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Genetic analysis for drought tolerance and biomass allocation in newly developed populations of bread wheat (triticum aestivum L.)

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Bread wheat (Triticum aestivum L., 2n = 6x = 42, AABBDD) is the most lucrative commodity crop cultivated worldwide. Wheat productivity is crucial for economic gains and food security to the growing global population. Global wheat production is affected by recurrent droughts that are further exacerbated by a changing climate characterized by rising temperatures and erratic rainfall. In response to these challenges, most wheat breeding programs have focused on increasing harvest index to improve grain yield and drought adaptation without considering below-ground root biomass. In recent years there has been a growing interest in using crops such as wheat to store some of the atmospheric carbon previously lost from soils due to past agricultural practices to sustain soil quality and to mitigate climate change. Increasing biomass allocation of new wheat genotypes to the root system may enhance carbon (C) extraction from the atmosphere and transfer to crop tissues and to soils through carbon sequestration while increasing resilience to drought stress by improving water and nutrient uptake. Therefore, this study aimed at improving drought tolerance and C sequestration ability of wheat for production under dryland farming systems. The specific objectives were: to provide information based on a retrospective quantitative genetic analysis on combining ability studies of wheat for yield and yield-related traits to predict potential genetic gains achievable in improving biomass allocation for drought tolerance and soil carbon storage; to determine the extent of genetic variation present in wheat germplasm collections for biomass allocation and drought tolerance based on complementary phenotypic and root attributes and high-density single nucleotide polymorphism (SNP) markers to select breeding parents; to estimate the magnitude of the relationships between root biomass and yield components and to identify influential traits to optimise genotype selection for enhanced biomass allocation, drought tolerance and carbon sequestration potential in bread wheat (Triticum aestivum L.); to determine the general and specific combining ability, maternal effects and the mode of gene action controlling the major yield-related traits and biomass allocation in wheat to identify good combiners for breeding and enhanced carbon sequestration, and; to determine the genetic variability of newly developed wheat populations for grain yield and biomass allocation under different water stress conditions to select the best-performing families for advancement. The first study compared data on the general combining ability (GCA) and specific combining ability (SCA) effects of wheat for yield and related traits under optimum and drought-stressed conditions from 40 studies worldwide. Days to heading (DTH), plant height (PH), number of tillers per plant (TN), kernels per spike (KPS), 1,000-kernel weight (TKW), shoot biomass (SB), and grain yield (GY) exhibited wide variation for GCA and SCA effects. Progeny performance increased by 14.30 and 4.04% for SB and GY, respectively, compared with parental values under optimum water conditions. The number of tillers and SB exhibited positive associations with GY (0.45 ≤ r ≤ 0.85, p < 0.05) under both water conditions. Meta effect sizes for drought stress were negative. The highest meta-effect sizes were calculated for DTH (−4.5) followed by SB (−2.0), whereas KPS (−1.25) had the lowest. The genetic gains for PH, SB, and other yield components showed that divergent crosses involving complementary parents could enhance biomass allocation patterns in wheat. This could be used as a basis for improving biomass allocation to roots. In the second study, a total of 97 bread wheat genotypes were evaluated in field and greenhouse trials under drought-stressed and non-stressed