Marker-assisted backcrossing: a useful method for rice improvement

Figures & data

Figure 1. Schematic representation of conventional backcrossing (Modified from George Acquaah [17]).

Table 1. Examples of marker-assisted backcross breeding in rice.

Sl number	Target trait	Gene (s)/QTL (s)	Type/name of marker(s) used	References	Remarks
1	Bacterial blight (BB) resistance	Xa21 and Xa13	SSR markers	[27]	MAS applied for marker-assisted backcross breeding (Target variety: Taraori Basmati and Basmati 386)
2		Xa4, xa5, xa13 and Xa21	SSR markers	[28]	MAS applied for marker-assisted backcross breeding (Target variety: PRR78 and KMR3)
3		Xa21	SSR markers	[29]	MAS applied for marker-assisted backcross breeding (Target variety: KDML105)
4		Xa7 and Xa21	SSR markers	[30]	MAS applied for marker-assisted backcross breeding (Target line: Yihui1577)
5		Xa7, Xa21, Xa22 and Xa23	SSR markers	[31]	MAS applied for marker-assisted backcross breeding (Target line: hybrid rice restorer line Huahui 1035)
6		Xa21	STS (pTA248)	[11]	MAS applied for marker-assisted backcross breeding
7		Xa21	STS (pTA248)	[32]	MAS applied for marker-assisted backcross breeding
8		xa5, xa13 and Xa21	CAPS for xa5(RG556+DraI) CAPS for xa13(RG136+HinfI) STS for Xa21(pTA248)	[33]	MAS applied for marker-assisted backcross breeding (Target variety: PR106)
9		xa5, xa13 and Xa21	CAPS for xa5(RG556+DraI) CAPS for xa13(RG136+HinfI) STS for Xa21(pTA248)	[34]	MAS applied for marker-assisted backcross breeding
10		xa5	CAPS (RG556+DraI)	[35]	MAS applied for marker-assisted backcross breeding
11		xa13, xa21	STS and SSR	[7]	MAS applied for marker-assisted backcross breeding
12		xa5, xa13 and Xa21	CAPS for xa5(RG556+DraI) CAPS for xa13 (RG136+HinfI) STS for Xa21(pTA248	[36]	MAS applied for backcross breeding (Target variety: Samba Mahsuri)
13		xa5 and xa13	CAPS for xa13(RG136+HinfI) STS for Xa21(pTA248)	[37]	MAS applied for backcross breeding (Target variety: Triguna)
14		xa13 and Xa21	CAPS for xa13(RG136+HinfI) STS for Xa21(pTA248)	[7,38]	MAS applied for backcross breeding (Target variety: Pusa Basmati 1)
15	Blast resistance	Pi-genes, Xa5	SSR markers	[39]	MAS applied for marker-assisted backcross breeding
16		Pi5 and Pi54	SSR markers	[40]	MAS applied for backcross breeding (Target variety: PRR78, Basmati rice)
17		Pi1 and Pi2	SSR markers	[41]	MAS applied for backcross breeding (Target variety: Ronfeng B hybrid rice)
18		Pi1	SSR and ISSR markers	[42]	MAS applied for backcross breeding (Target variety: Zhenshan 97A)
19	Submergence tolerance	sub1	SSR markers	[43]	MAS applied for backcross breeding (Target variety: AS996)
20		Sub1	SSR markers	[44]	MAS applied for backcross breeding (Target variety: OM1490)
21		Sub1QTL	SSR and STS	[8]	MAS applied for backcross breeding (Target variety: Swarna and Samba Mahsuri)
22		Sub1QTL	Phenotypic and SSR	[45]	MAS applied for backcross breeding (Target variety: Swarna and Samba Mahsuri)
23		Sub1QTL	SSR	[12]	MAS applied for backcross breeding (Target variety: Swarna and Samba Mahsuri)
24	Salt tolerance	Saltol	SSR markers	[46]	MAS applied for backcross breeding (Target variety: Q5DB)
25		Saltol QTL	SSR markers	[47]	MAS applied for backcross breeding (Target variety: ASS996)
26		Saltol QTL	SSR markers	[48]	MAS applied for backcross breeding (Target variety: Bacthom 7)
27	Drought tolerance	QTL	SSR markers	[49]	MAS applied for backcross breeding (Target variety: KMDL105)
28	Phosphorous tolerance	Pup1	SSR markers	[50]	MAS applied for backcross breeding
29	Brown Plant hopper resistance	Bph14 and Bph15	InDel marker B14 and B15	[51]	MAS applied for backcross breeding (Target variety: Shengdao 15, Shengdao 16 and Xudao 3)
30		Bph18	SSR markers	[52]	MAS applied for backcross breeding(Target variety: Junambyeo)
31	Gall midge resistance	Gm8	SSR markers	[53]	MAS applied for backcross breeding
32	Rice stripe resistance	Stv-bi	SSR markers	[51]	MAS applied for backcross breeding (Target variety: Shengdao 15, Shengdao 16 and Xudao 3)
33	Thermo sensitive genic male sterility	tms2, tgms and tms5	SSR markers	[54]	MAS applied for backcross breeding
34	Deep roots	QTLs on chromosomes 1, 2, 7 and 9	RFLP and SSR markers	[55]	MAS applied for backcross breeding
35	Root traits + Aroma	QTLs on chromosomes 2, 7, 8, 9 and 11	RFLP and SSR markers	[56]	MAS applied for backcross breeding
36	Submergence Tolerance + BPH resistance + Bacterial blight resistance + Blast resistance + quality	Subchr9 QTL, Xa21, Bph and blast QTLs, and quality loci	SSR and STS	[8]	MAS applied for backcross breeding
37	Heading date	QTLs for heading date (Hd1,Hd4, Hd5, or Hd6)	RFLP, STS, SSR, CAPS, dCAPs	[57]	MAS applied for backcross breeding
38	Quality	Waxy	RFLP	[58]	MAS applied for backcross breeding
39	Tolerance, disease	Bph and blast QTLs, and quality loci	SSR and STS	[8]	MAS applied for backcross breeding

