**4. Genetic and molecular basis of fragrance**

Inheritance of aroma is quite difficult to understand because it is controlled by number of unknown genes at different growth stages of rice and influenced by various concentrations of volatile and semi-volatile compounds. Although, plant breeders have reported the aroma inheritance by monogenic, digenic and polygenic pattern with recessive, dominant, complimentary and duplicate gene actions, indicating that complex genetic control of the trait. In majority of studies, the genetics of fragrance in rice is mainly due to single recessive gene [6, 9, 29–33] while other studies have also identified two, three or four genetic loci having influence on fragrance [9, 34–38]. Studies on the genetic control of aroma/fragrance/scent in rice have been presented in **Table 2**.

However, much of this conflicting information on the inheritance of aroma might have arisen due to (i) unreliable and cumbersome phenotyping methods used for fragrance determination [6], (ii) failure to consider the endosperm fragrance in rice seeds [29] and (iii) segregation distortion [9]. The nature of aroma inheritance appears to be cross/genotype specific due to the number of genes and the type of gene action varied with the genotype. However, the fragrance trait is a highly heritable as some of the lines derived from T142 (scented) x IR 20 (nonscented) cross, and some of the high yielding released aromatic rice varieties show strong scent.


The implementation of marker assisted selection is a significant supplement to traditional approaches, altering the selection process directly or indirectly from

#### **Table 2.** *Inheritance pattern of aroma in rice.*

*Rice Aroma: Biochemical, Genetics and Molecular Aspects and Its Extraction… DOI: http://dx.doi.org/10.5772/intechopen.98913*

phenotype to genes [75]. A novel compound namely 2AP (2-acetyl-1-pyrroline) plays a major role in most of the aromatic rice cultivars for the presence and absence of unique popcorn like characteristic aroma. Several attempts have been made at molecular level for genetic mapping the fragrance gene governing the 2AP synthesis in different aromatic rice varieties such as Della [30], Azucena [9, 76], Suyunuo [77, 78] and Wuxianjing [77]. Quantitative trait locus (QTL) mapping was also performed in indica aromatic rice KDML105 (Jasmine) [52, 79], Kyeema [80] and Wuxiangxian [77] (**Table 3**).

By using RFLP technique, a single recessive gene (*fgr*) that controls fragrance was mapped on chromosome 8 tightly linked with a single-copy marker RG28 and found that genetic distance between aroma gene and RG28 was 4.5 cM [30]. The close linkage between RG28 and *fgr* (5.8 cM) was confirmed by [9], also identified two quantitative trait loci for fragrance, one on chromosome 4 and the other on chromosome 12.

Further, a gene responsible for 2AP synthesis was mapped in a Jasmine rice variety KDML105 between the flanking regions of RG1 and RG28 [86]. The original region (1.13 Mb) flanking between RG1 and RG28 was narrowed down to 82.2 Kb in segregating population, within this region three KDML BACs were cloned and identified three new candidate genes. Among them, a single recessive gene (Os2AP) was identified which majorly contributing the 2AP synthesis in rice. The comparative analysis between aromatic KDML105 and Nipponbare for Os2AP gene sequences revealed two important mutational events within the exon 7 of Os2AP of KDML105, at positions 730 (A to T) and 732 (T to A), followed by the 8-bp deletion "GATTAGGC" starting at position 734 [87]. A similar mutational event was also reported by [79] within the flanking regions of RM515 and SSRJ07, a gene responsible for 2AP in Kyeema fragrant rice cultivar.


**Table 3.** *Molecular mapping of fragrance gene in rice.*

#### **Figure 2.**

*Structure of the fgr gene showing ATG, initiation codon, exons (15), introns (14) and the termination site (TAA).*

Using four BAC of Nipponbare spanning within a region of 386 bp from RM515 to SSRJ07, an in silico physical map was developed and suggested that one BAC clone (clone AP004463) as most likely to be having the gene. Further, resequencing of all 17 genes lying within the BACs helped in identification of a novel gene with 3 single nucleotide polymorphisms (SNPs) with the 8 bp deletion in the 7th exon of the gene, which resulted in a premature stop codon [10]. The newly identified gene was showing homolog with BAD1 (betaine aldehyde dehydrogenase 1) locus of chromosome 4 and hence named as BAD2 [79]. A comparative study between amino acids and sequences of Os2AP and BAD2 suggested them as one gene with two different names. Recent surveys of diverse fragrant germplasm support the association of *badh2* with fragrance [76, 78, 88], and transformation of a fragrant variety with the dominant non-fragrant allele has been proved to abolish aroma [21], confirming that *badh2* is the major and effective genetic determinant of aroma in rice (**Figure 2**).

The nucleotide sequences of 7 exon are shown for both the rice varieties. The fragrant variety shows a deletion of 8 bp with 3 SNPs that terminates prematurely, within this exon. Thus, fragrant varieties truncated protein might lack the conserved sequences which is encoded by 8, 9 and 10 exons and that are believed to be important for correct protein function [84].

**Figure 3.** *QTLs for aroma with respective candidate genes in rice.*

*Rice Aroma: Biochemical, Genetics and Molecular Aspects and Its Extraction… DOI: http://dx.doi.org/10.5772/intechopen.98913*

Since the *Badh2* gene was isolated and cloned, more than a dozen mutation sites have been found in *Badh2* [3, 89–91] and a series of molecular markers were designed for these loci, which could be used for the identification of gene responsible for aroma, selection of different aromatic rice varieties and cultivation of new varieties of aromatic rice.

#### **4.1 QTLs for aroma**

A number of QTLs for aroma have been identified on chromosomes 4, 8 and 12, at least three QTLs have been located on chromosomes 3, 4 and 8 in Pusa 1121 [9, 10, 92]. Recently, three QTLs were detected for rice grain aroma on chromosome 5 (one QTL) and chromosome 8 (two QTLs) [93]. However, until now only a few QTLs and associated markers have been confirmed (**Figure 3**).
