scholarly journals Dissection of closely linked QTLs controlling stigma exsertion rate in rice by substitution mapping

2021 ◽  
Author(s):  
Quanya Tan ◽  
Chengshu Wang ◽  
Xin Luan ◽  
Lingjie Zheng ◽  
Yuerong Ni ◽  
...  
Keyword(s):  
Complex Trait ◽  
Epistatic Effect ◽  
Open Reading Frames ◽  
Chromosome 3 ◽  
Chromosome 2 ◽  
Substitution Mapping ◽  
Mapping Strategy ◽  
Stigma Exsertion ◽  
Important Trait ◽  
Stigma Exsertion Rate

Abstract Key message Through substitution mapping strategy, two pairs of closely linked QTLs controlling stigma exsertion rate were dissected from chromosomes 2 and 3 and the four QTLs were fine mapped. Abstract Stigma exsertion rate (SER) is an important trait affecting the outcrossing ability of male sterility lines in hybrid rice. This complex trait was controlled by multiple QTLs and affected by environment condition. Here, we dissected, respectively, two pairs of tightly linked QTLs for SER on chromosomes 2 and 3 by substitution mapping. On chromosome 2, two linkage QTLs, qSER-2a and qSER-2b, were located in the region of 1288.0 kb, and were, respectively, delimited to the intervals of 234.9 kb and 214.3 kb. On chromosome 3, two QTLs, qSER-3a and qSER-3b, were detected in the region of 3575.5 kb and were narrowed down to 319.1 kb and 637.3 kb, respectively. The additive effects of four QTLs ranged from 7.9 to 9.0%. The epistatic effect produced by the interaction of qSER-2a and qSER-2b was much greater than that of qSER-3a and qSER-3b. The open reading frames were identified within the maximum intervals of qSER-2a, qSER-2b and qSER-3a, respectively. These results revealed that there are potential QTL clusters for SER in the two regions of chromosome 2 and chromosome 3. Fine mapping of the QTLs laid a foundation for cloning of the genes of SER.

scholarly journals Substitution mapping of the major quantitative trait loci controlling stigma exsertion rate from Oryza glumaepatula

2020 ◽  
Author(s):  
Quanya Tan ◽  
Tuo Zou ◽  
Mingmin Zheng ◽  
Yuerong Ni ◽  
Xin Luan ◽  
...  
Keyword(s):  
Quantitative Trait Loci ◽  
Quantitative Trait ◽  
Chromosome 1 ◽  
Rice Seed ◽  
Cultivated Rice ◽  
Rice Varieties ◽  
Substitution Mapping ◽  
Trait Loci ◽  
Stigma Exsertion ◽  
Stigma Exsertion Rate

Abstract Background: Stigma exsertion rate (SER) is a key determinant for outcrossing ability of male sterility lines (MSLs) in hybrid rice seed production. Outcrossing ability in cultivated rice varieties has diminished during the process of domestication, while wild Oryza species keep strong outcrossing ability. Here, we detected the quantitative trait loci (QTLs) controlling SER using a set of single-segment substitution lines (SSSLs) derived from O. glumaepatula, a wild Oryza species.Results: Seven QTLs for SER, qSER-1a, qSER-1b, qSER-3a, qSER-3b, qSER-5, qSER-9 and qSER-10, were located on 5 chromosomes. qSER-1a and qSER-1b were located on chromosome 1. qSER-3a and qSER-3b were mapped on chromosome 3, and qSER-3b was further located at an interval of 931.0kb by secondary substitution mapping. qSER-5, qSER-9 and qSER-10 were identified on chromosomes 5, 9 and 10, respectively, and qSER-9 was delimited to a region of 608.2kb by secondary substitution mapping. The additive effects of the 7 QTLs ranged from 10.6% to 14.8%, and the additive contribution variances explained by each of the QTLs were from 36.3% to 50.6%, which were higher than those of most loci for SER reported previously.Conclusions: qSER-1a and qSER-1b were novel loci for SER on chromosome 1. All of the 7 QTLs had major effects on SER. The major QTLs of SER will help to develop MSLs with strong outcrossing ability.

