Plant Breeding: QTL Mapping and Gene Identification Essay

Seedling energy in rice is a complex trait encoded by quantitative in nature. Consequently, QTL function and cistron designation for ESV trait is a major challenge to works breeders and biotechnologist. The complex inherited familial nature of ESV QTLs coincide with field and laboratory trial appraisals in rice cultivars. Some of these surveies have been demonstrated the engagement of genotype environment interactions in the look of seedling vigour traits ( Cui et al. 2002a ; Zhang et Al. 2005a ) . Due to the big environmental effects, it is normally hard to acquire duplicability in the field. Therefore, it is needed to be considered in laboratory word picture of physiological traits and their association with morphological traits to better ESV in rice. Several surveies have been reported in QTLs impacting in morphological and physiological traits related to ESV ( Cui et al. 2002a, B ; Zhang et Al. 2005a ; Zhou et Al. 2007 ) in field and controlled research lab status ( Table.2 ) ( Fig.3 ) . Recently, major QTLs confabulating ESV traits in several harvest species as Barley ( Mano and Takeda 1997 ) , Arabidopsis ( Clerkx et al. 2004 ) , Maize ( Hund et al. 2004 ) , Rice ( Miura et al. 2002 ; Fujino et Al. 2008, Sandhu et Al. 2014 ) , Tomato ( Foolad et al. 2007 ) and Lettuce ( Hayashi et al. 2008 ) have been mapped with different types of molecular markers in engendering programme

A big figure of QTLs have been identified in rice associated with morphological ( shoot length, fresh shoot weight, dry shoot weight, tiller figure /plant, mesocotyl length, root fresh weight and root dry weight ) and physiological ( sprouting rate, sprouting index, amylase activity, reducing-sugar content, root activity and chlorophyll content ) traits that significantly contributes to ESV. The ESV QTLs were identified from different mapping populations as biparental segregating population, recombinant inbred lines and twofold haploids ( Cui et al. 2002b ; Zhou et Al. 2006 ; Wang et Al. 2010 ; Diwan et Al. 2013 ; Dang et Al. 2014 ) .

Redona and Mackill ( 1996 ) , Cui et Al. ( 2002a ) , Huang et Al. ( 2004 ) , Zhang et Al. ( 2005a ) and ( Zhou et al. 2007 ) identified 11 QTLs commanding root length ( RL ) traits and were located on the chromosomes of 1, 2, 5, 6, 8 and 12 and the proportion of phenotypic discrepancy ( PV ) explained ranged from 5 to 15 % . Meanwhile, 19 QTLs commanding shoot length ( SL ) , shacking on the 8Thursdaychromosome and their PV ranged from 9.9 to 17 % and to boot 15 QTLs commanding shoot dry weight ( SDW ) were detected with PV runing from 3.4 to 15.8 % ( Redona and Mackill 1996 ; Huang et Al. 2004 ; Zhang et Al. 2005a ; Zhou et Al. 2007 ) . Shoot length is an of import trait for the seedling energy in rice. Six QTLs lending to hit length was observed by Diwan et Al. ( 2013 ) in the part of RM84-RM23 on chromosome 1 with 10-15 % important PV and the same part controls other traits related to seedling energy was reported by Redona and Mackill ( 1996 ) and Zhang et al. ( 2005a ) . QTLs related to entire dry weight was identified in the parts of chromosome 5 ( RM 26-C1447, RM 87-RM 334 and RM 178- RM 26 ) from different function populations ( Cui et al. 2002a ; Zhang et Al. 2005b ; McCouch et Al. 2001 ) .The QTLs of three traits for rate of sprouting, seedling dry weight and vigour index were besides found to be located in intervals of RM87-RM334, on chromosome 5, which might be due to either linkage or pleiotrophy.