Table 2. Expected recovery of recurrent parent genome comparing conventional and marker assisted backcrossing in subsequent generations

		% recurrent parent genome
Backcross generation	Number of individuals	Marker-assisted backcross	Conventional backcross
BC1	70	79.0	75.0
BC2	100	92.2	87.5
BC3	150	98.0	93.7
BC4	300	99.0	96.9

Source: Hospital [59]

Figure 2. Schematic representation of selection of homozygous plants for the donor allele. Source: modified from IRRI, (2014) with permission (www.knowledgebank.irri.org).

Figure 3. Schematic representation of transferring undesirable genes with target gene. Source: modified from IRRI, (2014) with permission (www.knowledgebank.irri.org).

Figure 4. Schematic representation of selection of heterozygous carrying resistance gene based on genotyping analysis resembling RP genome at BC₁F₁. Source: modified from IRRI, (2014) with permission (www.knowledgebank.irri.org).

Figure 5. Schematic representation of selection of heterozygous carrying resistance gene based on genotyping analysis resembling RP genome at BC₂F₁. Source: modified from IRRI, (2014) with permission (www.knowledgebank.irri.org).

Figure 6. Schematic representation of development of resistant rice variety through marker-assisted backcrossing (MABC). Source: modified from Babu et al. [67].

Figure 7. Schematic representation of difference between conventional backcrossing and marker-assisted backcrossing. Source: modified from IRRI, (2014) with permission (www.knowledgebank.irri.org).

Acquaah G. Principles of plant genetics and breeding. Oxford, UK: Blackwell Publishing; 2007.

