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