conditions and genotyped using 16 382 high-density single nucleotide polymorphism (SNP) markers. The analysis of molecular variance showed that the intrapopulation variance was very high at 99%, with a small minimal inter-population variance (1%). The genetic distance, polymorphic information content and expected heterozygosity varied from 0.20 to 0.88, 0.24 to 1.00 and 0.29 to 0.58, respectively. The cluster analysis based on SNP data showed that 44% and 28% of the assessed genotypes maintained their genetic groups compared to hierarchical clusters under drought-stressed and non-stressed phenotypic data, respectively. The joint analysis using genotypic and phenotypic data resolved three heterotic groups and allowed the selection of genotypes BW140, BW152, BW157, BW162, LM30, LM47, LM48, LM52, LM54 and LM70. The selected genotypes were the most genetically divergent, with high root biomass and grain yield and are recommended for production or breeding. The third study evaluated 100 wheat genotypes consisting of 10 parents and 90 derived F2 families under drought-stressed and non-stressed conditions at two different sites. Data were collected for DTH, days to maturity (DTM), PH, TN, spike length (SL), spikelets per spike (SPS), KPS, TKW, SB, root biomass (RB), total plant biomass (PB), root-to-shoot ratio (RS) and GY. There was significant (p < 0.05) genetic variation in most assessed traits except TN and RS. Root biomass had significant positive correlations with grain yield under drought-stressed (r = 0.28) and nonstressed (r = 0.41) conditions, but a non-significant correlation was recorded for RS and grain yield. Notably, both root and shoot biomass had significant positive correlations under both water regimes, revealing the potential to increase both traits with minimal biomass trade-offs. The highest positive direct effects on grain yield were found for KPS and PB under both water regimes. The present study demonstrated that selection based on KPS and PB rather than RS will be more effective in ideotype selection of segregating populations for drought tolerance and carbon sequestration potential. In the fourth study, the above dataset from the ten parental lines and their F2 progeny were subjected to combining ability analysis using a full-diallel mating design. Significant differences were recorded among the tested families revealing substantial variation for PH, KPS, RB, SB, PB and GY. Additive gene effects conditioned PH, SB, PB and GY under drought, suggesting the polygenic inheritance for drought tolerance. Strong maternal and reciprocal genetic effects were recorded for RB across the testing sites under drought-stressed conditions. The parental line LM75 maintained the GCA effects in a positive and desirable direction for SB, PB and GY. Early generation selection using PH, SB, PB and GY will improve drought tolerance by exploiting additive gene action under drought conditions. Higher RB production may be maintained by a positive selection of male and female parents to capture the significant maternal and reciprocal effects found in this study. The fifth study showed higher phenotypic coefficient of variation (PCV) than the genotypic coefficient of variation (GCV) for PH, KPS, SB, RB, PB and GY. Moderate heritability of 41.61% and 45.14% and genetic advance as a percentage of the mean (GAM) of 3.49% and 3.58% were observed for RB under drought and for KPS under non-stressed conditions, respectively. Based on correlation and principal component analysis, geometric mean productivity (GMP) and stress tolerance index (STI) were identified as the most efficient drought tolerance indices for selecting drought-tolerant families with high RB. Direct crosses such as BW162 × LM75, BW152 × LM75, LM70 × LM75, LM71 × LM75 and LM26 × LM75 and reciprocal crosses LM48 × BW140, LM71 × LM26, LM70 × BW152, LM70 × BW141 and LM75 × LMBW152 were identified as drought tolerant and are recommended for genetic advancement. The high root biomass production of these families will contribute to carbon inputs