**4.3 Root trait and aroma**

MABC strategy had adopted by high yielding India upland rice variety, Kalinga III to insert 5 segments of QTL including 4 QTL carrying root length and thickness and 1 QTL control recessive aroma trait from Azucena donor variety which come from Philippines japonica rice [31]. This experiment was performed until 8 generation which using 3000 SSR markers for almost 8 years to develop NIL. Twenty-two NIL successfully develop which carrying QTL on root length at chromosome number 9 linked with RM242-RM201 and RM248 on chromosome 7 control for delayed flowering.

#### **4.4 Submergence tolerance**

Ten improves lines from OM 1490/IR 64 -Sub1 was developed from Marker-assisted backcrossing and having 90–99% survival under field submergence treatment [78]. Foreground selection was carried out using microsatellite, RM23805 marker which identified allele as 240 and 230 bp bands, respectively from OM1490, susceptible parent and IR64-*Sub*1, tolerant parent. Entire lines of OM1490/IR64-*Sub*1 introgression possess an increase rate of survival from original parent. In India, high yielding mega variety, Swarna had been incorporated with *Sub*1 gene by using three selections namely foreground, recombinant, and background selection, respectively. Findings indicated that superior variety Swarna successfully transformed into submergence tolerant variety within 2–3 years with three backcross generations [33]. Popular rice variety, AS996 successful incorporated *sub1* gene from rice variety IR64 as a donor parent through MABC. Insertion of *sub1* was confirmed with foreground SSR marker, ART5 and SC3 [36]. Background analysis was screened with 53 polymorphic SSR markers to assess BC2F1 and BC3F1 generations. The highest recurrent background was achieved 100% donor parent. Results suggest the development a new submergence tolerant rice variety

**109**

*Current Applicable DNA Markers for Marker Assisted Breeding in Rice (*Oryza sativa *L.)*

ASS996-SUB1 to stand with climate change. Superior varieties from India (Samba Mahsuri and CR1009), IRRI, Philippines (IR64), Laos (Thadokkham 1) and Bangladesh (BR11) successfully introgress *sub1* gene exhibited an improve survival rate compare to parental variety by applying MABC approach. Septiningsih et al. [79] studied the expression level of sub genes revealed that *sub1C*-1 was dominant over the *sub1A* allele however no reduction of expression observed when intolerant *sub1C* allele merged with the tolerant *sub1A*-1 allele. Survival rates of heterozygous plant with *sub1A* expression higher compared to homozygous tolerant parent. Existence of *sub*1A-2 will not significantly function in intolerant plant with turn off expression of sub*1C*-1. Study by Ahmad et al. [38] developed 30 newly lines of BC2F3 population from backcross of MR219 and Swarna-Sub1 with 95.37% recurrent parent genome (RPG) recovery. Rahman et al. [39] stated a marker-assisted backcross breeding (MABB) approach to incorporate the *Sub1* locus into popular rice varieties of southern India, CO 43, from tolerant FR13A variety. An elite NILs of CO 43 harboring *Sub1* locus possessing 95.78% of the recurrent

parental CO 43 genome produced from genotyping and phenotyping analysis.

'Bengal) and identify 14 QTLs traits related to salinity tolerance.

ASS996 a high yielding and widely grown cultivar in Vietnam had been cross with FL478, a highly salt tolerant rice variety using MABC strategy [40]. Four *Saltol*-AS996 introgression lines, QF3–1, QF3–2, QF 4–3-3, QF6–4 was developed with 3 foreground SSR markers, AP3206, RM3412 and RM10793 and 63 polymorphic markers were applied across rice genome for background analysis. The promising lines showed significant salt tolerance or similar compare to recurrent parent, FL478. MABC approach had been applied for introgressed *Saltol* QTL from donor parent, FL478 into Bacthom 7 recipient rice cultivar. Eighty-nine polymorphic SSR markers including 8 foreground markers to screen heterozygous plant carrying *Saltol* locus in each backcrossed generation. Background analysis demonstrated the restoration of recipient genome up to 96.8–100% in the best plant of BC3F1 generation. Finding concluded that improve version of salt tolerance-Bacthom 7 is relevant for cultivation in coastal areas of the Vietnamese Deltas [41]. De leon et al. [43] reported the utilization of SSR and SNP markers to characterize the ILs (Pokkali x