We Will Write a Custom Essay Specifically
For You For Only $13.90/page!

order now

Nine QTLs were reported for seedling vigour traits in laboratory sprouting trials and besides in field conditions as drained dirt and afloat dirt ( Zhou et al. 2006 ) . Among them, three QTLs ( QFV-1-1, qFV- 1-2 and qFV-3-2) were observed under afloat status, four QTLs (qFV-2, qFV-3-1, qFV-3-3 and qFV-5-2) under drained intervention and two QTLs (qFV-5-1 and qFV- 10) were common between the two interventions as drouth and inundation. These QTLs were located on chromosomes 1, 2, 3, 5 and 10. In similar manner, Cui et Al. ( 2002a ) identified several seedling vigour QTLs under controlled status. Among them, QTL marked by markers RG532 and C86 located on chromosome 1 and another QTL marked by RZ403 observed on chromosome 3 were detected under nursery environment. Interestingly, a major QTLqFV-5-1reported to be on chromosome 5 was besides observed before by Redona and Mackill ( 1996 ) and Cui et Al. ( 2002a ) with rather different mapping populations although an exact comparing is slightly hard due to a deficiency of markers common between the different maps involved ( Fig.3 ) . Such QTL promises to be manipulated by MAS for betterment of rice seedling energy.

Recently, Dang et Al. ( 2014 ) reported morphological trait QTLs for seedling energy in the survey of familial diverseness and association function utilizing 540 rice cultivars using 262 simple sequence repetition ( SSR ) markers. Among the entire SSR markers employed, 11 SSR venue, were close to those reported in earlier surveies, including three QTL parts ( RM 84, RM 3453 and RM 5389 ) located on chromosome 1 for root length ( Cui et al. 2002b ) , seven QTL parts for shoot length ( RM 84, RM 3453 and RM 5389 ) on chromosome 1, ( RM 480 ) chromosome 5, ( RM 528 ) chromosome 6, ( RM 234 ) chromosome 7 and ( RM 7102 ) chromosome 12 ( Ishimaru et al. 2001 ; Moncada et Al. 2001 ; Marri et Al. 2005 ; Mei et Al. 2005 ) and one QTL part for shoot dry weight ( RM 20 ) on chromosome 12 ( Zhang et al. 2005a ) and staying 16 SSR venue ( 4 for RL, 5 for SL and 7 for SDW ) were identified as fresh marker venue for morphological traits. The important phenotypic discrepancies for root length of 27.1 % in 2011 and 25.3 % in 2012 were observed in RM3850 located on chromosome 2 and for shoot length phenotypic discrepancy of 58.8 % in 2011 and 55.6 % in 2012 were observed in RM573 of chromosome 2. The findings of erstwhile and fresh QTL linked markers could be utilized to better ESV traits in rice by using MAS in works genteelness.

Mesocotyl and coleoptile elongation plays an of import function in seedling outgrowth under DSR. Predominantly, mesocotyl elongation is considered as the major factor, controlled by complexness of familial and environmental factors. Consequently, by using of molecular marker engineering several QTLs for mesocotyl elongation was identified from interspecific or intrasubspecific crosses ( Cai and Morishima 2002 ; Cao et Al. 2002 ; Huang et Al. 2010 ) . Five QTLs for mesocotyl length were identified from F2derived population ( Redona and Mackill 1996 ) , three QTLs from F2:3population ( Katsuta-Seki et al. 1996 ) , eight QTLs from doubled monoploid population ( Cao et al. 2002 ) , 11 QTLs ( Cai and Morishima 2002 ) , five QTLs from recombinant inbred lines ( RILs ) ( Huang et al. 2010 ) and recent findings of five QTLs utilizing backcross inbred line ( BIL ) population ( Lee et al. 2012 ) . On the other manus, two QTLsqMel-1andqMel-3were identified by Lee et Al. ( 2012 ) in weedy rice PBR from chromosomes 1 with 37.3 % PV and chromosomes 3 with 6.5 % PV severally. These two QTLs for mesocotyl elongation were found to be colocalized with the QTL reported earlier for mesocotyl ( Cai and Morishima 2002 ; Cao et Al. 2002 ; Huang et Al. 2010 ; Lee et Al. 2012 ) . Therefore, these QTLs could be introgressed into an elect cultivar by marker assisted backcrossing to better the elongation of mesocotyl to do them suited for DSR.

Promising and consistent physiological traits could be used for the choice of parents or lines from big populations. Seed related traits, such as grade of seed filling, seed denseness, and seed weight could be used to better sprouting per centum, outgrowth of seedlings, activity of antioxidant enzymes and besides photosynthetic pigment. As these traits showed high relation expected familial progress and heritability and provides a better apprehension of seeds and seedlings for the finding of seedling energy in rice. This has been corroborated by Ali et Al. ( 1992 ) , seed weight was positively correlated with fresh shoot and root length, fresh shoot and root weight, and dry root weight.

