Breeding program management



Hybrid rice breeding and seed production



  • Describe what hybrids are and how they are developed

  • Explain two-line and three-line hybrid rice production

  • Understand the future opportunities of hybrids






What is a hybrid?


A hybrid is the first generation offspring of a cross between two genetically diverse parents.





How to obtain hybrid rice?

Hybrid rice is produced when the egg is fertilized by pollen from anthers of a rice plant from a different variety or line.

In order to produce great quantities of hybrid seeds, two kinds of parental lines are needed, a seed parent which is usually male sterile and a pollen parent.



A female plant X (left) and a male or pollen parent Y (right).





Why are we interested in hybrid rice?


Hybrids show a 15-20% of yield advantage giving higher economic returns.


Hybrid vigor or Heterosis is a universal phenomenon in which the F1 shows superiority to both parents in agronomic traits or yield.


It is present in all biological systems and has been exploited commercially in many agricultural crops.




How to measure heterosis?



* Standard heterosis is the most useful term in commercial crop production





Male Sterility Systems in Rice


Male sterility is a condition in which the pollen grain is unviable or cannot germinate and fertilize normally to set seeds.


Male Sterility Systems (genetic and non-genetic):

  • Cytoplasmic genetic male sterility (CMS)

Male sterility is controlled by the interaction of genetic factors (S) present in the cytoplasm and the nucleus (s).


  • Environment-sensitive genic male sterility (EGMS)

Male sterility system is controlled by nuclear gene expression, which is influenced by environmental factors such as temperature (TGMS), daylength (PGMS), or both (TPGMS).


  • Chemically induced male sterility

Male sterility is induced by some chemicals (gametocides)





Brief history of hybrid rice


1926 - Heterosis in rice reported


1964 - China started hybrid rice research


1970 - China discovered a commercially usable genetic tool for hybrid rice (male sterility in a wild rice = Wild Abortive )


1973 - PTGMS rice was found in China


1974 - First commercial three-line rice hybrid released in China


1976 - Large scale hybrid rice commercialization began in China


1979 - IRRI revived research on hybrid rice


1981 - PTGMS rice genetics and application was confirmed


1982 - Yield superiority of rice hybrids in the tropics confirmed (IRRI)


1990s - India and Vietnam started hybrid rice programs with IRRI


1991 - More than 50% of China’s riceland planted to hybrids


1994 - First commercial two-line rice hybrid released in China


1994 - 1998 - Commercial rice hybrids released in India, Philippines Vietnam






Rice and Hybrid Rice Production in China


In the graph below, you can see the increase of hybrid rice area in China since 1976.






Rice Grain Yield in China


The graph below compares the grain yield of hybrid rice and inbred rice. Both show an increase in yield but the yield of hybrid rice is still much higher.






What is the hybrid rice area in other Asian countries?


The table below shows that hybrid rice area continuously expands in most rice growing countries.






The 2 commercial systems for hybrid rice


Two-line hybrid rice cultivation




Three-line hybrid rice cultivation






Desirable characteristics of the 3 lines  in the CMS system



  • Stable Sterility

  • Well developed floral traits for outcrossing

  • Easily, wide-spectum, & strongly to be restored



  • Well developed floral traits with large pollen load

  • Good combining ability



  • Strong restore ability

  • Good combining ability

  • Taller than A-line

  • Large pollen load, normal flowering traits and timing




TGMS and two-line hybrid


  • Based on the discovery of P(T)GMS mutant

  • Male sterility controlled by 1 or 2 pairs of recessive gene(s)



Model of Sterility / Fertility Expression for TGMS Rice






Advantages & disadvantages of the 3-line hybrid rice system




  • Stable male sterility


  • Limited germplasm source (CMS, Restorer)

  • WA, which is the most popular CMS cytoplasm today is used in a very large area.

  • This system requires an extra step for parental seed production

  • CMS breeding is time consuming




Click on the icon to see a flowchart of 3-Line Hybrid Rice Evaluation and Seed Production





Advantages & disadvantages of the 2-line hybrid rice system




  • Simplified procedure of hybrid seed production

  • Multiple and diverse germplasm available as parents:

--> Any line could be bred as female:

--> 97% (2-line) vs 5% (3-line) of germplasm as male

  • Increased chance of developing desirable & heterotic hybrids

  • Multiple cytoplasm sources as female parents

  • Unpredictable environmental condition may affect sterility expression during seed production resulting to seed purity problems.