scholarly journals Substitution mapping of the major quantitative trait loci controlling stigma exsertion rate from Oryza glumaepatula

2020 ◽  
Author(s):  
Quanya Tan ◽  
Tuo Zou ◽  
Mingmin Zheng ◽  
Yuerong Ni ◽  
Xin Luan ◽  
...  
Keyword(s):  
Quantitative Trait Loci ◽  
Quantitative Trait ◽  
Chromosome 1 ◽  
Oryza Species ◽  
Rice Seed ◽  
Substitution Mapping ◽  
Trait Loci ◽  
Stigma Exsertion ◽  
Stigma Exsertion Rate ◽  
Wild Oryza Species

Abstract Background: Stigma exsertion rate (SER) is a key determinant for the outcrossing ability of male sterility lines (MSLs) in hybrid rice seed production. In the process of domestication, the outcrossing ability of cultivated rice varieties decreased, while that of wild Oryza species kept strong. Here, we detected the quantitative trait loci (QTLs) controlling SER using a set of single-segment substitution lines (SSSLs) derived from O. glumaepatula , a wild Oryza species. Results: Seven QTLs for SER were located on 5 chromosomes. qSER-1a and qSER-1b were located on chromosome 1. qSER-3a and qSER-3b were mapped on chromosome 3, and qSER-3b was further located at an estimated interval of 898.8kb by secondary substitution mapping. qSER-5 , qSER-9 and qSER-10 were identified on chromosomes 5, 9 and 10, respectively, and qSER-9 was delimited to an estimated region of 551.9kb by secondary substitution mapping. The additive effects of the 7 QTLs ranged from 10.6% to 14.8%, which were higher than those of most loci for SER reported previously. Conclusions: qSER-1a and qSER-1b are novel loci for SER on chromosome 1. All of the 7 QTLs have major effects on SER. The major QTLs of SER will help to develop MSLs with strong outcrossing ability.

scholarly journals Rearrangements of the DNA in Carbon Ion-Induced Mutants of Arabidopsis thaliana

Genetics ◽  
2001 ◽  
Vol 157 (1) ◽  
pp. 379-387 ◽  
Author(s):  
Naoya Shikazono ◽  
Atsushi Tanaka ◽  
Hiroshi Watanabe ◽  
Shigemitsu Tano
Keyword(s):  
Arabidopsis Thaliana ◽  
Nonhomologous End Joining ◽  
Chromosome 3 ◽  
Chromosome 2 ◽  
Carbon Ions ◽  
Induced Mutations ◽  
End Joining ◽  
Carbon Ion ◽  
Induced Mutants ◽  
Dna Strand

Abstract To elucidate the nature of structural alterations in plants, three carbon ion-induced mutations in Arabidopsis thaliana, gl1-3, tt4(C1), and ttg1-21, were analyzed. The gl1-3 mutation was found to be generated by an inversion of a fragment that contained GL1 and Atpk7 loci on chromosome 3. The size of the inverted fragment was a few hundred kilobase pairs. The inversion was found to accompany an insertion of a 107-bp fragment derived from chromosome 2. The tt4(C1) mutation was also found to be due to an inversion. The size of the intervening region between the breakpoints was also estimated to be a few hundred kilobase pairs. In the case of ttg1-21, it was found that a break occurred at the TTG1 locus on chromosome 5, and reciprocal translocation took place between it and chromosome 3. From the sequences flanking the breakpoints, the DNA strand breaks induced by carbon ions were found to be rejoined using, if present, only short homologous sequences. Small deletions were also observed around the breakpoints. These results suggest that the nonhomologous end-joining (NHEJ) pathway operates after plant cells are exposed to ion particles.

