Genetics of sterility in hybrids between wild and cultivated ...
Transcript of Genetics of sterility in hybrids between wild and cultivated ...
Genetics of sterility in hybrids between wild and cultivated rice strains
Division seminar 24/ Sep/ 08
Yohei Koide
Introduction
Topics 1
Hybrid sterility between Oryza sativa and O. glaberrima
Topics 2
Hybrid sterility within Asian rice species
What is Hybrid sterility??
Equus caballus
HorseEquus asinus
Donkey
Equus asinus x Equus caballus
x
Sterile…
Mule
What is Hybrid sterility??
O. glaberrima
O. sativa
F1 Hybrid
Hyb
rid
vig
or
Genetic divergence
Inbreeding depression
Hybrid inviabilityHybrid sterility
Heterosis
RaceWithin Species
Differentspecies
Barrier between species
Reproductive barrier
Fig. General pattern of vigor in hybrids and genetic divergence between the parents.
Fertilization Reproductivephase
Vegetativephase
F1 F2
Cross incompatibility(Pre- and Post zygotic)
Hybrid inviability
Hybrid sterility
Fig. Reproductive barriers in plant hybrids.
Species No. of genesAction Reported
Cross incompatibility and Hybrid inviabilityOryza 4Gossypium 1Crepis 1Triticum 4Nicotiana 1
Hybrid sterilityOryza 37Triticum 2Lycoperusicon 1Nicotiana 1Hordeum 2Silene 1Hordeum 1
Hybrid breakdownOryza 11Mimurus 1Brasica 1
Gene
Table number of reproductive isolation related-genes reported in plants
reviewed by Koide et al. 2008a
In Oryza, there are many hybrid sterility genes reported.
Hybrid sterility is important in Oryza (?)
More interestingly…
No. of Species No. of genesAction Loci Reported
Hybrid sterilityGametophytic 1 Oryza 30
Triticum 2Lycoperusicon 1Nicotiana 1
Gametophytic 2 Oryza 6Hordeum 1Silene 1
Sporophytic 1 Hordeum 1Sporophytic 2 Oryza 1
Gene
reviewed by Koide et al. 2008a
One locus gametophytic hybrid sterility genes have been frequently observed in Oryza.
What is ‘one locus gametophytic hybrid sterility gene’??
S/S Sa/Sa
Strain A Strain B
x
S/Sa
Hybrid
S S
SaSa S/S
Sa/Sa
S/SaS/Sa
PollenEm
bryo s
ac
Sa/SaS/SaS/S
1 2 1
What is ‘one locus gametophytic hybrid sterility gene’??
S/S Sa/Sa
Strain A Strain B
x
S/Sa
Hybrid
S S
SaSa
PollenEm
bryo s
ac
Sa/SaS/SaS/S
1 2 1
S/S
Sa/Sa
S/SaS/Sa
Segregationdistortion
Semi-sterile Semi-sterile
Selfish!!
Segregation distortion
After Harushima et al. 2002
Segregation distortion may prevent the introgression of useful genes.
What is the importance of studying hybrid sterility??
1. for breeding
1-1. Sterility decreases yield.
1-2. Hybrid sterility genes prevent the introgression of useful genes.
2. for studying evolution
Hybrid sterility is one of the mechanisms of reproductive barrier between species.
We can answer the question of ‘What is the species?’
Topics 1
Hybrid sterility between Oryza sativa and O. glaberrima
Topics 2
Hybrid sterility within Asian rice genepool
Hybrid sterility gene, S1
Hybrid sterility gene, S6
S1 S1a
S1/S1a
S1a
S1
S1 S1a
S1/S1
♀♂
O. glaberrima
T65S1 (W025BC)
O. sativa
T65wxWx
OsC1
Hd1
R111
R32
RM3140Chromosome
6
S1
Hybrid sterility between Oryza sativa and O. glaberrima
Pollen semi-sterility
Normal embryo sac Abnormal embryo sac
Cytological observation of F1 hybrids
What is the causative gene?
Wx pollen
wx pollenS1a
S1Wx
wx
OSR19(Waxy)*****OSR25*****RM204*****G039*****
RM253*****C
Se-1
RM3a
RM30
G342
Chromosome 6
Linkage map constructed by Lorieux et al. 2000
Pollen fertility QTL and segregation distortion detected by Doi et al. 1998.
Is this gene common in hybrids between Asian and African rice?
