Construction of a linkage map of the Rennell Island Tall coconut type (Cocos nucifera L.) and QTL analysis for yield characters

AFLP and SSR DNA markers were used to construct a linkage map in the coconut (Cocos nucifera L.; 2n = 32) type Rennell Island Tall (RIT). A total of 227 markers were arranged into 16 linkage groups. The total genome length corresponded to 1971 cM for the RIT map, with 523 markers per linkage group. QTL analysis for yield characters in two consecutive sampling periods identified nine loci. Three and two QTLs were detected for number of bunches and one and three QTLs for number of nuts. The correlation of trait values between characters and evaluation periods is partially reflected in identical QTLs. The QTLs represent characters that are important in coconut breeding. The cosegregation of markers with these QTLs provides an opportunity for marker-assisted selection in coconut breeding programmes.Key words: coconut, QTL, AFLP, SSR, marker-assisted selection (MAS).

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Mapping of quantitative trait loci underlying resistance to cassava anthracnose disease

The Journal of Agricultural Science ◽

10.1017/s0021859615001057 ◽

2015 ◽

Vol 154 (7) ◽

pp. 1209-1217 ◽

Cited By ~ 3

Author(s):

A. BOONCHANAWIWAT ◽

S. SRAPHET ◽

S. WHANKAEW ◽

O. BOONSENG ◽

D. R. SMITH ◽

...

Keyword(s):

Quantitative Trait Loci ◽

Linkage Map ◽

Dna Markers ◽

Quantitative Trait ◽

Genetic Linkage ◽

Genetic Linkage Map ◽

Gene Annotation ◽

Linkage Groups ◽

Anthracnose Disease ◽

Trait Loci

SUMMARYCassava (Manihot esculenta Crantz) is an economically important root crop in Thailand, which is ranked the world's top cassava exporting country. Production of cassava can be hampered by several pathogens and pests. Cassava anthracnose disease (CAD) is an important disease caused by the fungus Colletotrichum gloeosporioides f. sp. manihotis. The pathogen causes severe stem damage resulting in yield reductions and lack of stem cuttings available for planting. Molecular studies of cassava response to CAD will provide useful information for cassava breeders to develop new varieties with resistance to the disease. The current study aimed to identify quantitative trait loci (QTL) and DNA markers associated with resistance to CAD. A total of 200 lines of two F1 mapping populations were generated by reciprocal crosses between the varieties Huabong60 and Hanatee. The F1 samples were genotyped based on simple sequence repeat (SSR) and expressed sequence tag-SSR markers and a genetic linkage map was constructed using the JoinMap®/version3·0 program. The results showed that the map consisted of 512 marker loci distributed on 24 linkage groups with a map length of 1771·9 centimorgan (cM) and a mean interval between markers of 5·7 cM. The genetic linkage map was integrated with phenotypic data for the response to CAD infection generated by a detached leaf assay test. A total of three QTL underlying the trait were identified on three linkage groups using the MapQTL®/version4·0 program. Those DNA markers linked to the QTL that showed high statistically significant values with the CAD resistance trait were identified for gene annotation analysis and 23 candidate resistance genes to CAD infection were identified.

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Construction of a linkage map of the Rennell Island Tall coconut type (Cocos nucifera L.) and QTL analysis for yield characters

Genome ◽

10.1139/gen-44-6-962 ◽

2001 ◽

Vol 44 (6) ◽

pp. 962-970 ◽

Cited By ~ 7

Author(s):

P. Lebrun ◽

L. Baudouin ◽

R. Bourdeix ◽

J. Louis Konan ◽

J.H.A. Barker ◽

...