 Google Scholar

Pandey MK, Rani NS, Sundaram RM, Laha GS, Madhav MS, Rao KS, Sudharshan I, Hari Y, Varaprasad GS, Rao LVS, Suneetha K, Sivaranjani AKP, Viraktamath BC. Improvement of two traditional Basmati rice varieties for bacterial blight resistance and plant stature through morphological and marker-assisted selection. Mol Breed. 2013;31:239–246.

 Web of Science ®Google Scholar

Guvvala L D, Koradi P, Shenoy V, Marella LS. Improvement of resistance to bacterial blight through marker assisted backcross breeding and field validation in rice (Oryza sativa). Res J Biol. 2013;1:52–66.

 Google Scholar

Win KM, Korinsak S, Jantaboon J, Siangliw M, Lanceras-Siangliw J, Sirithunya P, Vanavichit A, Pantuwan G, Jongdee B, Sidhiwong N, Toojinda T. Breeding the Thai jasmine rice variety KDML105 for non-age-related broad-spectrum resistance to bacterial blight disease based on combined marker-assisted and phenotypic selection. Field Crops Res. 2012;137:186–194.

 Web of Science ®Google Scholar

Xu J, Jiang J, Dong X, Ali J, Mou, T. Introgression of bacterial blight (BB) resistance genes Xa7 and Xa21 into popular restorer line and their hybrids by molecular marker-assisted backcross (MABC) selection scheme. Afr J Biotechnol. 2012;11(33):8225–8233.

 Google Scholar

Huang B, Xu JY, Hou MS, Ali J, Mou TM. Introgression of bacterial blight resistance genes Xa7, Xa21, Xa22 and Xa23 into hybrid rice restorer lines by molecular marker-assisted selection. Euphytica. 2012;187:449–459.

 Web of Science ®Google Scholar

Chen S, Lin XH, Xu CG, Zhang QF. Improvement of bacterial blight resistance of ‘Minghui 63’, an elite restorer line of hybrid rice, by molecular marker-assisted selection. Crop Sci. 2000;40:239–244.

 Web of Science ®Google Scholar

Ronald PC, Albano B, Tabien R, Abenes MLP, Wu KS, McCouch SR, Tanksley SD. Genetic and physical analysis of the rice bacterial blight disease resistance locus Xa-21. Mol Gen Genet. 1992;236:113–120.

 PubMedGoogle Scholar

Singh S, Sidhu JS, Huang N, Vikal Y, Li Z, Brar DS, Dhaliwal HS, Khush GS. Pyramiding three bacterial blight resistance genes (xa5, xa13 and Xa21) using marker-assisted selection into indica rice cultivar PR106. Theor Appl Genet. 2001;102:1011–1015.

 Web of Science ®Google Scholar

Sanchez AC, Brar DS, Huang N, Li Z, Khush GS. Sequence Tagged site marker-assisted selection for three bacterial blight resistance genes inrRice. Crop Sci. 2000;40:792–797.

 Web of Science ®Google Scholar

Toenniessen GH, O'Toole JC, DeVries J. Advances in plant biotechnology and its adoption in developing countries. Curr Opin Plant Biol. 2003;6:191–198.

 PubMed Web of Science ®Google Scholar

Joseph M, Gopalakrishnan S, Sharma RK, Singh VP, Singh AK, Mohapatra T. Combining bacterial blight resistance and Basmati quality characteristics by phenotypic and molecular marker-assisted selection in rice. Mol Breed. 2004;13:377–387.

 Web of Science ®Google Scholar

Sundaram RM, Vishnupriya MR, Biradar SK, Laha GS, Reddy AG, Rani NS, Sarma NP, Sonti RV. Marker assisted introgression of bacterial blight resistance in Samba Mahsuri, an elite indica rice variety. Euphytica. 2008;160:411–422.

 Web of Science ®Google Scholar

Sundaram RM, Priya MRV, Laha GS, Rani NS, Rao PS, Balachandran SM, Reddy GA, Sarma NP, Sonti RV. Introduction of bacterial blight resistance into Triguna, a high yielding, mid-early duration rice variety by molecular marker assisted breeding. Biotechnol J. 2009;4:400–407.