Hybrid sterility between Oryza sativa and O. glaberrima
Topics 1
1. What gene(s) are involving in this phenomenon?
2. How does it distribute in Asian and African rice strains?
Fine mapping
Test crossing
Koide et al. 2008b
Fig. Fine mapping of S1 locus
Os06g0141400
Os06g0141600
Os06g0141700
Os06g0141800
Os06g0142000
Os06g0142100
Os06g0142200
Os06g0142300
Similar to early nodulin
Early nodulin 93
Similar to early nodulin
Similar to Ribosome biogenesis regulatory protein homolog
Conserved hypothetical protein
Cyclin-like F-box domain containing protein
Early nodulin
Early nodulin 93
Locus name Function
Table Predicted ORFs in candidate region of S1 locus
Normal Distortion
high low
Normal
high
Distortion
low
Fertility
?=Sa
?=S
Fertility
Segregation
Segregation
M
M M
M S
SSa
+
+ +
?
??
x x
Tester line A Tester line BUnknown genotype
Sa
Test crosses to determine the distribution of the S1 gene.
Pollen Seed Pollen Seed
O.sativa
Acc414 indica India 27.4 1.0 59.1 10.2 0.0 3.9 S 1a
Kasalath India 66.4 56.5 44.9 40.7 0.0 4.2 S 1a
Acc27590 Bangladesh 95.9 94.3 52.9 53.3 35.4 2.8 S 1a
Acc27593 Bangladesh 95.3 88.5 57.3 51.8 13.4 4.4 S 1a
Nipponbare japonica Japan 95.0 22.5 47.9 54.9 1.3 3.4 S 1a
A58 Japan 100.0 93.0 52.9 55.6 25.5 96.82) S 1a
Acc775 China 76.1 36.5 48.7 24.1 0.6 1.0 S 1a
C9064 javanica Thailand 88.4 42.3 49.6 46.1 1.4 95.12) S 1a
O. rufipogon
W106 Annual India 88.0 88.3 45.9 62.7 37.3 4.0 S 1a
W107 India 59.1 46.2 48.5 45.0 0.7 4.0 S 1a
W1551 Thailand 86.2 41.2 47.9 56.6 24.2 3.9 S 1a
Acc105451 Sri Lanka 28.5 9.7 58.4 15.3 1.5 3.6 S 1a
W130 Intermediate India 64.3 56.4 47.5 26.5 0.2 2.2 S 1a
W593 Malaysia 76.4 26.5 52.1 39.5 0.2 4.1 S 1a
W1807 Sri Lanka 50.5 39.4 58.6 29.9 0.8 4.3 S 1a
W120 Perennial India 59.7 50.6 52.7 1.3 0.2 nd3) S 1a
W149 India 90.1 78.9 41.1 39.9 52.2 1.4 S 1a
W1681 India 58.4 28.4 52.8 26.5 2.7 1.6 S 1a
W2005 India 60.3 37.6 59.1 46.2 4.6 4.1 S 1a
W2007 India 38.0 6.3 46.8 3.1 0.0 nd3) S 1a
W172 Thailand 55.5 12.9 44.8 41.9 0.2 3.5 S 1a
W1294 Philippines 85.2 8.2 46.0 12.8 0.7 1.6 S 1a
W1944 China 10.2 25.8 40.5 3.6 3.2 nd3) S 1a
W1952 China 61.1 31.9 48.7 35.8 0.4 2.2 S 1a
W1714 Weedy Brazil 54.8 26.2 42.2 23.3 0.5 4.5 S 1a
O. glaberrimaT65Wx (C7631) Nigeria 48.3 30.8 97.3 95.9 88.3 51.5 S 1
O. barthii T65Wx (B19) Mali 57.1 42.4 98.2 93.4 83.7 52.2 S 1
3) No data was obtained due to a low level of pollen fertility.
Crossing with the S 1 carriers(T65wxS 1 or T65S 1 )
% of Wxpollen
1) A58 and C9064 were tested with T65 and T65S 1, since A58 and C9064 carried the wx allele, while the other lines weretested with T65wx and T65wxS 1 .2) The high frequency of Wx pollen grains reflects the linkage between the S 1 and Wx alleles.
Speciesandaccession
Subspecies ortype
OriginAlleleestimatedFertility (%) % of Wx
pollenFertility (%)
Crossing with the S 1a carriers
(T65wx or T65 )1)
LowDistortion
LowDistortion
S1a
S1
O. sativa - O. rufipogon
complex
O. glaberrimaO. barthii
Allelic distribution of the S1 locus
Tester line with S1Tester line with S1a
Hybrid sterility between Oryza sativa and O. glaberrima
Topics 1
1. What gene(s) are involving in this phenomenon?
2. How does it distribute in Asian and African rice strains?
S1 locus was delimited to a 40kb region.There were four repeated early nodulin genes, a ribosome biogenesis regulatory protein homolog, and unknown ORFs.
The allelic states of the S1 locus was clearly diverged between Asian and African rice species.
S1 gene is one of the candidate speciation genes between Asian and African rice species.