In Indonesia, *Hd*2 gene located at chromosome 7 from Nipponbare was transferred to Code variety [44]. Two markers linked with early maturation trait, RM1362 and RM7601 was used to identify heterozygous carrying this gene in 2 backcross and 1 selfing generation. Improved lines showed a similar agronomic characteristic with code variety except for heading time which 73–85 days in improved version compared to recipient parents, 89 days. Maturation days for improved version of Code carrying *Hd*2 gene were 103–104 day which is at considerable maturation days. Result concluded the availability to use these improved lines

Koshihikari and Kasalath were crossed by using MABC strategy to introgress 3 QTL segment which code for *Qdth*3, *Qdth*6 and *Qdth*8 [47]. Genotyping analysis was performed using five different types of DNA marker including RFLP, STS, SSR, CAPS and dCAPs. Three NIL successfully produced namely Wakei 367, Wakei 371 and Kanto IL1 which carrying Hd2 gene coded for heading time. All NIL exhibited

*DOI: http://dx.doi.org/10.5772/intechopen.93126*

**4.5 Salt tolerance**

**4.6 Early maturation**

**4.7 Heading time**

in Indonesia for increasing rice production.

*Current Applicable DNA Markers for Marker Assisted Breeding in Rice (*Oryza sativa *L.) DOI: http://dx.doi.org/10.5772/intechopen.93126*

ASS996-SUB1 to stand with climate change. Superior varieties from India (Samba Mahsuri and CR1009), IRRI, Philippines (IR64), Laos (Thadokkham 1) and Bangladesh (BR11) successfully introgress *sub1* gene exhibited an improve survival rate compare to parental variety by applying MABC approach. Septiningsih et al. [79] studied the expression level of sub genes revealed that *sub1C*-1 was dominant over the *sub1A* allele however no reduction of expression observed when intolerant *sub1C* allele merged with the tolerant *sub1A*-1 allele. Survival rates of heterozygous plant with *sub1A* expression higher compared to homozygous tolerant parent. Existence of *sub*1A-2 will not significantly function in intolerant plant with turn off expression of sub*1C*-1. Study by Ahmad et al. [38] developed 30 newly lines of BC2F3 population from backcross of MR219 and Swarna-Sub1 with 95.37% recurrent parent genome (RPG) recovery. Rahman et al. [39] stated a marker-assisted backcross breeding (MABB) approach to incorporate the *Sub1* locus into popular rice varieties of southern India, CO 43, from tolerant FR13A variety. An elite NILs of CO 43 harboring *Sub1* locus possessing 95.78% of the recurrent parental CO 43 genome produced from genotyping and phenotyping analysis.

### **4.5 Salt tolerance**

*Recent Advances in Rice Research*

morphological characters of plant.

Four QTL (chromosome 1, 2, 7 and 9) was introgressed to NIL developed from crossed between Azucena (donor parent) and IR64 (recipient parent) [29]. Twentynine NIL successfully developed in which three NIL carrying target 1 demonstrated significantly increased trait over IR64 while 3 out of 8 NIL consist combination target 1 and 7 exhibited higher root mass and depth. Four NIL carrying targets 9 showed increased maximum number of root length and 2 NIL showed no significant difference on root phenotypic compare to IR64. Results suggest the introgression of genes linked to root improvement is an ideal system compared to change the

Waxy locus (*wx*-MH) from Mighui 63 was successfully introgressed into Zhenshan 97 which having poor agronomically quality including amylose content (AC), gel consistency (GC), gelatinization temperature (GT) and endosperm [30]. MABC scheme had been used to develop 3 backcross and 1 selfing generation. Improved variety of Minghui 63 (Shanyou 63) carrying *wx*-MH gene at 6.1 cm length have similar agronomy characteristic as Minghui 63 with low AC, high GC and GT with low grain opacity. Result indicated that waxy region gives significant

MABC strategy had adopted by high yielding India upland rice variety, Kalinga III to insert 5 segments of QTL including 4 QTL carrying root length and thickness and 1 QTL control recessive aroma trait from Azucena donor variety which come from Philippines japonica rice [31]. This experiment was performed until 8 generation which using 3000 SSR markers for almost 8 years to develop NIL. Twenty-two NIL successfully develop which carrying QTL on root length at chromosome number 9 linked with RM242-RM201 and RM248 on chromosome 7 control for