 PubMedGoogle Scholar

Gopalkrishnan RK, Sharma, Rajkumar AK, Josheph M, Singh VP, Singh AK, Bhat KV, Singh NK, Mohapatra T. Integrating marker assisted background analysis with foreground selection for identification of superior bacterial blight resistant recombinants in Basmati rice. Plant Breed. 2008;127:131–139.

 Web of Science ®Google Scholar

Pinta W, Toojinda T, Thummabenjapone P, Sanitchon J. Pyramiding of blast and bacterial leaf blight resistance genes into rice cultivar RD6 using marker assisted selection. Afr J Biotechnol. 2013;12(28):4432–4438.

 Google Scholar

Singh VK, Singh A, Singh SP, Ellur RK, Choudhary V, Sarkel S, Singh D, Krishnan SG, Nagarajan M, Vinod KK, Singh UD, Rathore R, Prashanthi Sk, Agrawal PK, Bhatt JC, Mohapatra T, Prabhu KV, Singh AK. Incorporation of blast resistance into “PRR78”, an elite Basmati rice restorer line, through marker assisted backcross breeding. Field Crops Res. 2012;128:8–16.

 Web of Science ®Google Scholar

Fu C, Wu T, Liu W, Wang F, Li J, Zhu X, Huang H, Liu ZR, Liao Y, Zhu M, Chen J, Huang Y. Genetic improvement of resistance to blast and bacterial blight of the elite maintainer line Rongfeng B in hybrid rice (Oryza sativa L.) by using marker-assisted selection. Afr J Biotechnol. 2012;11(67):13104–13124.

 Google Scholar

Liu DW, Oard SV, Oard JH. High transgene expression levels in sugarcane (Saccharum officinarurn L) driven by rice ubiquitin promoter RUBQ2. Plant Sci. 2003;165:743–750.

 Web of Science ®Google Scholar

Cuc LM, Huyen LTN, Hien PTM, Hang VTT, Dam NQ, Mui PT, Quang VD, Ismail AM, Ham LH. Application of marker assisted backcrossing to introgress the submergence tolerance QTL SUB1 into the Vietnam elite rice variety-AS996. Am J Plant Sci. 2012;3:528–536.

 Google Scholar

Lang N T, Tao NV, Buu BC. Marker-assisted backcrossing (mab) for rice submegence tolerance in Mekong delta. Omonrice. 2011;18:11–21.

 Google Scholar

Toojinda T, Tragoonrung S, Vanavichit A, Siangliw JL, Pa-In N, Jantaboon J, Siangliw M, Fukai S. Molecular breeding for rainfed lowland rice in the Mekong region. Plant Prod Sci. 2005;8:330–333.

 Web of Science ®Google Scholar

Mackill DJ. Breeding for resistance to abiotic stresses in rice: the value of quantitative trait loci. In: K.R. Lamkey and M. Lee, editors. Plant breeding: the Arnel R. Hallauer international symposium. Ames, IA: Blackwell; 2006. p. 201–212.

 Google Scholar

Neeraja CN, Maghirang-Rodriguez R, Pamplona A, Heuer S, Collard BCY, Septiningsih EM, Vergara G, Sanchez, D, Xu K, Ismail AM, Mackill DJ. A marker-assisted backcross approach for developing submergence-tolerant rice cultivars. Theor Appl Genet. 2007;115:767–776.

 PubMed Web of Science ®Google Scholar

Huyen LTN, Cuc LM, Ham LH, Khanh TD. Introgression the SALTOL QTL into Q5DB, the elite variety of Vietnam using marker assisted selection (MAS). Am J BioSci. 2013;1(4):80–84.

 Google Scholar

Huyen LTN, Cuc LM, Ismail AM, Ham LH. Introgression the salinity tolerance QTLs Saltol into AS996, the elite rice variety of Vietnam. Am J Plant Sci. 2012;3:981–987.

