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1.
R. K. Kapila S. Naryal K. C. Dhiman 《Journal of plant biochemistry and biotechnology.》2012,21(2):286-291
Genetic diversity among 31 genotypes of field and garden pea including primitive cultivated forms and widely cultivated varieties of India was studied using 40 random decamer and 9 ISSR primers. A total of 274 amplicons were detected using both types of markers, which amplified 192 RAPD and 82 ISSR amplicons. Average number of bands amplified per primer was higher in case of ISSR (9.1) as compared to RAPDs (4.8). ISSR primers also exhibited higher average polymorphism (89.0%) and resolving power (4.50) than RAPDs (72.4%, 1.87, respectively). Genetic similarity estimates based on the pooled data of both types of markers using Jaccard??s coefficient ranged from 0.58 to 0.85 delineating considerable diversity among the pea genotypes studied. The 31 genotypes clustered in two major groups based on pooled data. Popular cultivars of garden and field pea of the region exhibited high similarities among themselves. However, primitive cultivated forms collected from the higher Indian Himalayas were diverse from the current varieties and hold potential in pea breeding programmes. 相似文献
2.
A. Bagheri J. G. Paull P. Langridge A. J. Rathjen 《Molecular breeding : new strategies in plant improvement》1995,1(2):193-197
The optimisation of polymerase chain reaction (PCR) for random amplified polymorphic DNA (RAPD) analysis in pea was investigated and the results were applied to an analysis of five representative Australian varieties and five selected boron-tolerant accessions derived from different geographical regions. Genotypes were compared using 34 random primers (Operon Technologies, Alameda, CA) which generated 180 polymorphic bands. Genetic similarity among genotypes was estimated on the basis of the percentage of common bands between genotypes and a dendrogram was constructed by the unweighted pair grouping method. A pattern of RAPD reaction corresponding to two main groups was discerned. The genetic divergence between Australian varieties and the boron-tolerant accessions suggests an intensive back-crossing programme would be required to transfer boron tolerance to a locally adapted genetic background. Our results show RAPD to be useful for clarifying phylogenic relationships within a species and also to provide useful genetic markers for varietal identification in pea. 相似文献
3.
An influence of some Random Amplified Polymorphic DNA (RAPD) reaction factors on resulting banding pattern and the ability
of RAPD technique to detect DNA polymorphism among six economically important pea cultivars was tested. Relatively high level
of DNA polymorphism among peas was observed, using polyacrylamide/urea gels and silver staining. Altogether 13 arbitrarily
designed primers produced 313 amplification products. In addition 59 polymorphisms were found. These polymorphisms can serve
as potential genetic markers. RAPD data were processed using cluster analysis and plotted as dendrogram. Each tested cultivar
was clearly distinguished from the others. Moreover,Pisum sativum andP. sativum subsp.arvense cultivars were separated into 2 different clusters, according to their systematic relationships. 相似文献
4.
Tribulus terrestris is well known for its medicinal importance in curing urino-genital disorders. Amplified fragment length polymorphism (AFLP),
selective amplification of microsatellite polymorphic loci (SAMPL), inter-simple sequence repeat (ISSR) and randomly amplified
polymorphic DNA (RAPD) markers were used for the first time for the detection of genetic polymorphism in this medicinal herb
from samples collected from various geographical regions of India. Six assays each of AFLP and SAMPL markers and 21 each of
ISSR and RAPD markers were utilized. AFLP yielded 500 scorable amplified products, of which 82.9% were polymorphic. SAMPL
primers amplified 488 bands, 462 being polymorphic (94.7%). The range of amplified bands was 66 [(TC)8G + M-CAG] to 98 [(CA)6AG + M-CAC] and the percentage polymorphism, 89.9 [from (CT)4C (AC)4A + M-CTG] to 100 [from (GACA)4 + M-CTA]. The ISSR primers amplified 239 bands of 0.4–2.5 kb, 73.6% showed polymorphism. The amplified products ranged from
5 to 16 and the percentage polymorphism 40–100. RAPD assays produced 276 bands, of which 163 were polymorphic (59%). Mantel
test employed for detection of goodness of fit established cophenetic correlation values above 0.9 for all the four marker
systems. The dendrograms and PCA plots derived from the binary data matrices of the four marker systems are highly concordant.