Keyword(s):

Linkage Map ◽

Qtl Analysis ◽

Cocos Nucifera ◽

Type I

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A new intervarietal linkage map and its application for quantitative trait locus analysis of "gigas" features in bread wheat

Genome ◽

10.1139/g04-092 ◽

2005 ◽

Vol 48 (1) ◽

pp. 65-75 ◽

Cited By ~ 47

Author(s):

Kazuhiro Suenaga ◽

Mireille Khairallah ◽

H M William ◽

David A Hoisington

Keyword(s):

Quantitative Trait Locus ◽

Linkage Map ◽

Qtl Analysis ◽

Simple Sequence Repeat ◽

Sequence Repeat ◽

Linkage Groups ◽

Spike Number ◽

Trait Locus ◽

Dh Lines ◽

Simple Sequence

A doubled-haploid (DH) population from an intervarietal cross between the Japanese cultivar 'Fukuho-komugi' and the Israeli wheat line 'Oligoculm' was produced by means of wheat × maize crosses. One hundred seven DH lines were genotyped to construct a simple sequence repeat (SSR) based linkage map with RFLP, RAPD, and inter-simple sequence repeat markers. Out of 570 loci genotyped, 330 were chosen based on their positions on the linkage map to create a "framework" map for quantitative trait locus (QTL) analysis. Among the 28 linkage groups identified, 25 were assigned to the 21 chromosomes of wheat. The total map length was 3948 cM, including the three unassigned linkage groups (88 cM), and the mean interval between loci was 12.0 cM. Loci with segregation distortion were clustered on chromosomes 1A, 4B, 4D, 5A, 6A, 6B, and 6D. After vernalization, the DH lines were evaluated for spike number per plant (SN) and spike length (SL) in a greenhouse under 24-h daylength to assess the "gigas" features (extremely large spikes and leaves) of 'Oligoculm'. The DH lines were also autumn-sown in the field in two seasons (1990–1991 and 1997–1998) for SN and SL evaluation. QTL analysis was performed by composite interval mapping (CIM) with the framework map to detect QTLs for SN and SL. A major QTL on 1AS, which was stable in both greenhouse and field conditions, was found to control SN. This QTL was close to the glume pubescence locus (Hg) and explained up to 62.9% of the total phenotypic variation. The 'Oligoculm' allele restricted spike number. The SSR locus Xpsp2999 was the closest locus to this QTL and is considered to be a possible marker for restricted tillering derived from 'Oligoculm'. Eight QTLs were detected for SL. The largest QTL detected on 2DS was common to the greenhouse and field environments. It explained up to 33.3% of the total phenotypic variation. The second largest QTL on 1AS was common to the greenhouse and the 1997–1998 season. The position of this QTL was close to that for the SN detected on 1AS. The association between SN and SL is discussed.Key words: linkage map, microsatellite, QTL, spike length, spike number.

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An updated doubled haploid oat linkage map and QTL mapping of agronomic and grain quality traits from Canadian field trials

Genome ◽

10.1139/g2012-017 ◽

2012 ◽

Vol 55 (4) ◽

pp. 289-301 ◽

Cited By ~ 18

Author(s):

Pirjo Tanhuanpää ◽

Outi Manninen ◽

Aaron Beattie ◽

Peter Eckstein ◽

Graham Scoles ◽

...

Keyword(s):

Linkage Map ◽

Doubled Haploid ◽

Avena Sativa ◽

Dna Markers ◽

Grain Quality ◽

Field Trials ◽

Diversity Array Technology ◽

Linkage Groups ◽

Array Technology ◽

Reference Map

The first doubled haploid oat linkage map constructed at MTT Agrifood Research Finland was supplemented with additional microsatellites and Diversity Array Technology (DArT) markers to produce a map containing 1058 DNA markers and 34 linkage groups. The map was used to locate quantitative trait loci (QTLs) for 11 important breeding traits analyzed from Finnish and Canadian field trials. The new markers enabled most of the linkage groups to be anchored to the ‘Kanota’ × ‘Ogle’ oat ( Avena sativa L.) reference map and allowed comparison of the QTLs located in this study with those found previously. Two to 12 QTLs for each trait were discovered, of which several were expressed consistently across several environments.

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Linkage mapping and QTL analysis in coconut (Cocos nucifera L.)