 Google Scholar

Vu HTT, Le DD, Ismail AM, Le HH. Marker-assisted backcrossing (MABC) for improved salinity tolerance in rice (Oryza sativa L.) to cope with climate change in Vietnam. Aust J Crop Sci. 2012;6(12):1649–1654.

 Google Scholar

Suji KK, Prince KSJ, Mankhar PS, Kanagaraj P, Poornima R, Amutha K, Kavitha S, Biji KR, Gomez M, Babu RC. Evaluation of rice (Oryza sativa L.) near iso-genic lines with root QTLs for plant production and root traits in rainfed target populations of environment. Field Crops Res. 2012;137:89–96.

 Web of Science ®Google Scholar

Chin JH, Gamuyao R, Dalid C, Bustamam M, Prasetiyono J, Moeljopawiro S, Wissuwa M, Heuer S. Developing rice with high yield under phosphorus deficiency: Pup1 sequence to application. Plant Physiol. 2011;156:1202–1216.

 PubMed Web of Science ®Google Scholar

Xu J. Pyramiding of two BPH resistance genes and Stv-bi gene using marker-assisted selection in japonica rice. Crop Breed Appl Biotechnol. 2013;13:99–106.

 Web of Science ®Google Scholar

Suh JP, Yang SJ, Jeung JU, Pamplona A, Kim JJ, Lee JH, Hong HC, Yang CI, Kim YG, Jena KK. Development of elite breeding lines conferring Bph18 gene-derived resistance to brown plant hopper (BPH) by marker-assisted selection and genome-wide background analysis in japonica rice (Oryza sativa L.). Field Crops Res. 2011;120:215–222.

 Web of Science ®Google Scholar

Sama VSAK, Himabindu K, Naik SB, Sundaram RM, Viraktamath BC, Bentur JS. Mapping and marker-assisted breeding of a gene allelic to the major Asian rice gall midge resistance gene Gm8. Euphytica. 2012;187:393–400.

 Web of Science ®Google Scholar

Nas TMS, Sanches DL, Diaz GQ, Mendioro MS, Virmani SS. Pyramiding of thermosensitive genetic male sterility (TGMS) genes and identification of a candidate tms5 gene in rice. Euphytica. 2005;145:67–75.

 Web of Science ®Google Scholar

Shen ZK, Wang M, Li Y, Jackson D, Yin A, Dong D, Peng F. Crustal deformation associated with the Altyn Tagh fault system, western China, from GPS. J Geophys Res. 2001;106(30):607–621.

 Google Scholar

Steele AD, Emsley JG, Ozdinler PH, Lindquist S, Macklil DJ. Prion protein (PrPc) positively regulates neural precursor proliferation during developmental and adult mammalian neurogenesis. Proc Natl Acad Sci USA. 2006;103:3416–3421.

 PubMed Web of Science ®Google Scholar

Takeuchi N, Ebitani T, Yamamato T, Sato H, Ohta H, Nemoto H, Imbe T, Yano M. Development of isogenics of rice cultivar Koshihikari with early and late heading by marker-assisted selection. Breed Sci. 2006;56:405–413.

 Web of Science ®Google Scholar

Zhou PH, Tan YF, He YQ, Xu CG, Zhang Q. Simultaneous improvement for four quality traits of Zhenshan 97, an elite parent of hybrid rice, by molecular marker-assisted selection. Theor Appl Genet. 2003a;106:326–331.

 PubMed Web of Science ®Google Scholar

Babu, R, Nair SK, Kumar A, Venkatesh S, Sekhar JC, Singh NN, Srinivasan G, Gupta HS. Two-generation marker-aided backcrossing for rapid conversion of normal maize lines to quality protein maize (QPM). Theor Appl Genet. 2005;111:888–897.

 PubMed Web of Science ®Google Scholar