Chromosome polymorphism in natural populations of Anopheles quadrimaculatus Say species A and B

Genome ◽  
1988 ◽  
Vol 30 (2) ◽  
pp. 138-146 ◽  
Author(s):  
P. E. Kaiser ◽  
J. A. Seawright ◽  
B. K. Birky
Keyword(s):  
X Chromosome ◽  
Southeastern United States ◽  
Polytene Chromosomes ◽  
Natural Populations ◽  
Chromosome 3 ◽  
Chromosome Polymorphism ◽  
Chromosome 2 ◽  
Anopheles Quadrimaculatus ◽  
The Right ◽  
Maculipennis Complex

Ovarian polytene chromosomes from eight populations of Anopheles quadrimaculatus in the southeastern United States were observed for chromosomal polymorphisms. Two sibling species, species A and B, each with intraspecific inversions, were distinguished. Species A correlates with the previously published standard maps for salivary gland and ovarian nurse-cell polytene chromosomes. Species A was found at all eight collection sites, and five of these populations also contained species B. Three inversions on the right arm of chromosome 3 were observed in species A. Species B contained a fixed inversion on the X chromosome, one fixed and one floating inversion on the left arm of chromosome 2, and one fixed and one floating inversion on the right arm of chromosome 3. The fixed inversion on the X chromosome makes this the best diagnostic chromosome for distinguishing species A and B. An unusual dimorphism in the left arm of chromosome 3, found in both species A and B, contained two inversions. The heterokaryotypes, as well as two distinct homokaryotypes, were seen in all of the field populations. Intraspecific clinal variations in the frequencies of the species A inversions were noted. The Florida populations were practically devoid of inversions, the Georgia and Alabama populations contained some inversions, and the Arkansas population was mostly homozygous for two of the inversions. The phylogenetic relationships of species A and B to the Maculipennis complex (Nearctic) are discussed.Key words: Anopheles, inversion, populations, chromosome polymorphism, phylogenetics.

Seven genes on the short arm of human chromosome 3 map to two regions on Macropus eugenii (tammar wallaby) chromosome 2

1994 ◽  
Vol 65 (4) ◽  
pp. 228-232 ◽  
Author(s):  
D.A. Miller ◽  
O.J. Miller ◽  
D. Francis ◽  
P.F.R. Little ◽  
J.A.M. Graves
Keyword(s):  
Human Chromosome ◽  
Tammar Wallaby ◽  
Chromosome 3 ◽  
Chromosome 2 ◽  
Macropus Eugenii ◽  
Human Chromosome 3

138. GENOME-WIDE LINKAGE SCAN FOR FAMILIAL DIZYGOTIC TWINNING

2010 ◽  
Vol 22 (9) ◽  
pp. 56
Author(s):  
J. N. Painter ◽  
G. Willemsen ◽  
D. R. Nyholt ◽  
C. Hoekstra ◽  
D. Duffy ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Complex Trait ◽  
Potential Candidate ◽  
Chromosome 2 ◽  
Family Work ◽  
Linkage Analyses ◽  
Genome Wide ◽  
A Genome ◽  
The Usa ◽  
Genetic And Environmental Factors

The tendency to conceive dizygotic (DZ) twins is a complex trait influenced by genetic and environmental factors. To search for new candidate loci for twinning we have conducted a genome-wide linkage scan in 525 families using microsatellite and single nucleotide polymorphism (SNP) marker panels. Non-parametric linkage analyses including 523 families containing a total of 1115 mothers of DZ twins (MODZT) from Australia and New Zealand (ANZ) and The Netherlands (NL) produced four linkage peaks above the threshold for suggestive linkage, including a highly suggestive peak at the extreme telomeric end of chromosome 6 with an exponential (exp)LOD score of 2.813 (P = 0.0002). Since the DZ twinning rate increases steeply with maternal age independent of genetic effects, we also investigated linkage including only families where at least one MODZT gave birth to her first set of twins before the age of 30. These analyses produced a maximum expLOD score of 2.718 (p = 0.0002), largely due to linkage signal from the ANZ cohort, however, ordered subset analyses indicated this result is most likely a chance finding in the combined dataset. Linkage analyses were also performed for two large DZ twinning families from the USA, one of which produced a peak on chromosome 2 in the region of two potential candidate genes. Sequencing of FSHR and FIGLA, along with INHBB in MODZTs from two large NL families with family-specific linkage peaks directly over this gene, revealed a potentially functional variant in the 5’ untranslated region of FSHR that segregated with the DZ twinning phenotype in the UT family. Work is continuing screening candidate genes. Our data provide further evidence for complex inheritance of familial DZ twinning.

