Current Scenario of Breeding Approaches in Rice

Rice is the predominant crop in India and is the staple food in eastern and southern Indian populations. One of the oldest grown crops is rice. The initial discovery of cytoplasmic male sterile (CMS) three-line system made it possible to produce hybrids that significantly increase rice yields compared to its inbred counterparts. Further genetic and molecular studies help elucidate the mechanisms involved in CMS male sterility. Additional CMS types were also discovered with similar genetic control from wild sources by interspecific hybridization. In India more than 1200 varieties were released for cultivation suitable different ecosystems and out of them 128 varieties have been contributed from NRRI, Cuttack. A list of these varieties are furnished below with their duration, grain type, yield potential, reaction to major disease and insects grain quality and tolerance to different adverse situations. Recent advances in molecular approaches used in modern rice breeding include molecular marker technology and marker-assisted selection (MAS); molecular mapping of genes and QTLs and production of hybrids and alien introgression lines (AILs). Genomic selection (GS) has been projected as alternative to conventional MAS. GS has huge potential to enhance breeding efficiency by increasing gain per selection per unit time. Due to the adaptation of semi dwarf high yielding varieties, combined with intensive input management practices, the country witnessed an impressive rice production growth in the post-independent period. Rice production was increased four times, productivity three times while the area increase was only one and half times during this period. The projected rice requirement by 2025, in order to keep up with increasing population, is about 130 m.t. The challenge of growing rice production is made more difficult by declin-ing trends in HYV’s yields, decreasing and degrading natural resources such as land and water and a severe labour shortage.


Introduction
Rice (Oryza sativa L.) is one of the most important staple foods that feed more than half of the world's population; Asia and Africa are the major consuming regions [1]. For at least half of the world's population, rice is the most significant source of calories. As a result, many countries have developed strategies to achieve rice self-sufficiency by growing the area under cultivation or increasing yield per unit area. In case of rice, however, grain quality is just as critical as yield. Heterosis is the ability of F 1 offspring to outperform either parent and it is the only way to achieve full hybrid vigor in crop plants. For decades, this has been a factor in the production of superior cultivars for many crops in agriculture and enthusiastic geneticists [2]. In a hybrid compared to HYVs, the appropriate combination and manipulation have produced benefits [3]. Since the discovery and growth of the cytoplasmic male sterile (CMS) source in the middle of the twentieth century, heterosis was possible due to its self-pollinating existence (0.3-3.0% outcrossing). Nanyou 2, the first indica rice hybrid, was released for cultivation in China in 1974.
Subsequently, relatively heterotical hybrid rice (HR) breeding approaches were adopted, such as two-line system and super hybrids, which complemented Chinese food security and liveling standards significantly in India. In 1989, the Indian Council of Agricultural Research (ICAR) launched a special goal-oriented and time-bound project for rice called "Promotion of Research and Development Efforts on Hybrids in Selected Crops," which included 12 network centres. Around four years of intensive research (1989)(1990)(1991)(1992)(1993) paid off handsomely, and India became the second country after China to grow and commercialize hybrid rice. APRRI, Maruteru, launched the first hybrid variety APRH-1 in 1993-1994 for Andhra Pradesh. So far, 117 rice hybrids (36 from public organization and 81 from private sector) have been produced, with duration ranging from 115 to 150 days and a total area of 3.0 mha, accounting for 7.0 percent of India's total rice acreage [4]. As a result, breeding for consumer-favored grain qualities has become a major target for breeding programs all over the world. Grain quality must be clearly identified and the genes underlying their regulation deciphered before it is possible to breeder for fastidious customer preference. Rice is a staple food crop that accounts for more than a fifth of all calories consumed by humans [5]. Since rice is the most common cereal crop in most Asian countries and is the staple food for more than half of the world's population, even a small increase in rice grain micronutrient content could have a major effect on human health. Hybrid rice is the product of a cross between two rice parents with genetically different traits. When the right parents are chosen, the hybrid can outperform both parents in terms of vigor and yield. Higher yields, increased vigor, and increased resistance to diseases and insect resistance are all advantages of hybrid rice [6].

Hybrid rice breeding program in India
Rice is the predominant crop in India and is the staple food in eastern and southern Indian populations. One of the oldest grown crops is rice. The two cultivated species of rice are (i) Oryza sativa -Asian rice Cultivated Species of Rice (A) Asian Rice (Oryza sativa L.). It is predominant species which has spread to different part of world. (B) African Rice (Oryza glaberrima L.) [7]. It's also only found in Africa's tropical region. Based on morphological and physiological characteristics as well as geographical adaptation, Asian rice is divided into three ecological forms.