High bootstrap values were obtained at major nodes of phenograms through WINBOOT software. The relative efficiency of the
four molecular marker systems calculated on the basis of multiplex ratio, marker index and average heterozygosity revealed
SAMPL to be the best. Distinct DNA fingerprinting profile, unique to every geographical region could be obtained with all
the four molecular marker systems. Clustering can be a good indicator for clear separation of genotypes from different regions
in well-defined groups that are supported by high bootstrap values. 相似文献
5.
Noor Zafirah Ismail Hasni Arsad Mohammed Razip Samian Abdul Hafiz Ab Majid Mohammad Razak Hamdan 《Physiology and Molecular Biology of Plants》2016,22(4):523-534
Three polymerase chain reaction (PCR) techniques were compared to analyse the genetic diversity of Clinacanthus nutans eight populations in the northern region of Peninsular Malaysia. The PCR techniques were random amplified polymorphic deoxyribonucleic acids (RAPD), inter-simple sequence repeats (ISSR) and random amplified microsatellite polymorphisms (RAMP). Leaf genomic DNA was PCR amplified using 17 RAPD, 8 ISSR and 136 RAMP primers . However, only 10 RAPD primers, 5 ISSR primers and 37 RAMP primers produced reproducible bands. The results were evaluated for polymorphic information content (PIC), marker index (MI) and resolving power (RP). The RAMP marker was the most useful marker compared to RAPD and ISSR markers because it showed the highest average value of PIC (0.25), MI (11.36) and RP (2.86). The genetic diversity showed a high percentage of polymorphism at the species level compared to the population level. Furthermore, analysis of molecular variance revealed that the genetic diversity was higher within populations, as compared to among populations of C. nutans. From the results, the RAMP technique was recommended for the analysis of genetic diversity of C. nutans. 相似文献
6.
S. K. Chakrabarti D. Pattanayak D. Sarkar V. P. Chimote P. S. Naik 《Biologia Plantarum》2006,50(4):531-536
Variations in random amplified polymorphic DNA (RAPD) profiles from leaf, stem, root, and tuber tissues were observed in case
of two glasshouse grown potato cultivars using 40 decamer primers suggesting possible danger of cultivar misidentification.
Genomic DNA extracted from the above four tissues of four in vitro grown potato cultivars, however, produced more uniform RAPD fingerprints. A significant effect of random primers on fingerprint
uniformity was observed in case of both glasshouse and in vitro grown samples. A new concept of stability index for random primers based on homogeneity of RAPD profiles obtained from different
tissues of a single plant have been introduced. It is concluded that RAPD analysis of genomic DNA extracted from any tissue
of in vitro grown potato plants using 14 selected decamer primers could be used to develop RAPD fingerprints for identification of Indian
potato cultivars. 相似文献
7.
Velayutham V Shanmugavel S Munusamy A Sundaram J 《Experimental & applied acarology》2012,56(4):375-383
The genomic DNA from ten isolates of the cattle tick, Boophilus microplus collected in and around Chennai, India, was analyzed by random amplified polymorphic DNA (RAPD) using PCR. Selected five
random primers were used for the study of genetic variability among different isolates of B. microplus. A high degree of genetic polymorphism with a different pattern of RAPD profiles for each tick isolate was detected with
all these random primers. This variability was also confirmed by similarity coefficient values and dendrogram which were performed
using mean RAPD profiles for all the primers between various isolates of ticks. The findings suggest the existence of a complex
genotypic diversity of the tick B. microplus in an endemic region such as Chennai. 相似文献
8.
RAPD markers for constructing intraspecific tomato genetic maps 总被引:8,自引:0,他引:8
The existing molecular genetic maps of the tomato, Lycopersicon spp, are constructed based on isozyme and RFLP polymorphisms between tomato species. These maps are useful for certain applications but have few markers that exhibit sufficient polymorphisms for intraspecific analysis and manipulations within the cultivated tomato. The purpose of this study was to investigate the relative potential of RAPD technology, as compared to isozymes and RFLPs, to generate polymorphic DNA markers within cultivated tomatoes. Sixteen isozymes and 25 RFLP clones that were known to detect polymorphism between L. esculentum and L. pennellii, and 313 random oligonucleotide primers were examined. None of the isozymes and only four of the RFLP clones (i.e., 16%) revealed polymorphism between the cultivated varieties whereas up to 63% of the RAPD primers detected one or more polymorphic DNA fragments between these varieties. All RAPD primers detected polymorphism between L. esculentum and L. pennellii genotypes. These results clearly indicate that RAPD technology can generate sufficient genetic markers exploiting sequence differences within cultivated tomatoes to facilitate construction of intraspecific genetic maps.Abbreviations RFLP
restriction fragments length polymorphism
- RAPD
random amplified polymorphic DNA
- PCR
polymerase chain reaction
- QTLs
quantitative trait loci 相似文献
9.
