat (SSR) markers (RM527, AP4791, AP5659-1, AP5659-5) closely linked to Pi-z, and was verified using pathogenicity assays with an avirulent strain (IE1k) and two virulent races (IB33 and IB49). Among 111 germplasm accessions evaluated, 73 were found to contain the Pi-z gene using both SSR markers and pathogenicity assays. The remaining 38 germplasm accessions were found to be inconsistent in their responses to the blast races IB33, IEIk and IB49 with expected SSR marker alleles, suggesting the presence of unexpected SSR alleles and additional R gene(s). These characterized germplasm can be used for genetic studies and marker-assisted breeding for improving blast resistance in rice.

Introgression of Root‐Knot Nematode Resistance into Tetraploid Cottons

Root‐knot nematode (RKN) resistance introgression into tetraploid cotton (Gossypium spp.) and its ancestral genome origin were examined. Resistance sources (‘Acala NemX’, ‘Clevewilt 6’, Auburn 623 RNR) were compared with diverse germplasm using simple sequence repeat (SSR) markers from chromosomes 7, 11, and 14 and DNA sequence information. Differences (P < 0.05) were observed for mean root galling index (GI; scale 0–10) between the 56 resistant and susceptible entries. In resistance sources, GI ranged from 0.3 to 2.9, but no consistent differences were observed at allele‐marker or DNA sequence level. Except for CIR316 allele (206–207 bp) on chromosome 11, no alleles from other SSRs were observed on resistant entries (GI < 3). Allotetraploid G. hirsutum L. (AD1) and G. barbadense L. (AD2) showing the same SSR marker alleles as G. arboreum L. (A2) might suggest resistance introduction from the diploid cotton A2 genome (genetic distance 0.19 to 0.27). However, percent sequence identity from MUCS088 and CIR316 revealed G. barbadense and resistant G. hirsutum (206–207 bp) also were close to diploids G. herbaceum L. (A1), G. thurberi Tod. (D1), and G. trilobum (DC.) Skovst. (D8). Other G. hirsutum DNA sequences were closer to G. raimondii Ulbr. (D5). These analyses indicated resistance introgression into G. hirsutum allotetraploid cottons occurred by artificial hybridization with ancestral genome origin from G. arboreum as well as G. thurberi and not during cotton genome evolution.

Genetic diversity of resistance genes controlling fusarium head blight with simple sequence repeat markers in thirty-six wheat accessions from east asian origin

Fusarium head blight (FHB) is a serious disease of wheat worldwide that may cause substantial yield and quality losses. Breeding for FHB-resistant cultivars is the most cost-effective approach to control FHB. The objective of the present study was to determine the relationship of resistance between new resistant sources and Sumai 3 using five simple sequence repeat (SSR) markers closely linked to the major QTL for FHB resistance on chromosome arms 3BS and 6BS. All five SSR markers were highly polymorphic between Sumai 3 (and its derivatives) and susceptible Canadian wheat lines. Most of the Sumai 3-derived Chinese wheat accessions and three Canadian FHB-resistant lines had all the Sumai 3 SSR marker alleles on chromosome arms 3BS and 6BS. The Chinese landrace Wangshuibai and two Japanese accessions Nobeokabozu and Nyu Bai had the same banding patterns as Sumai 3 for all five SSR marker alleles, and another Chinese landrace Fangshanmai had three of the five SSR markers in common with Sumai 3, and therefore most likely carries the same QTL as Sumai 3 on 3BS and 6BS. The Brazilian cultivar Frontana had no alleles in common with Sumai 3 on either QTL, and the Chinese landrace Hongheshang had only one of the five SSR markers in common with Sumai 3, therefore likely carrying resistance genes different from Sumai 3. The Italian cultivar Funo is not the donor of either the 3BS QTL or 6BS QTL. All five SSR seem to be effective candidates for marker-assisted selection to increase the level of resistance to FHB in wheat breeding programs.

Genetic Improvement of New Mexico Acala Cotton Germplasm and Their Genetic Diversity

The New Mexico cotton breeding program was established in 1926 and has been led by five generations of breeders and geneticists. The program has released more than 30 Acala 1517 cotton (Gossypium hirsutum L.) cultivars and numerous germplasm lines known for high fiber quality and Verticillium wilt (caused by Verticillium dahliae Kleb.) tolerance that have made substantial contributions to cotton breeding in the USA. The present project was initiated in 2003 to evaluate the genetic improvement of Acala 1517 cultivars and lines released over the past 75 yr in yield, boll size, seed index, lint percentage, fiber length, fiber strength, and micronaire. Their genetic divergence was also estimated by simple sequence repeat (SSR) markers. On the basis of the data available from annual yield trials, lint yield and lint percentage in Acala 1517 cotton have steadily increased since the 1930s, while boll size and seed index have gradually decreased since the 1960s. Fiber strength has been enhanced since the 1960s, which has been accompanied by steady increase in micronaire. However, fiber length in Acala 1517 cultivars tended to shorten from 31.0 to 30.0 mm from 1960 to 1990, whereas newly released Acala 1517 cultivars (Acala 1517‐95, 1517‐99, 1517‐02, 1517‐03, and 1517‐04) have fiber greater than 30.5 mm. Genetic distance among Acala 1517 genotypes ranged from 0.06 to 0.38 with an average of 0.18 on the basis of 189 SSR marker alleles, indicating a substantial genetic diversity among Acala 1517 cotton germplasm. Divergent germplasm introgression in the program has contributed to genetic diversity of Acala cotton germplasm and continuous genetic gain in Acala cotton cultivar improvement.