Wild species
The genus Oryza contains tweny valid species, two of which are cultivated, namely Oryza sativa and Oryza glaberrima. There are nine diploid species among the remaining 18 species ( Table 2). Six of them are tetraploid. Some of the wild species utilized in breeding programme are Oryza perennis -Co 31 GEB 24 x O. perennis [8][9][10].

Breeding component and system in hybrid rice development
For breeding technique, there are three approaches (1) the three-line method also known as CMS (cytoplasmic male sterility) system (2) the two-line method also known as the PTGMS (photo/temperature sensitive genic male sterility) system and (3) the one-line method, also known as the apomixis system. Inter-varietal hybrids, Inter-sub-specific hybrids and inter-specific or intergeneric hybrids are three ways to increase the degree of heterosis ( Table 3).

Two-line hybrid rice
The two-line hybrid rice research began in China and was successfully scaled up in 1995. The thermo-sensitive male sterile lines (TGMS) lines are those whose sterility expression is regulated by temperature, whereas photoperiod-sensitive male sterile (PGMS) lines are those whose expression is controlled by day-length duration. Backcrossing has successfully transferred the PGMS trait to many Indica and Japonica rice cultivars in China. In China, rice hybrids produced by this male sterile system are being tested in multiple locations. The degree of heterosis in two-line hybrid rice is close to that of three-line hybrid rice, but the technique methods is different. Unlike three-line hybrids, the male parent of two-line hybrid is not limited by restorer genes, allowing us to use both good restorer lines with high combining potential and good traditional varieties without restorer genes as male have many advantages for hybrid combinations, such as larger freedom for crossing, higher yielding, better quality and diseases resistance. The yield of improved two-line hybrid rice combinations is usually higher than of three-line hybrids used as controls. Meanwhile, seed processing and cultivation techniques for two-line hybrids have advanced to the point that they can be used in commercial production. Breeding of elite restorer lines is the key for matching heterotic combinations [13] ( Table 4).

Identification and utilization of cytoplasm male sterility
The role of rice cytoplasm in male sterility was first discovered in 1954 [16]. They studied cytoplasmic differences among rice varieties in 1965 and formed a male sterile line for the first time by transferring the nuclear genotype of rice cultivar Fujisaka [17]. However, due to its instability, poor plant form and photoperiod sensitivity, this cytoplasm male sterility (CMS) line could not be used to breed rice. Yuan Long Ping proposed the concept of using heterosis in rice in 1964, and for the    [18][19][20]. In another word, the discovery of WA led to successful breakthrough in hybrid rice production, resulting in the establishment of three-line hybrid rice system. As a result, China became the first country in the world to commercialize hybrid rice for food production. For commercial rice hybrids processing, a three-line hybrid system with the CMS line (A), maintainer line (B) and restorer line (R) is used. The A line cannot produce viable pollen due to the interaction between cytoplasmic and nuclear genes, so called  cytoplasmic male sterile, which anthers are pale or white and shriveled. The A line is also known as the CMS line and the seed parent because it is used as a female parent for hybrid seed development. Since the CMS line is male sterile, it cannot replicate itself and requires the assistance of a maintainer. The B line is the maintainer line, and its morphology is very similar to that of its CMS line, with the exception of its reproductive feature. However, the B line has viable pollen grains and normal seed setting, it may pollinate the A line, resulting in male sterile F1 plants. In this way, the male sterility of the A line is maintained, and the A line can be reproduced for further use or commercial purposes. Similarly, the R line will pollinate the A line because it has viable pollen grains and normal seed setting. Unlike the pollination with the B line, the F1 plants from the pollination with R line are extremely fertile, or the male sterility of the A line is restored into fertility in their progeny by R line. As a result, the R line is often referred to as the pollen parent or restoring line [21][22][23][24][25].