R. K. Kakani S. K. Singh Anjly Pancholy R. S. Meena Rakesh Pathak Aparna Raturi 《Plant Molecular Biology Reporter》2011,29(2):315-323
Fenugreek (Trigonella foenum-graecum) is receiving global attention due to rare medicinal properties of significance to human health. Gene banks possess scanty
germplasm and very little background information regarding its genetic variability that has hampered its improvement. We investigated
the extent of variability among 17 Indian varieties of fenugreek using phenotypic and genetic markers. Multilocus genotyping
by ten random amplified polymorphic DNA (RAPD) primers detected an average of intraspecific variations amounting to 64.7%
polymorphism in banding patterns. Analysis of molecular variance indicated that a greater proportion of total genetic variation
exists within population (91%) rather than among populations. Higher values of Nei’s gene diversity (h) and Shannon Information Index (i) and genetic distance analysis validate higher genetic diversity among Indian fenugreek varieties. SNPs at 14 sites of rDNA
region revealed further lineages of distinct varieties with main RAPD clusters. The representative sequences of each subgroup
and all distinct varieties have been submitted to NCBI database and assigned Gen Accession numbers HM 176640–176649. The measures
of relative genetic distances among varieties of fenugreek did not completely correlate with the geographical distances of
places of their development. The homogeneous phenotypic markers proved insufficient in exhibiting genetic divergence among
fenugreek varieties studied. Eventually, the knowledge of their genetic relationships, DNA bar coding and phylogenies might
contribute for the designing of intraspecific crosses between cultivars of this fenugreek collection with potential interest
in seed spices breeding programme. 相似文献
10.
Tui Ray Indrajit Dutta Prasenjit Saha Sampa Das S.C. Roy 《Plant Cell, Tissue and Organ Culture》2006,85(1):11-21
An efficient micropropagation protocol produced large number of plants of the three elite banana (Musa spp.) cultivars Robusta (AAA), Giant Governor (AAA) and Martaman (AAB) from shoot tip meristem. The genetic relationships
and fidelity among the cultivars and micropropagated plants as assessed by random amplified polymorphic DNA (RAPD) and inter-simple
sequence repeat (ISSR) markers, revealed three somaclonal variants from Robusta and three from Giant Governor. A total of
5330 RAPD and 2741 ISSR fragments were generated with 21 RAPD and 12 ISSR primers in micropropagated plants. The percentage
of polymorphic loci by RAPD and ISSR were found to be 1.75, 5.08 in Robusta and 0.83, 5.0 in Giant Governor respectively.
Among the two marker systems used, ISSR fingerprinting detected more polymorphism than RAPD in Robusta and Giant Governor
with most of the primers showing similar fingerprinting profile, whereas Martaman revealed complete genetic stability. 相似文献
11.
Salvia miltiorrhiza (SM), a widely popular Chinese herb, is grown in various regions in China. Identifying SMs grown in different provinces of
China is difficult, and therefore genotyping these collections would be highly valuable. Based on the techniques of sequence-related
amplified polymorphism and target region amplified polymorphism, a novel PCR-based molecular marker technique called conserved
region amplification polymorphism (CoRAP) is reported in this study to genotype SMs. The CoRAP technique is based on the use
of two primers: fixed and arbitrary primers. The former is derived from target EST sequences deposited in Genbank; while,
the core sequence (CACGC) of the latter is a conserved region found in most introns. In the present study, we utilized CoRAP
to genotype SMs from different geographical origins. PCR amplification is performed for 30 cycles at an annealing temperature
of 52°C. Each PCR reaction has generated as many as 30–50 fragments of 50 to 1,000 bp in size. The successful DNA genotyping
of SMs by CoRAP was achieved. This new genotyping method is rapid, efficient, and reproducible. 相似文献
12.