Frequencies of genotype
S6
T65wx homozygote
W593 homozygoteT65wx×W593A F2
99 plants
Wx
OsC1
Hd1
R111
R32
RM3140Chromosome
6
100%
50%
25%
0%
75%
heterozygote
Segregation distortion
S6
S6
S6a
S6a
S6/S6
♂
♀
S6/S6a
S6 S6ax
F1
Gametogenesis
Fig. S6 genetic model
O. sativa
T65wx
O. rufipogon
W593A (NIL)
Topics 2Hybrid sterility within Asian rice species
Fig. Segregation distortion detected in the F2 population derived from the cross between T65wx and W593A.
S6 fine mapping
Due to the deficit of recombination near the centromere, the S6 locus was delimited to a region of more than 8Mb, even with a large mapping population.
8Mb!!
F1 F2 F1 F2Subspecies Seed Seed putative
Species Strain or type Origin fertility (A)a st1 % fertility (B)a st1 % A/B allele
O. sativa T65 ssp. japonica Taiwan 34.1 58.4** 72.3 23.9 0.47 S 6a
Koshihikari ssp. japonica Japan 41.5 60.2** 88.0 22.6 0.47 S 6a
A58 ssp. japonica Japan 46.2 57.3** 86.7 22.8 0.53 S 6a
PTB10 ssp. indica India 16.7 20.3 14.0 17.8 1.19 S 6n
IR36 ssp. indica Philippines 80.2 17.1** 76.7 17.2 1.05 S 6n
Patpaku ssp. indica Taiwan 72.7 23.3 67.0 21.3 1.09 S 6n
Acc27590 ssp. indica Bangladesh 82.1 - 79.0 - 1.04 S 6n
Acc27591 ssp. indica Bangladesh 31.7 9.2 ** 44.1 24.1 0.72 S 6n
444 ssp. indica India 65.2 17.8 54.9 26.5 1.19 S 6n
O. rufipogon W107 Annual India 42.1 29.7 55.1 20.5 0.76 S 6n
W2002 Annual Myammer 80.3 21.6 74.4 22.2 1.08 S 6n
W630 Annual Myammer 47.6 12.5** 42.7 - 1.11 S 6n
W2048 Perennial China 20.4 45.1** 25.7 23.5 0.79 S 6a
W1718 Perennial China 52.5 - 40.8 - 1.29 S 6n
W1943 Perennial China 71.0 - 73.3 - 0.97 S 6n
W1944 Perennial China 31.1 18.4 23.5 26.3 1.32 S 6n
W1945 Perennial China 54.6 20.9 47.6 20.5 1.15 S 6n
W1952 Perennial China 47.6 13.6* 42.3 - 1.13 S 6n
W1681 Perennial India 82.1 - 74.9 - 1.10 S 6n
W593 Perennial Malaysia 81.4 15.0* 39.1 2.7** 2.08 S 6
W172 Perennial Thailand 67.2 11.2 25.5 3.6** 2.64 S 6
W1294 Perennial Philippines 67.9 20.6 28.0 2.6** 2.43 S 6
W1807b Perennial Sri Lanka 77.1 26.7 26.6 0.1** 2.90 S 6
Crossed with T65st1S 6 Crossed with T65st1
S6
S6a
S6a
S6n
S6n
Allelic distribution of the S6 locus
Neutral allele, S6n
Neutral allele, S6n
Koide et al. 2008c
S6n was located in the region where S6 was located
Fine mapping of the S6n allele by using an indica strain, Patpaku, which suggested to contain S6n allele.
This locus has same genetic history as mutation locus
This locus has different genetic history as mutationlocus because of the recombination
Even the locus is near the mutation, it doesn’t have same genetic history as mutation locus
Is there association between genetic diversity and allelic state of the S6 locus?
Genetic association
Thus, association between phenotype and marker genotype is
1. strong if marker is near the mutation.
2. strong if mutation appeared recently.
Individuals with
phenotype
Individuals without
phenotype
A
B
Geneticdiversity A B
The relative ratio of the genetic diversity of the strains with S6 to the strains with S6n
Decreasing near the centromere
Genetic diversities of S6 S6a and S6n
The genetic diversities of S6 and S6a were decreased at specific chromosomal region.The causative alleles might locate near the locus.
The genetic diversity of S6n was not decreased.S6n has longer history than S6 and S6a.
Topics 2Hybrid sterility within Asian rice species
There were three alleles at the S6 locus.
S6n were distributed widely in O. sativa and O. rufipogon.
A prominent reduction in the genetic diversity of S6 and S6a was detected.
Hybrid sterility gene, S6
Association mapping is potentially useful in this region.
S6 and S6a are newly arisen allele.
S6 and S6a were found in limited geographic area.
S6 and S6a were originated independently (from S6n??).S6 S6a
S6n
S x Sa = incompatible
Selfish genes evolved without selective advantages???
Thank you very much