Theoretical and Applied Genetics ◽

10.1007/s001220051482 ◽

2000 ◽

Vol 101 (1-2) ◽

pp. 292-300 ◽

Cited By ~ 25

Author(s):

A. Herrán ◽

L. Estioko ◽

D. Becker ◽

M. J. B. Rodriguez ◽

W. Rohde ◽

...

Keyword(s):

Qtl Analysis ◽

Linkage Mapping ◽

Cocos Nucifera ◽

Cocos Nucifera L

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QTL Analysis of Domestication Syndrome in Zombi Pea (Vigna vexillata), an Underutilized Legume Crop

10.1101/353029 ◽

2018 ◽

Cited By ~ 1

Author(s):

Sujinna Dachapak ◽

Norihiko Tomooka ◽

Prakit Somta ◽

Ken Naito ◽

Akito Kaga ◽

...

Keyword(s):

Linkage Map ◽

Seed Size ◽

Qtl Analysis ◽

Leaf Size ◽

Interval Mapping ◽

Linkage Groups ◽

Legume Crop ◽

Vigna Vexillata ◽

Length Width ◽

Trait Locus

AbstractZombi pea (Vigna vexillata (L.) A. Rich) is an underutilized crop belonging to the genus Vigna. Two domesticated forms of zombi pea are cultivated as crop plants; seed and tuber forms. The cultivated seed form is present in Africa, while the cultivated tuber form is present in a very limited part of Asia. Genetics of domestication have been investigated in most of cultivated Vigna crops by means of quantitative trait locus (QTL) mapping. In this study, we investigated genetics of domestication in zombi pea by QTL analysis using an F2 population of 139 plants derived from a cross between cultivated tuber form of V. vexillata (JP235863) and wild V. vexillata (AusTRCF66514). A linkage map with 11 linkage groups was constructed from this F2 population using 145 SSR, 117 RAD-seq and 2 morphological markers. Many highly segregation distorted markers were found on LGs 5, 6, 7, 8, 10 and 11. Most of the distorted markers were clustered together and all the markers on LG8 were highly distorted markers. Comparing this V. vexillata linkage map with a previous linkage map of V. vexillata and linkage maps of other four Vigna species demonstrated several macro translocations in V. vexillata. QTL analysis for 22 domestication-related traits was investigated by inclusive composite interval mapping in which 37 QTLs were identified for 18 traits; no QTL was detected for 4 traits. Number of QTLs detected in each trait ranged from 1 to 5 with an average of only 2.3. Tuber traits were controlled by five QTLs with similar effect locating on different linkage groups. Large-effect QTLs (PVE > 20%) were on LG4 (pod length), LG5 (leaf size and seed thickness), and LG7 (for seed-related traits). Comparison of domestication-related QTLs of the zombi pea with those of cowpea (Vigna unguiculata), azuki bean (Vigna angularis), mungbean (Vigna radiata) and rice bean (Vigna umbellata) revealed that there was conservation of some QTLs for seed size, pod size and leaf size between zombi pea and cowpea and that QTLs associated with seed size (weight, length, width and thickness) in each species were clustered on same linkage.

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Cuticular wax composition in Cocos nucifera L.: physicochemical analysis of wax components and mapping of their QTLs onto the coconut molecular linkage map

Tree Genetics & Genomes ◽

10.1007/s11295-008-0168-7 ◽

2008 ◽

Vol 5 (1) ◽

pp. 53-69 ◽

Cited By ~ 15

Author(s):

M. Riedel ◽

M. Riederer ◽

D. Becker ◽

A. Herran ◽

A. Kullaya ◽

...