M. Vafale-Tabar Shanti Chandrashekaran M. K. Rana K. V. Bhaf 《Journal of plant biochemistry and biotechnology.》2004,13(1):81-84
Random Amplified Polymorphic DNA (RAPD) analysis was used to evaluate genetic diversity among commercial Indian cotton varieties. Fifteen varieties belonging to Gossypium hirsutum L and seven to G. arboreum L were analyzed with 50 random decamer primers using the polymerase chain reaction (PCR). Twenty six of the primers detected polymorphism in all 22 cotton varieties. A total of 371 bands were amplified, 87% of which were polymorphic. Cluster analysis by the unweighted pair group method of arithmetic means (UPGMA) showed that diploids and tetraploids can be divided in two groups at a similarity of 30%. Diploid variety C402W showed the least similarity to all the others in the group. Among tetraploids, closely related varieties Pusa 8-6, 4515 and RS 875 were distinctly different from the rest. The analysis revealed that the intervarietal genetic relationships of several varieties is related to their pedigree. The results also revealed that tetraploids show a much narrower genetic base (similarity range of 65–95%) than the diploids (similarity range 54–88%). The results obtained can be used for the selection of parents to generate a mapping population and begin a breeding programme. 相似文献
13.
Germplasm characterization and evolutionary process in viable populations are important links between the conservation and
utilization of plant genetic resources. Here, an investigation is made, based on molecular and biochemical techniques for
assessing and exploiting the genetic variability in germplasm characterization of taro, which would be useful in plant breeding
and ex situ conservation of taro plant genetic resources. Geographical differentiation and phylogenetic relationships of Indian
taro, Colocasia esculenta (L.) Schott, were analyzed by random amplified polymorphic DNA (RAPD) and isozyme of seven enzyme systems with specific reference
to the Muktakeshi accession, which has been to be proved resistant to taro leaf blight caused by P. colocasiae. The significant differentiations in Indian taro cultivars were clearly demonstrated by RAPD and isozyme analysis. RAPD markers
showed higher values for genetic differentiation among taro cultivars and lower coefficient of variation than those obtained
from isozymes. Genetic differentiation was evident in the taro accessions collected from different regions of India. It appears
that when taro cultivation was introduced to a new area, only a small fraction of genetic variability in heterogeneous taro
populations was transferred, possibly causing random differentiation among locally adapted taro populations. The selected
primers will be useful for future genetic analysis and provide taro breeders with a genetic basis for selection of parents
for crop improvement. Polymorphic markers identified in the DNA fingerprinting study will be useful for screening a segregating
population, which is being generated in our laboratory aimed at developing a taro genetic linkage map. 相似文献
14.
Trigonella is recognized as a medicinal therapist throughout the globe due to its multifaceted rare medicinal properties. It is indigenous from Iran to Northern India but has gained global acceptance towards cultivation and consumption for its yellow-to-amber colored seed which substantially contributes to food, pharmaceutical, nutraceutical and cosmetic industry. Genetic diversity serves as an excellent tool for developing improved crop varieties with breeder preferred traits. Unfortunately, very little information available on variability existing in commercial Trigonella genotypes considerably impedes the crop improvement. In this study, ninety Trigonella genotypes belonging to most productive North Indian states were subjected to multilocus genotyping using RAPD (49) and SSR (13) primers and detected an average of 55.60 and 50.16% polymorphism, respectively. The percentage polymorphism range (RAPD, 16.7–90.90; SSR, 33.30–66.66) average band informativeness (RAPD, 0.182–0.85; SSR, 0.21–0.91) and resolving power (RAPD, 0.95–9.984; SSR, 1.68–7.28) obtained revealed the wide range of diversity prevailing among these genotypes. Hierarchical clustering of genotypes in nine different clusters showed Trigonella’s genetic variability has wide genetic distribution across different agro-climatic zones. No consistency was observed while grouping Trigonella varieties based on eco-geographical region. Eventually, knowledge of these genetic differences significantly contributes in designing intra-specific crosses with potential interest to spice breeding programs. To the best of our knowledge, this is the first report of genetic diversity using SSR molecular markers in Trigonella foenum-graecum L. 相似文献
15.
