The document discusses marker-assisted breeding methods in rice, highlighting their advantages for selecting desirable traits and increasing efficiency in breeding programs. It presents multiple case studies on the successful integration of disease resistance genes into prominent rice varieties in India, showcasing techniques like marker-assisted backcrossing and pyramiding. The research emphasizes the importance of early generation selection and combining traits to enhance yield and resilience against environmental stressors.

1. Markers-Assisted Breeding in Rice
Banoth Madhu
Ph.D Research Scholar
Genetics and Plant Breeding
Tamil Nadu Agricultural University, Coimbatore

2. Marker-Assisted Selection for Conventional Breeding: Why?
• Difficult traits
• Traits with low heritability
• Pyramiding of resistance genes
• Selection at seedling stage
• Distinguish homo & heterozygotes
• Selection for recessive genes
• No question of biosafety and bioethics, etc.

3. Case study-1
Marker assisted selection in rice
Authors: Sabina Akhtar et al. (SKUAST-K, J & K, India)
Published: Journal of Phytology (2010)
Steps involved in MAS:
1. Selection of parents
2. Development of breeding population
3. Isolation of DNA from each plant
4. Scoring DNA markers and
5. Correlation with morphological traits
MAS Breeding schemes:
1. Marker- assisted backcrossing
2. Marker- assisted pyramiding
3. Early generation selection
4. Combined approaches

4. Marker-Assisted Backcrossing (MAB)
 MAB has several advantages over conventional backcrossing:
Effective selection of target loci- Foreground selection
Minimize linkage drag- Recombinant selection
Accelerated recovery of recurrent parent- Background selection

5. Case study-2
Marker assisted introgression of bacterial blight resistance in Samba
Mahsuri, an elite indica rice variety
Authors: Sundaram et al. (DRR and CCMB)
Published: Euphytica (2008)
 Samba Mahsuri (BPT5204) is a leading rice variety of AP. But it is susceptible to BLB.
 A rice line called SS1113 that contains Xa21, xa13 and xa5 genes in the genetic
background of PR106 has been developed at PAU. SS1113 is resistant to BLB disease
but scores low on other characteristics

9. Generation Number of
plantsscored
Number of plants that are
triple heterozygotes
Estimated maximum %
contribution of recurrent
parent genome to selectedBC
plant
Expected % contribution of
recurrent parent genome
to selected BC pant
BC1F1 145 11 72 75
BC2F1 126 10 80 87.5
BC3F1 120 8 89 93.754
BC4F1 80 6 96 96.875
Table: Number of triple ‘R’ gene heterozygotes identified and estimation of recurrent parent genome
contribution
S.No. Gene combinations SS1113 X BPT 5204 BC4 F2 Line numbers
1 Xa21/Xa21 xa13/xa13 xa5/xa5 5 B-170, 189, 197, 210, 226
2 Xa21/Xa21 xa13/xa13 Xa5/Xa5 5 B-24, 29, 60, 69, 277
3 Xa21/Xa21 Xa13/Xa13 xa5/xa5 4 B-159, 199, 261, 266
4 xa21/xa21 xa13/xa13 xa5/xa5 2 B-48, 173
5 Xa21/Xa21 Xa13/Xa13 Xa5/Xa5 4 B-142, 249, 270, 276
6 xa21/xa21 xa13/xa13 Xa5/Xa5 4 B-9, 32, 182, 187
7 xa21/xa21 Xa13/Xa13 xa5/xa5 2 B-136, 184
Table: Number of lines with multiple ‘R’ gene combinations

10. Conclusion;
• At BC4F1, a line possessing the BB resistance genes along with maximum recurrent parent genome
introgression was selfed to generated homozygous BC4F2 lines
• The lines were evaluated for their morphology, yield, quality and BB resistance from BC4F2 generation
onwards
• Four homozygous lines possessing high BB resistance, yield and grain quality similar to Samba Mahsuri were
nominated for AICRIP trials - IET 19026 - IET 19045 - IET 19046 - IET 19590

12. Improved Samba Mahsuri (IET 19046) - A first variety from MAS in India

13. Marker-assisted pyramiding
Objectives:-
 Enhancing trait performance
 Remedying deficits
 Increasing the durability
 Broadening the genetic basis

15. Early generation MAS
 MAS conducted at F2 or F3 stage
 The main advantage is to discard many plant with unwanted gene combinations
 Advantages for later stages of the breeding program because resources can be used to
focus on fewer lines

16. Case study-3
Introduction of bacterial blight resistance into Triguna, a high yielding, mid-
early duration rice variety
Authors: Sundaram et al. (DRR and CCMB)
Published: Biotechnology Journal (2009)

17. Combined approaches
 “Marker directed phenotyping or Tandem selection”
 To maximize genetic gain
 Level of recombination between marker and QTL
 To reduce population sizes
 Save time and reduce cost

18. Case study-4
Combining drought and submergence tolerance in rice: marker-assisted
breeding and QTL combination effects
Authors: Shalabh Dixit and Anshuman Singh et al. (IRRI and DRR)
Published: Molecular Breeding (2017)
 TDK1 is a popular rice variety from the Lao PDR. Originally developed for irrigated conditions,
this variety suffers a high decline in yield under drought conditions.
 Studies have identified three quantitative trait loci (QTLs) for grain yield under drought conditions,
qDTY3.1, qDTY6.1, and qDTY6.2, that show a high effect in the background of this variety.
 We report here the pyramiding of these three QTLs with SUB1 that provides 2–3 weeks of
tolerance to complete submergence, with the aim to develop drought- and submergence-tolerant
near-isogenic lines (NILs) of TDK1.

20. Achievements of MAS in India
1. Three BB resistance genes (Xa5, Xa13, Xa21) introgress into the rice variety Sambha
Mahsuri (BPT-5204) released in India as “Improved Sambha Mahsuri” (IET 19046)-
DRR & CCMB
2. BB resistance genes (Xa13, Xa21) introgress into the rice variety Pusa Basmati 1 (PB 1)
and released as “Improved Pusa Basmati (IPB 1)”- IARI
3. Blast resistance genes - Pi1, Pi2 (CRRI & UAS)
4. Gall midge resistance genes - Gm1, Gm10 (TNAU)
5. Submergence tolerance variety: Swarna- Sub 1 and Sambha Mahsuri- Sub1 Show
increased submergence tolerance (IRRI, DRR and CRRI)
6. Improved Pusa RH10 - resistant to BB and blast (IARI)