Keyword(s):

Linkage Map ◽

Cocos Nucifera ◽

Physicochemical Analysis ◽

Cuticular Wax ◽

Molecular Linkage Map ◽

Cocos Nucifera L

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Penyebaran Polen Berdasarkan Analisis SSR Membuktikan Penyerbukan

Buletin Palma ◽

10.21082/bp.v16n1.2015.77-92 ◽

2016 ◽

Vol 16 (1) ◽

pp. 77 ◽

Cited By ~ 6

Author(s):

SITI HALIMAH LAREKENG ◽

ISMAIL MASKROMO ◽

AGUS PURWITO ◽

NURHAYATI ANSHORI MATTJIK ◽

SUDARSONO SUDARSONO

Keyword(s):

Ssr Marker ◽

Cocos Nucifera ◽

Pollen Dispersal ◽

Paternity Analysis ◽

Font Size ◽

Cross Pollination ◽

Ssr Analysis ◽

Self Pollination ◽

Marker Loci ◽

Cocos Nucifera L

ABSTRAK Analisis paternitas digunakan untuk mengetahui pola penyebaran serbuk sari pada kelapa (Cocos nucifera L.) tipe Dalam Kalianda. Tujuan penelitian ini adalah untuk (1) mengevaluasi pola penyebaran serbuk sari dan menentukan kisaran jarak penyebaran serbuk sari pada kelapa tipe Dalam Kalianda, (2) menentukan persentase penyerbukan silang (outcrossing) dan penyerbukan sendiri (selfing) yang terjadi pada kelapa tipe Dalam Kalianda, dan (3) menentukan frekuensi pola penyerbukan silang antara kelapa tipe Dalam normal (N) dengan kelapa Dalam Kopyor (K), KxN dan KxK yang terjadi pada populasi campuran antara kelapa tipe Dalam Kopyor dan kelapa Dalam normal Kalianda. Populasi yang digunakan terdiri atas 60 pohon kelapa tipe Dalam dewasa, 21 pohon merupakan kelapa tipe Dalam berbuah normal (homozigot KK) dan 39 merupakan pohon kelapa tipe Dalam Kopyor (heterosigot Kk). Empat belas pohon (5 pohon KK dan 9 pohon Kk) digunakan sebagai tetua betina. Sebanyak 49 progeni dipanen dari 15 induk terpilih dan dikecambahkan untuk sumber DNA dalam analisis paternitas. Enam lokus marka SSR polimorfik, yaitu CnCir_B12, CnCir_86, CnCir_87, CnCir_56, CnZ_51, CnZ_18 dan empat lokus marka SNAP polimorfik, yaitu CnSUS1#14,CnSUS1#3, CnWRKY6#3 dan CnWRKY19#1 digunakan untuk menentukan genotipe seluruh progeni, seluruh kandidat tetua jantan, dan semua tetua betina yang digunakan. Hasil penelitian menunjukkan bahwa serbuk sari kelapa tipe Dalam Kalianda menyebar dengan jarak terjauh 63 m. Jarak penyebaran serbuk sari terbanyak pada jarak 40-50 m, dengan frekuensi sebesar 13 kejadian polinasi (27%). Dari 47 progeni yang dievaluasi, hanya satu (2%) progeni yang berasal dari penyerbukan sendiri (self pollination) dan 48 (98%) berasal dari penyerbukan silang. Dari progeni hasil penyerbukan silang, 24 (49,0%) progeni teridentifikasi sebagai hasil persilangan antara induk dan tetua jantan kelapa tipe Dalam kopyor heterosigot Kk, 11 (22,4%) sebagai hasil persilangan antara induk kelapa tipe Dalam Kopyor heterosigot Kk dan normal homosigot KK, 10 (20,5%) sebagai hasil persilangan antara induk kelapa tipe Dalam normal homosigot KK dan Kopyor heterosigot Kk, serta 3 (6,1%) sebagai hasil persilangan antara induk dan tetua jantan tipe Dalam normal homosigot KK.Kata kunci : Kelapa Dalam Kopyor, kelapa Kopyor Kalianda, tingkat penyerbukan sendiri, tingkat penyerbukan silang. Pollen Dispersal Based on SSR Analysis Proves Kalianda to Kopyor Coconut PollinationsABSTRACT Paternity analysis was applied to determine the pattern of pollen spread among Kalianda Tall coconut (Cocos nucifera L.) in Kalianda, Lampung. The objectives of this research are to (1) evaluate patterns of pollen dispersal and ranges of pollen spread, (2) determine percentage of outcrossing or selfing rates, and (3) determine the frequency of cross pollination among normal (N) to kopyor (K), KxN and KxK in the mix population of Kalianda Tall coconut at Kalianda, Lampung. The population used in this study was 60 palms, consisted of 21 Kalianda Tall Normal coconuts (homozygous KK) and 39 Kalianda Tall Kopyor coconuts (Heterozygous Kk). Fourteen palms out of those were selected as female parents. Progeny arrays (49 nuts) were harvested from 15 female parents and they were germinated. The DNA was isolated from young leaf of all adult palms and germinated coconut seedlings and they were used in paternity analysis. Six polymorphic SSR marker loci used were CnCir_B12, CnCir_86, CnCir_87, CnCir_56, CnZ_51, CnZ_18 and the four polymorphic SNAP markers used were CnSUS1#14, CnSUS1#3, CnWRKY6#1 and CnWRKY19#3. The markers were used to genotype all the progenies, the potential male and the female parents. Results of the experiment indicated pollen of Kalianda Tall Kopyor coconut farthest disperse was 63 m. Distance of the mostpollen dispersal was between 40-50 m,with the frequency of 13 pollination events (27%). Among the evaluated progenies, only one (2%) comes from self pollination event and 48 (98%) comes from cross pollination. Results of the progeny evaluation also indicated 24 progenies (49.0%) are results of outcrossing among Kalianda Tall kopyor heterozygous Kk parents, 11 progenies (22.4%) are outcrossing among kopyor heterozygous Kk female and normal homozygous KK male parents, 10 progenies (20.5%) are outcrossing among normal homozygous KK female and kopyor heterozygous Kk male parents, and 3 progenies (6.1%) are outcrossing among normal homozygous KK female and male parents.Keywords : Tall kopyor coconut, Kalianda Kopyor coconut, self polination, cross pollination rate.