QTL analysis of seed sprouting has been reported in Arabidopsis, rice, beans, boodle and soya bean ( Price et al. 2002 ; Fujino et Al. 2004 ; Hayashi et Al. 2008 ; Park et Al. 2009 ; Yano et Al. 2009 ; Wang et Al. 2011 ; Sasaki et Al. 2013 ) . In rice, at least 38 QTLs for sprouting rate, sprouting index, sprouting per centum, and intend sprouting clip have been identified ( Miura et al. 2002 ; Fujino et Al. 2004 ; Zhang et Al. 2005a ; Ji et Al. 2009 ; Wang et Al. 2011 ) . Thirty one QTLs were observed by Cui et Al. ( 2002a ) for the five seedlings energy traits, from Minghui 63 and Zhenshan 97 RIL population, of which eight were for sprouting rate, accounting for 54.7 % of the PV. Further, Cui et Al. ( 2002a ) observed important difference for amylase activity, ?-amylase activity and reducing-sugar content between the two parents. They reported three QTLs for entire amylase activity, two QTLs for ?-amylase activity, and six QTLs for reducing-sugar content with important PV of 20.5 % , 14.4 % and 18.4 % severally. Wang et Al. ( 2010 ) identified 10 QTLs for the sprouting capacities under optimal conditions utilizing population of 150 RILs in rice. Among the entire QTLs, four QTLs viz. ,qGP-4, qGP-6, qGP-8, and qGP-11represents sprouting per centum, three QTLs viz. ,qGR-1, qGR-2, andqGR-11controls sprouting rate and three QTLs viz. ,qGI-1, qGI-7,andqGI-11were responsible for sprouting index. With the above of three standards of sprouting, major QTLs asqGP-6 ( LOD=5.3 ) with Roentgen2of 24.0 % ,qGR-1( LOD=11.0 ) with Roentgen2=68.5 % andqGI-11( LOD=5.1 ) with Roentgen2=54.9 % in sprouting per centum, sprouting rate and sprouting index severally with PV of 7.5 % to 68.5 % .

Designation of major QTLs of physiological traits by MAS and their mechanisms are assuring attack in harvest betterment programme. Wang et Al. ( 2010 ) corroborated earlier studies of major QTLs, interestingly QTL ofqGR-1for sprouting rate was familiar with the part of 1000-seed weight (gw1.1andgw1.2) on chromosome 1 ( Moncada et al. 2001 ) ,qGP6for sprouting per centum on chromosome 6 was co-localized with part of seed quiescence (sd6.1) ( Li et al. 2006 ) and 1000-seed weight ( qGW-6 ) ( Wan et al. 2005 ) . In add-on, some other minor QTLs,qGR2,qGP11andqGP4were besides corresponded with 1000-seed weight ( Li et al. 2000 ; Marri et Al. 2005 ) , grain width ( Bai et al. 2010 ) and seed quiescence ( Gu et al. 2004 ) severally. Recently, Diwan et Al. ( 2013 ) reported eight QTLs for sprouting parametric quantities. The major QTL was identified in first and concluding histories of sprouting were located on chromosome 1 in the part between RM5 and RM306 markers. Interestingly, the ?-amylase cistronamy1B/Alocated in the same chromosome nearer to the marker RM5 at 13cM apart ( Temnykh et al. 2001 ) . However, the same QTLs were commanding ESV in rice and normally detected across other mapping population ofO. rufipogonandjaponicacultivarJefferson( Thomson et al. 2003 ) .

Development of high giving assortments with inundation tolerant during sprouting and early growing is indispensable for harvest constitution under direct seeding. QTL mapping for anaerobiotic sprouting ( AG ) tolerance in rice has begun in 2004 by Jiang et al. to place assuring venue that promote sprouting under deluging. Subsequently, major QTLs were reported by several research workers, Jiang et Al. 2006, Angaji et Al. 2010 and Septiningsih et Al. 2013 ( Fig.3 ) . Jiang et Al. ( 2004 ) identified QTLs on chromosomes 1, 2 and 7 from DV85 and on chromosome 5 from Kinmaze with PV of 10.5–19.6 % . In another survey, Jiang et Al. ( 2006 ) reported QTLs on chromosome 5 of USSR5, a japonica assortment ( R2=15.51 % ) . Further, Angaji et Al. ( 2010 ) observed five putative QTLs of qAG-1-2, qAG-3-1, qAG-7-2, qAG-9-1 and qAG-9-2 clarifying 17.9 to 33.5 % of the PV, with LOD tonss of 5.69–20.34 from Khao Hlan On ( Angaji et al. 2010 ) . In 2013, Septiningsih et Al. reported six QTLs on chromosomes 2, 5, 6 and 7 from the landrace Ma-Zhan Red. Among them, QTL on chromosome 7, had LOD mark of 14.5 and an Roentgen2of 31.7 % , was confirmed utilizing a BC2F3population. QTL named qAG7, was detected on chromosome 7 with an LOD of 13.93 and 22.3 % of the PV from Nanhi ( Baltazar et al. 2014 ) . Minor QTLs of qAG11 and qAG2.1 was identified from Nanhi and IR64 severally.