Ten improves lines from OM 1490/IR 64 -Sub1 was developed from Marker-assisted backcrossing and having 90–99% survival under field submergence treatment [78]. Foreground selection was carried out using microsatellite, RM23805 marker which identified allele as 240 and 230 bp bands, respectively from OM1490, susceptible parent and IR64-*Sub*1, tolerant parent. Entire lines of OM1490/IR64-*Sub*1 introgression possess an increase rate of survival from original parent. In India, high yielding mega variety, Swarna had been incorporated with *Sub*1 gene by using three selections namely foreground, recombinant, and background selection, respectively. Findings indicated that superior variety Swarna successfully transformed into submergence tolerant variety within 2–3 years with three backcross generations [33]. Popular rice variety, AS996 successful incorporated *sub1* gene from rice variety IR64 as a donor parent through MABC. Insertion of *sub1* was confirmed with foreground SSR marker, ART5 and SC3 [36]. Background analysis was screened with 53 polymorphic SSR markers to assess BC2F1 and BC3F1 generations. The highest recurrent background was achieved 100% donor parent. Results suggest the development a new submergence tolerant rice variety

**4. Abiotic stresses**

**4.1 Deep root**

**4.2 Quality**

effect on quality trait.

delayed flowering.

**4.4 Submergence tolerance**

**4.3 Root trait and aroma**

**108**

ASS996 a high yielding and widely grown cultivar in Vietnam had been cross with FL478, a highly salt tolerant rice variety using MABC strategy [40]. Four *Saltol*-AS996 introgression lines, QF3–1, QF3–2, QF 4–3-3, QF6–4 was developed with 3 foreground SSR markers, AP3206, RM3412 and RM10793 and 63 polymorphic markers were applied across rice genome for background analysis. The promising lines showed significant salt tolerance or similar compare to recurrent parent, FL478. MABC approach had been applied for introgressed *Saltol* QTL from donor parent, FL478 into Bacthom 7 recipient rice cultivar. Eighty-nine polymorphic SSR markers including 8 foreground markers to screen heterozygous plant carrying *Saltol* locus in each backcrossed generation. Background analysis demonstrated the restoration of recipient genome up to 96.8–100% in the best plant of BC3F1 generation. Finding concluded that improve version of salt tolerance-Bacthom 7 is relevant for cultivation in coastal areas of the Vietnamese Deltas [41]. De leon et al. [43] reported the utilization of SSR and SNP markers to characterize the ILs (Pokkali x 'Bengal) and identify 14 QTLs traits related to salinity tolerance.

#### **4.6 Early maturation**

In Indonesia, *Hd*2 gene located at chromosome 7 from Nipponbare was transferred to Code variety [44]. Two markers linked with early maturation trait, RM1362 and RM7601 was used to identify heterozygous carrying this gene in 2 backcross and 1 selfing generation. Improved lines showed a similar agronomic characteristic with code variety except for heading time which 73–85 days in improved version compared to recipient parents, 89 days. Maturation days for improved version of Code carrying *Hd*2 gene were 103–104 day which is at considerable maturation days. Result concluded the availability to use these improved lines in Indonesia for increasing rice production.

## **4.7 Heading time**

Koshihikari and Kasalath were crossed by using MABC strategy to introgress 3 QTL segment which code for *Qdth*3, *Qdth*6 and *Qdth*8 [47]. Genotyping analysis was performed using five different types of DNA marker including RFLP, STS, SSR, CAPS and dCAPs. Three NIL successfully produced namely Wakei 367, Wakei 371 and Kanto IL1 which carrying Hd2 gene coded for heading time. All NIL exhibited

same morphological trait with Koshihikari with early heading time for Kanto IL1 (12 days), Wakei 367 (10 days) and Wakei 371 (11 days) compare to 95 days on Koshihikari.

### **4.8 Phosphorus tolerance**

MABC approach had been successfully adapted to introgress a major quantitative trait locus (QTL), *Phosphorus uptake1* (*Pup1*), positioned on rice (*Oryza sativa*) chromosome 12 into two types of Indonesian rice varieties, irrigated and upland. SNP and CAPs had been used as foreground marker to identify desirable traits and background selection had been conducted using 47 to 61 polymorphic SSRs markers and restored 89–93% of the recipient genome in BC2F3 population. Phenotyping finding suggests that *Pup1* is effective to enhance grain yield under field treatment [48].