Click on the icon to see a flowchart of 2-Line Hybrid Rice Evaluation and Seed Production




Two-line hybrid production in China






Hybrid rice seed standard






IRRI's hybrid rice program


Its mission:

  • Developing germplasm, parents and hybrids as international public goods

  • Research and development of new technology for breeding and seed production

  • Collaboration with NARS and private sectors in hybrid rice research and production

  • Promotion of exchange of information, technology, scientist and germplasm




Its strategy:

  • Focus on conventional tools and integrate them with proven non-conventional methods to develop the technology

  • Develop parental lines, especially female parents with high outcrossing and high quality, to promote the adoption of the hybrid rice technology.

  • Facilitate development of close partnership between public and private sectors in national programs

  • Intensify agronomic research to maximize manifestation of heterosis in hybrids





Its released varieties:

Click on the icon to see:

  1. a list of the hybrids IRRI released in different countries between 1994 and 2005 and  

  2. a list of the hybrids released in different countries by using IRRI germplasm between 1994 and 2004

  3. germplasm shared by IRRI in 2004 and 2005

 IRRI hybrids



“Super high-yielding” hybrid rice breeding in China






Morphological Model of Super High-yielding Hybrid Rice


  • Plant height = 100 cm, with culm length = 70 cm

  • Uppermost three leaves:

  • Flag leaf, long, 50 cm, higher than the panicle top 20 cm. The 2nd leaf from the top: 10% longer than the flag leaf, and over the top of the panicle. The 3rd leaf = the middle position of the panicle

  • Erect: the leaf angles of the flag, 2nd and 3rd leaves are around 5, 10, 20 degrees, till mature

  • Narrow, V-shape and thick: narrow with 2 cm when flattened.

  • Plant type: moderate compact with moderate tillering capacity; drooping panicles after filled, above ground ~ 60 cm, erect-leaved canopy without appearance of the panicles

  • Panicle weight and number: grain weight per panicle = 5 g, 2.7 million panicles per hectare.

  • Leaf area index (LAI) and ratio of leaf area to grains: the LAI is ~ 6.5 based on the uppermost three leaves, the ratio of leaf area to grain weight is 100 : 2.2-2.3, meaning that to produce 2.2-2.3 grams of rice, 100 cm2 of the upper three functional leaves are needed.

  • Harvest index > 0.55


The "super high-yielding" hybrid rice






Which crosses give the highest hybrid heterosis in rice?


A hybrid from Indica and Japonica gives the highest heterosis





Inter-subspecific hybrid rice breeding


What are difficulties in breeding inter-subspecific hybrid rice?

  • Low seed set

  • Tall plant height

  • Poor grain-filling

  • Late maturity

  • Grain quality market


What are solutions for breeding of inter-subspecific hybrid rice?

  • use of wide compatibility (WC) genes

  • use of allelic dwarf gene

  • grow indica/javanica hybrids in indica rice growing region

  • grow japonica/javanica hybrids in japonica rice growing





What are the future opportunities?


1. Enhance yield heterosis


-->Exploiting subspecies heterosis


-->Applying biotechnology for parent selection (heterotic groups and/or heterotic gene blocks)







2. Increase yield of hybrid seed production


Developing high outcrossing parents

  • Improving seed production technology

  • Training seed growers

  • Selecting adequate location / season






The production of hybrid rice seed in China shows a steady increase between 1976 and 2002 despite the decrease of available land.





The pictures below show differences in hybrid rice seed production in Asia and the USA.





3. Improve hybrid rice grain quality


What is measured to determine rice grain quality?

  • Milling yield (Total milling yield + Whole milling yield)

  • Chalk

  • Amylose content

  • Gel Temperature (ASV)

  • Length, width, L/W

  • Protein

  • Aroma




The table above shows that hybrid rice has a lower whole milling yield

and that it is chalkier than inbred rice.



For more on grain quality go to lesson III.3





4. Develop hybrids for unfavorable environments


Hybrids have substantially higher yield than inbred rices under severe lowland stress of circa 1 ton per ha. (IRRI, G. Atlin, 2005)


Yield comparison of hybrid and inbred varieties under stress (Dry season 2004 and 2005, IRRI)



5. Improve agronomic management and deployment strategy






Additional materials:


For more information on hybrid rice seed production, please visit the Rice Knowledge bank online at:



Click on the icon to open a manual on two-line hybrid rice breeding.


Next lesson


In the next lesson, we will discuss intellectual property. You will also see germplasm can be exchanged with IRRI.