Traits associated with seed sprouting of 13 QTLs in wet emphasis and nine QTLs in control ( Non-stress ) status were identified by Zahra et Al. ( 2013 ) in F2:4derived population. Among the QTLs identified, six QTLsqGR-1( sprouting rate ) ,qCOL-3( coleorhiza length ) ,qGP-4( sprouting per centum ) ,qCL-4( Coleoptile length ) ,qGP-7( sprouting per centum )and qRL-12( extremist length ) were detected in emphasis and non-stress environments and they were located on chromosomes 1, 3, 4, 7 and 12 severally.

Eight QTLs modulating seedling energies at low and optimum temperature, (qSVaˆ?1, qSVaˆ?5a, qSVaˆ?5b, qSVaˆ?5c, qSVaˆ?6a, qSVaˆ?6b, qSVaˆ?8, andqSVaˆ?11 )were observed by Xie et Al. ( 2014 ) . The places ofqSVaˆ?5a, qSVaˆ?5c,andqSVaˆ?6bhave been identified as QTLs for ESV were besides reported earlier and among them, the venue ofqSVaˆ?5ais a hot topographic point for seedling energy. The major effectual venueqSVaˆ?1( chromosome 1 ) andqSVaˆ?5c( chromosome 5 ) for seedling constitution and sprouting in low temperature were narrowed down to 1.13 Mbp and 400 kbp genomic parts, severally ( Lucas et al. 2013 ) . QTLs, for seed quiescence ( Miura et al. 2002 ) , sprouting rate, shoot/ root dry weight, and physiological traits such as cut downing sugar and entire amylase activity ( Cui et al. 2002b ; Zhang et Al. 2005a ) were earlier mapped to a part similar toqSVaˆ?5a. The venueqSVaˆ?5cof chromosome 5 contains QTLs for sprouting rate, cut downing sugar content, root dry weight, entire dry weight ( Cui et al. 2002b ) , and shoot length ( Redone and Mackill 1996 ) . The findings suggested that, these parts might incorporate candidate cistrons that are effectual for seed sprouting and seedling growing.

For convenience of works breeders and physiologist, we have gathered information of promising and co-localized QTLs linked with microsatellite markers of different function populations in rice related to ESV and summarized in table 3. Among the markers assembled from different research publications, RM259 and RM84 of chromosome 1, RM282, RM148 and RM85 of chromosome 3, RM26 of chromosome 5, and RM11 of chromosome 7 were found assuring for assorted seedling vigour traits such as coleoptile length, fresh weight, sprouting rate, leaf country, figure of foliages, root activity, root dry weight, root length, cut downing sugar content, shoot dry weight, shoot length, entire dry weight and weight of mobilized seed modesty.

Aerobic rice is specifically developed to unite drought tolerance of highland rice and give potency of lowland rice. Therefore, aerophilic rice is “ improved highland rice ” in footings of output potency, and “ improved lowland rice ” in footings of drouth tolerance. In an aerophilic rice production, the seeds are direct-seeded in aerophilic dirt without any standing H2O bed, which minimizes H2O usage and boosts up H2O productiveness by extinguishing uninterrupted ooze and infiltration, cut downing vaporization and extinguishing wetland readying ( Singh et al. 2008 ; Nie et Al. 2012 ) . Under aerophilic cultivation system, lower output are expected than afloat rice due to H2O handiness, hapless sprouting, uneven harvest base, high weed force per unit area and alimentary emphasis. Bettering early growing of rice seedlings was suggested to heighten seedling early constitution ( Nie et al. 2012 ) .