through rhizodeposition in agricultural soils. Further research studies should investigate the link between changes in biomass allocation and atmospheric carbon transfer to soils for improving soil quality and mitigating climate change. The present study revealed that maternal and reciprocal effects should be considered when selecting root biomass and biomass allocation traits. Also, the study identified drought tolerant genotypes and developed new families with high biomass production for enhanced carbon sequestration. The identified families should be advanced for variety development and further evaluated for their net carbon contribution to the soil. IQOQA Ukolweni wesinkwa (iTriticum aestivum L., 2n = 6x = 42, AABBDD) yisivuno sezimpahla esinenzuzo kakhulu esitshalwa emhlabeni wonke. Umkhiqizo kakolweni ubalulekile ekuzuzeni umnotho nokuvikeleka kokudla ekukhuleni kwabantu emhlabeni wonke. Ukukhiqizwa kukakolweni emhlabeni jikelele kuthinteka ngenxa yesomiso esiphindaphindiwe esiphinde sikhuliswe yisimo sezulu esishintshayo esibonakala ngokukhuphuka kwamazinga okushisa kanye nemvula engaqondakali. Ekuphenduleni lezi zinselelo, izinhlelo eziningi zokuzalanisa ukolweni ziye zagxila ekwandiseni inkomba yokuvuna ukuthuthukisa isivuno sokusanhlamvu kanye nokuzivumelanisa nesomiso ngaphandle kokucabangela ibiomass yezimpande ezingaphansi komhlaba. Eminyakeni yamuva kuye kwaba nentshisekelo ekhulayo ekusebenziseni izilimo ezifana nokolweni ukugcina ezinye zekhabhoni yomkhathi ebikade ilahlekile emhlabathini ngenxa yemikhuba yezolimo edlule ukugcina ikhwalithi yomhlabathi kanye nokunciphisa ukuguquka kwesimo sezulu. Ukwandisa ukwabiwa kwebiomass yegenotypes entsha kakolweni ohlelweni lwezimpande kungathuthukisa ukukhishwa kwekhabhoni, icarbon (C) emkhathini futhi kudluliselwe ezicutshini zezitshalo nasemhlabathini ngokusebenzisa icarbon sequestration ngenkathi kwandiswa ukuqina kokucindezeleka kwesomiso ngokuthuthukisa amanzi nokuthathwa kwezakhi zomzimba. Ngakho-ke, lolu cwaningo lwaluhlose ukuthuthukisa ukubekezelela isomiso kanye nekhono le-C sequestration likakolweni lokukhiqiza ngaphansi kwezinhlelo zokulima ezomile. Izinhloso ngqangi zazimi kanje: i. ukunikeza ulwazi olusekelwe ekuhlaziyweni kwezakhi zofuzo zobuningi obubuyela emuva ekuhlanganiseni izifundo zekhono likakolweni wesivuno kanye nezici ezihlobene nesivuno ukubikezela inzuzo engaba khona yofuzo efinyelelekayo ekuthuthukiseni ukwabiwa kwebiomass yokubekezelela isomiso nokugcinwa kwekhabhoni yomhlabathi; ii. ukunquma ubukhulu bokuhlukahluka kwezakhi zofuzo ezikhona emaqoqweni kakolweni wegermplasm wokwabiwa kwebiomass kanye nokubekezelela isomiso okusekelwe kuphenotypic ehambisanayo kanye nezici zezimpande kanye nezimpawu eziphezulu zenucleotide polymorphism (SNP) ukukhetha abazali abazalayo; iii. ukulinganisa ubukhulu bobudlelwane phakathi kwebiomass yezimpande kanye nezingxenye zesivuno kanye nokuhlonza izici ezinethonya ukwenza ngcono ukukhethwa kwegenotype yokwabiwa kwebiomass okuthuthukisiwe, ukubekezelela isomiso kanye namandla ecarbon sequestration kukolweni wesinkwa (Triticum aestivum L.); iv. ukunquma ikhono lokuhlanganisa okujwayelekile nokuqondile, imiphumela yomama kanye nendlela yesenzo sofuzo esilawula izici ezinkulu ezihlobene nesivuno kanye nokwabiwa kwebiomass kukolweni ukuhlonza ukuxhumana okuhle kokuzalanisa nokuthuthukisa icarbon sequestration, futhi; v. ukunquma ukuguquguquka kwezakhi zofuzo lwenani likakolweni elisanda kuthuthukiswa ngokwesivuno sokusanhlamvu kanye nokwabiwa kwebiomass ngaphansi kwezimo ezahlukene zokucindezeleka kwamanzi ukukhetha imindeni eyenza kahle kakhulu ukuze ithuthuke. Ucwaningo lokuqala lwaqhathanisa imininingo ngekhono lokuhlanganisa jikelele, igeneral combining ability (GCA) kanye nemiphumela ethile yokuhlanganisa ikhono, ispecific combining ability (SCA) likakolweni wesivuno kanye nezici ezihlobene ngaphansi kwezimo ezinhle kakhulu nalezo ezicindezelekile yisomiso ezivela ezifundweni ezi-40 emhlabeni wonke. Izinsuku zokubheka, amadays to heading (DTH), ukuphakama kwezitshalo, iplant