Mohd Arif N. W. Zaidi Y. P. Singh Qazi Mohd Rizwanul Haq U. S. Singh 《Plant Molecular Biology Reporter》2009,27(4):488-495
Shisham (Dalbergia sissoo) is one of the most preferred timber tree species of South Asia. Two DNA-based molecular marker techniques, intersimple sequence
repeat (ISSR) and random amplified polymorphism DNA (RAPD), were compared to study the genetic diversity in this species.
A total of 30 polymorphic primers (15 ISSR and 15 random) were used. Amplification of genomic DNA of 22 genotypes, using ISSR
analysis, yielded 117 fragments, of which 64 were polymorphic. Number of amplified fragments with ISSR primers ranged from
five to ten and varied in size from 180 to 1,900 bp. Percentage polymorphism ranged from 0 to 87.5. The 15 RAPD primers produced
144 bands across 22 genotypes, of which 84 were polymorphic. The number of amplified bands varied from five to 13, with size
range from 180 to 2,400 bp. Percentage polymorphism ranged from 0 to 100, with an average of 58.3 across. RAPD markers were
relatively more efficient than the ISSR assay. The mental test between two Jaccard’s similarity matrices gave r ≥ 0.90, showing very good fit correlation in between ISSR- and RAPD-based similarities. Clustering of isolates remained more
or less the same in RAPD and combined data of RAPD and ISSR. The similarity coefficient ranged from 0.734 to 0.939, 0.563
to 0.946, and 0.648 to 0.920 with ISSR, RAPD, and combined dendrogram, respectively. 相似文献
16.
In order to develop more specific markers that characterize particular regions of the pea genome, the data on nucleotide sequences of RAPD fragments were used for choosing more extended primers, which may be helpful in amplifying a fragment corresponding to the particular DNA region. Of the 14 STS markers obtained from 14 polymorphic RAPD fragments, 12 were polymorphic, i.e., they are SCAR markers that can be used in genetic analysis. The transition from complex RAPD spectra to amplification of a particular SCAR marker substantially facilitates analysis of large samples for the presence or absence of the examined fragment. Inheritance of the developed SCAR markers was studied in F1 and F2. SCAR markers were used to identify various pea lines, cultivars, and mutants. It was established that the study of amplification of STS markers in various pea genotypes at varying temperatures of annealing and the comparison with amplification of the original RAPD fragments in the same genotypes provide an approach for analysis of RAPD polymorphism origin. 相似文献
17.
Qualitative and quantitative characterization of RAPD variation among snap bean (Phaseolus vulgaris) genotypes 总被引:1,自引:0,他引:1
P. W. Skroch J. Nienhuis 《TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik》1995,91(6-7):1078-1085
Ten snap bean (Phaseolus vulgaris) genotypes were screened for polymorphism with 400 RAPD (random amplified polymorphic DNA) primers. Polymorphic RAPDs were scored and classified into three categories based on ethidium bromide staining intensity. An average of 5.19 RAPD bands were scored per primer for the 364 primers that gave scorable amplification products. An average of 2.15 polymorphic RAPDs were detected per primer. The results show that primer screening may reduce the number of RAPD reactions required for the analysis of genetic relationships among snap-bean genotypes by over 60%. Based on the analysis of the distribution of RAPD amplification, the same number of polymorphic RAPDs were amplified from different genotypes for all RAPD band intensity levels. A comparison of RAPD band amplification frequency among genotypes for the three categories of bands classified by amplification strength revealed a measurable difference in the frequencies of RAPDs classified as faint (weakly amplifying) compared to RAPD bands classified as bold (strongly amplifying) indicating a possible scoring error due to the underscoring of faint bands. Correlation analysis showed that RAPD bands amplified by the same primer are not more closely correlated then RAPD bands amplified by different primers but are more highly correlated then expected by chance. Pairwise comparisons of RAPD bands indicate that the distribution of RAPD amplification among genotypes will be a useful criterion for establishing RAPD band identity. For the average pairwise comparison of genotypes, 50% of primers tested and 15.8% of all scored RAPDs detected polymorphism. Based on RAPD data Nei's average gene diversity at a locus was 0.158 based on all scorable RAPD bands and 0.388 if only polymorphic RAPD loci were considered. RAPD-derived 1 relationships among genotypes are reported for the ten genotypes included in this study. The data presented here demonstrate that many informative, polymorphic RAPDs can be found among snap bean cultivars. These RAPDs may be useful for the unique identification of bean varieties, the organization of bean germplasm, and applications of molecular markers to bean breeding. 相似文献
18.