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A framework linkage map of perennial ryegrass based on SSR markers

Genome ◽

10.1139/g05-120 ◽

2006 ◽

Vol 49 (4) ◽

pp. 354-364 ◽

Cited By ~ 43

Author(s):

G P Gill ◽

P L Wilcox ◽

D J Whittaker ◽

R A Winz ◽

P Bickerstaff ◽

...

Keyword(s):

Linkage Map ◽

Ssr Markers ◽

Lolium Perenne ◽

Perennial Ryegrass ◽

Simple Sequence Repeat ◽

Ssr Marker ◽

Sequence Repeat ◽

Linkage Groups ◽

Marker Loci ◽

Simple Sequence

A moderate-density linkage map for Lolium perenne L. has been constructed based on 376 simple sequence repeat (SSR) markers. Approximately one third (124) of the SSR markers were developed from GeneThresher® libraries that preferentially select genomic DNA clones from the gene-rich unmethylated portion of the genome. The remaining SSR marker loci were generated from either SSR-enriched genomic libraries (247) or ESTs (5). Forty-five percent of the GeneThresher SSRs were associated with an expressed gene. Unlike EST-derived SSR markers, GeneThresher SSRs were often associated with genes expressed at a low level, such as transcription factors. The map constructed here fulfills 2 definitions of a "framework map". Firstly, it is composed of codominant markers to ensure map transferability either within or among species. Secondly, it was constructed to achieve a level of statistical confidence in the support-for-order of marker loci. The map consists of 81 framework SSR markers spread over 7 linkage groups, the same as the haploid chromosome number. Most of the remaining 295 SSR markers have been placed into their most likely interval on the framework map. Nine RFLP markers and 1 SSR marker from another map constructed using the same pedigree were also incorporated to extend genome coverage at the terminal ends of 5 linkage groups. The final map provides a robust framework with which to conduct investigations into the genetic architecture of trait variation in this commercially important grass species.Key words: Framework map, perennial ryegrass, SSR, simple sequence repeat, GeneThresher, Lolium perenne.

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