Genetic mechanism of rice heterosis
Heterosis, also known as hybrid vigor, is the phenomenon in which progeny of diverse inbred varieties outperform both parents in terms of yield, panicle size, and number of spikelets per panicle, number of productive tillers, stress tolerance and other factors. This phenomenon has been extensively exploited in crop production as a powerful force in plant evolution. After the successful development of hybrid maize in 1930, other crop breeders, including rice breeders, were inspired to use the concept of hybrid production by exploiting heterosis. In fact, the exploitation of heterosis has been the most practical achievement of genetics and plant breeding research [26]. The impact of this phenomenon can be judged by the fact that the number of grains per square meter in rice varies significantly between (1) wild ancestors with just a few hundred (2) improved inbred varieties with about 40,000, and (3) rice hybrids with about 52,000. Rice heterosis was first reported by Jones (1926) who observed that some F1 hybrids had more culms and greater yield than their parents. Between 1962 and 1967, a variety of proposal came from around the world for commercial exploitation of heterosis to become a major component of national and international rice improvement programs. Rice breeders from Japan, China, United States, India, the former Soviet Union and Philippines, for example, began working on projects to use rice heterosis. However, progress had been hampered by rice's inability to be strictly self-pollinated crop, as opposed to corn which is needed for hybrid seed development, extremely difficult [27][28][29].

Molecular technique to enhance rice breeding activities
Recent progress in molecular biology and biotechnology increases opportunities to use rice genetic tools not addressed in previous programs for rice production. The availability of genomic, phenotypic, geographical, and ecological information among other sequence data, when analyzed together, enables researchers to strategically plan experiments based on established models predicting plant performance [3,30]. Molecular marker technology and marker-assisted selection (MAS), molecular mapping of genes and QTLs and the generation of hybrids and alien introgression lines [31][32][33][34] are just a few of the molecular approaches used in modern rice breeding. MAS is a form of genomic assisted breeding that uses molecular markers to map QTLs or unique genes linked to phenotypes or target traits in order to select individuals with desirable alleles for desired traits [32]. MAS has many benefits over traditional phenotypic selection, including the fact that it is easier than phenotypic screening, that selection can be performed at the seedling level, and that a single plant can be selected based on its genotype [35].
Breeding for improved grain is complex because many of the quality traits are phenotyped using subjective and or expensive biochemical methods. As a result, scientists have been able to map/clone several QTLs/genes for various quality traits and developed molecular markers to aid in grain quality selection. Co-dominant marker, making it ideal for marker-assisted backcrossing for recessive trait like aroma, since lines carrying the aroma gene can be selected in the heterozygote state without having to screen progeny [36,37]. Other researchers have produced markers for the 8-bp deletion in exon 7 of chromosome 8. Other alleles in the BADH2 gene, such as a 7-bp deletion in exon 2 [38][39][40] and a 3-bp insertion in exon 13 found in aromatic rice varieties from Myanmar [41], have also been functionally identified. Around the world, functional markers for RM 190, a waxy gene SSR and waxy SNPS on intron (In1), exon 6 (Ex6) and exon 10 (Ex10) are used to select for AAC and RVA around the world [42]. The waxy SNP haplotypes have been found to be more effective in selecting for AAC and RVA than the RM 190 haplotype across these three SNPs in the waxy genome [43][44][45][46][47].

Outstanding elite hybrid rice varieties in India
In India many verities of rice have been released by Indian Council of Agriculture Research (ICAR) institute, state agricultural universities and private seed companies.

Future trends in rice breeding
Rice production would have to double by 2050 to keep up with population growth. If the world's population grows, so will consumers demands for higherquality rice. In addition to this challenge, climate change is combining new biotic and abiotic stresses. As a result, when designing new lines, rice breeders must consider a large number of simple and quantitative traits in combination while preserving and enhancing grain quality. MAS has been effective in improving certain biotic, abiotic and quality traits in rice, but it is purposeful on broad impact QTLs/genes and ignores epistatic and genetic context effects. Most traits of interest to rice breeders are regulated by a combination of several small effect and/or major genes rather than a few large-effect genes. The use of genomic selection (GS) as an alternative to traditional MAS has been proposed. By the benefits per selection per unit time, GS has a huge potential to improve breeding efficiency. GS breeding enables breeders to use genome-wide DNA marker data to choose the most suitable parents for the next generation. The association between genome-wide markers and phenotypes of the individuals under selection is used to choose these parents. The major benefits of GS over MAS is that genotyping is not limited to a subset of markers that target genes with significant effects, but instead uses all available marker data to predict breeding value. This aids in the prevention of data loss. Genes with a minor effect can be tracked and chosen based on all of the markers results. As the cost of genotyping decreases, GS will become more efficient method for improving rice breeding performance [48,49].