scholarly journals An ion beam–induced Arabidopsis mutant with marked chromosomal rearrangement

2017 ◽  
Vol 58 (6) ◽  
pp. 772-781 ◽  
Author(s):  
Ayako N Sakamoto ◽  
Vo Thi Thuong Lan ◽  
Satoru Fujimoto ◽  
Sachihiro Matsunaga ◽  
Atsushi Tanaka
Keyword(s):  
Ion Beam ◽  
Ion Beams ◽  
Large Chromosome ◽  
Chromosome 3 ◽  
Fish Analysis ◽  
Chromosome 2 ◽  
45S Rdna ◽  
Uvb Radiation ◽  
Centromeric Repeat ◽  
Arabidopsis Mutant

Abstract Ion beams have been used as an effective tool in mutation breeding for the creation of crops with novel characteristics. Recent analyses have revealed that ion beams induce large chromosomal alterations, in addition to small mutations comprising base changes or frameshifts. In an effort to understand the potential capability of ion beams, we analyzed an Arabidopsis mutant possessing an abnormal genetic trait. The Arabidopsis mutant uvh3-2 is hypersensitive to UVB radiation when photoreactivation is unavailable. uvh3-2 plants grow normally and produce seeds by self-pollination. SSLP and CAPS analyses of F2 plants showed abnormal recombination frequency on chromosomes 2 and 3. PCR-based analysis and sequencing revealed that one-third of chromosome 3 was translocated to chromosome 2 in uvh3-2. FISH analysis using a 180 bp centromeric repeat and 45S ribosomal DNA (rDNA) as probes showed that the 45S rDNA signal was positioned away from that of the 180 bp centromeric repeat in uvh3-2, suggesting the insertion of a large chromosome fragment into the chromosome with 45S rDNA clusters. F1 plants derived from a cross between uvh3-2 and wild-type showed reduced fertility. PCR-based analysis of F2 plants suggested that reproductive cells carrying normal chromosome 2 and uvh3-2–derived chromosome 3 are unable to survive and therefore produce zygote. These results showed that ion beams could induce marked genomic alterations, and could possibly lead to the generation of novel plant species and crop strains.

scholarly journals Effect Of Ga3 And Row Ratio On Floral Traits Of Component Lines Of BRRI Hybrid Dhan2

2013 ◽  
Vol 38 (1) ◽  
pp. 155-163 ◽  
Author(s):  
MH Rahman ◽  
MM Khatun ◽  
MSR Khan ◽  
MM Haque ◽  
MG Rasul
Keyword(s):  
Seed Production ◽  
Hybrid Rice ◽  
Environmental Influence ◽  
Floral Traits ◽  
Rice Seed ◽  
Filament Length ◽  
Anther Length ◽  
Cms Line ◽  
Stigma Exsertion ◽  
Stigma Exsertion Rate

Component lines (A and R lines) of BRRI hybrid dhan2 were assessed under treatment of GA3 application and row ratio on days to 5% and 50% flowering, duration of opening of floret, angle of open floret, filament length, anther length, stigma length, panicle exsertion rate, stigma exsertion rate and outcrossing rate. The CMS line viz; BRRI 10A have been found to be usable female parents for hybrid rice seed production due to their stigma length, stigma exsertion rate, duration of blooming, anther length and filament length. The different between genotypic and phenotypic variation was not remarkable for most of the characters studied indicating negligible environmental influence on the traits. The maximum duration of opening of floret (158.10 min) and angle of floret opening (28.870) were obtained with the application of 350 g GA3 ha-1. The improvement in the floral traits with increased GA3 level might be due to increased availability of GA3 which enhanced floral traits. The CMS line can be used as potential female parent in hybrid rice seed production of BRRI hybrid dhan2. Bangladesh J. Agril. Res. 38(1): 155-163, March 2013 DOI: http://dx.doi.org/10.3329/bjar.v38i1.15202

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