Two approaches were used to detect variability within 23 pea cultivars. Eight random amplified polymorphic DNA (RAPD) primers
produced 163 bands (114 polymorphic), whereas five isoenzyme systems produced 25 bands (20 polymorphic). Both methods provided
good results in finger-printing and identified all cultivars tested. Genetic similarity analysis (UPGMA) gave different results
from RAPD and isoenzyme data. This could reflect different properties of both marker types. These data were also analysed
using the bootstrap method, which supported the idea of one common progenitor of cultivated peas.
This revised version was published online in July 2006 with corrections to the Cover Date. 相似文献
19.
Madhu Koundal D. R. Sharma T. Mohapatra K. R. Koundal 《Journal of plant biochemistry and biotechnology.》2006,15(1):15-19
The present investigation was carried out with an objective of evaluating genetic diversity in brinjal (Solanum melongena) using DNA markers. A total of 38 brinjal accessions including one wild-species, Solanum sisymbrifolium were characterized using random amplified polymorphic DNA (RAP D) and amplified fragment length polymorphism (AFLP) techniques. Out of 45 primers employed to generate RAPD profiles, reproducible patterns were obtained with 32 primers and 30 (93.7%) of these detected polymorphism. A total of 149 bands were obtained, out of which 108 (72.4%) were polymorphic. AFLP analysis was carried out using four primer combinations. Each of these primers was highly polymorphic. Out of 253 fragments amplified from these four primer combinations, 237 (93.6%) were polymorphic. The extent of pair-wise similarity ranged from 0.264 to 0.946 with a mean of 0.787 in RAPD, in contrast to a range of 0.103 to 0.847 with a mean of 0.434 in AFLP. The wild species clustered separately from the brinjal genotypes. In the dendrogram constructed separately using RAPD and AFLP markers, the brinjal genotypes were grouped into clusters and sub-clusters, and the varieties released by IARI remained together on both the dendrograms. All the 30 RAPD primers in combination and each of the four primer pairs in AFLP could distinguish the brinjal accessions from each other. AFLP was thus found to be more efficient than RAPD in estimation of genetic diversity and differentiation of varieties in brinjal. 相似文献
20.
Mastan SG Sudheer PD Rahman H Ghosh A Rathore MS Ravi Prakash Ch Chikara J 《Molecular biology reports》2012,39(4):4383-4390
Jatropha curcas L. (Euphorbiaceae) has acquired a great importance as a renewable source of energy with a number of environmental benefits.
Very few attempts were made to understand the extent of genetic diversity of J. curcas germplasm. In the present study, efforts were made to analyze the genetic diversity among the elite germplasms of J. curcas, selected on the basis of their performance in field using random amplified polymorphic DNA (RAPD), amplified fragment length
polymorphism (AFLP) and simple sequence repeats (SSR). The plants were selected on the basis of height, canopy circumference,
number of seeds per fruit, weight of 100 seeds, seed yield in grams per plant and oil content. Out of 250 RAPD (with 26 primers),
822 AFLP (with 17 primers) and 19 SSR band classes, 141, 346 and 7 were found to be polymorphic, respectively. The percentage
polymorphism among the selected germplasms using RAPD, AFLP and SSR was found to be 56.43, 57.9, and 36.84, respectively.
The Jaccard’s similarity coefficient was found 0.91, 0.90 and 0.91 through RAPD, AFLP and SSR marker systems, respectively.
Principle component analysis (PCA) and dendrogarm analysis of genetic relationship among the germplasm using RAPD, AFLP and
SSR data showed a good correlation for individual markers. The germplasm JCC-11, 12, 13, 14 and 15 whose yield found to be
high were clustered together in dendrogram and PCA analysis though JCC11 is geographically distinct from others. In overall
analysis JCC6 (in RAPD), JCC8 (in AFLP) and JCC 6 and JCC10 (in SSR) were found genetically diverse. Characterization of geographically
distinct and genetically diverse germplasms with varied yield characters is an important step in marker assisted selection
(MAS) and it can be useful for breeding programs and QTL mapping. 相似文献