height (PH), inani lamatillers ngesitshalo ngasinye, inumber of tillers per plant (TN), ama-kernels nge-spike, amakernels per spike (KPS), isisindo se-1,000-kernel, ikernel weight (TKW), ishoot biomass (SB), kanye nesivuno sokusanhlamvu, igrain yield (GY) kubonise ukuhlukahluka okubanzi kwemiphumela ye-GCA ne-SCA. Ukusebenza kwenzalo kukhuphuke ngo-14.30 no-4.04% ngokwe-SB ne-GY, ngokulandelana, uma kuqhathaniswa namanani abazali ngaphansi kwezimo zamanzi ezinhle kakhulu. Inani lamatillers kanye ne-SB libonise izinhlangano ezinhle ne-GY (0.45 ≤ r ≤ 0.85, p < 0.05) ngaphansi kwezimo zombili zamanzi. Ubukhulu bomphumela wemeta wokucindezeleka kwesomiso babububi. Ubukhulu obuphezulu kakhulu bemeta-effect bubalwa ku-DTH (−4.5) kulandele i-SB (−2.0), kanti i-KPS (−1.25) yayiphansi kakhulu. Izinzuzo zofuzo ze-PH, i-SB, nezinye izingxenye zesivuno zabonisa ukuthi iziphambano ezahlukene ezibandakanya abazali abahambisanayo zingathuthukisa amaphethini okwabiwa kwebiomass kukolweni. Lokhu kungasetshenziswa njengesisekelo sokuthuthukisa ukwabiwa kwebiomass ezimpandeni. Ocwaningweni lwesibili, isamba segenotypes kakolweni wesinkwa esingama-97 sahlolwa ekuhlolweni kwensimu kanye negreenhouse ngaphansi kwezimo ezicindezelekile zesomiso futhi ezingacindezelekile kanye negenotyped kusetshenziswa izimpawu ze-16 382 eziphezulu zesingle nucleotide polymorphism (SNP). Ukuhlaziywa kokuhlukahluka kwamangqamuzana kubonise ukuthi ukuhlukahluka kwe-intra-population kwakuphezulu kakhulu ku-99%, ngokuhlukahluka okuncane kwe-inter-population (1%). Ibanga lofuzo, okuqukethwe kolwazi lwepolymorphic kanye neheterozygosity elindelekile kwahluka kusuka ku-0.20 kuya ku-0.88, 0.24 kuya ku-1.00 no-0.29 kuya ku-0.58, ngokulandelana. Ukuhlaziywa kweqoqo okusekelwe kumininingo ye-SNP kubonise ukuthi ama-44% nama-28% wegenotypes ehloliwe bagcina amaqembu abo ofuzo uma kuqhathaniswa namaqoqo ehierarchical ngaphansi kwemininingo yephenotypic ecindezelekile yesomiso futhi engacindezelekile, ngokulandelana. Ukuhlaziywa ngokuhlanganyela kusetshenziswa imininingo yegenotypic nephenotypic kuxazulule amaqembu amathathu eheterotic futhi kwavumela ukukhethwa kwegenotypes BW140, BW152, BW157, BW162, LM30, LM47, LM48, LM52, LM54 ne-LM70. Amagenotypes akhethiwe ayehluke kakhulu ngofuzo, anebiomass ephezulu yezimpande kanye nesivuno sokusanhlamvu futhi anconywa ukukhiqizwa noma ukuzala. Ucwaningo lwesithathu luhlole amagenotypes kakolweni ayi-100 aqukethe abazali abayi-10 nemindeni ye-F2 engama-90 etholakala ngaphansi kwezimo ezicindezelekile zesomiso nezingacindezelekile ezindaweni ezimbili ezahlukene. Imininingo yaqoqwa i-DTH, izinsuku zokuvuthwa, days to maturity (DTM), PH, TN, ispike length (SL), amaspikelets per spike (SPS), i-KPS, i-TKW, i-SB, ibiomass yezimpande, iroot biomass (RB), inani lebiomass yezitshalo, iplant biomass (PB), isilinganiso sezimpande zokudubula, iroot-to-shoot ratio (RS) ne-GY. Kwakukhona ukuhlukahluka okuphawulekayo (p < 0.05) kwezakhi zofuzo ezicini eziningi ezihloliwe ngaphandle kwe-TN ne-RS. Iroot biomass yayinokuhambisana okuhle okuphawulekayo nesivuno sokusanhlamvu ngaphansi kwezimo ezicindezelekile zesomiso (r = 0.28) kanye nezimo ezingacindezelekile (r = 0.41), kodwa ukuhambisana okungabalulekile kwaqoshwa isivuno se-RS nokusanhlamvu. Ngokuphawulekayo, kokubili impande nokuqhuma ibiomass kwakunokuhambisana okuhle okuphawulekayo ngaphansi kwemibuso yomibili yamanzi, kuveza amandla okwandisa zombili izici ngokuhweba okuncane kwebiomass. Imiphumela ephezulu kakhulu emihle eqondile ekuvuneni okusanhlamvu yatholakala ku-KPS ne-PB ngaphansi kwemibuso yomibili yamanzi. Ucwaningo lwamanje lwabonisa ukuthi ukukhethwa okusekelwe ku-KPS ne-PB kunokuba i-RS kuzosebenza kakhulu ekukhethweni kwe-ideotype yokuhlukanisa inani lokubekezelela isomiso kanye namandla okuqothulwa kwekhabhoni. Esifundweni sesine, idataset engenhla evela emigqeni eyishumi yezinzali kanye nenzalo yazo ye-F2 yabhekana nokuhlaziywa kwekhono lokuhlanganisa usebenzisa umklamo ogcwele wokukhwelana. Umehluko obalulekile waqoshwa phakathi kwemindeni ehloliwe eveza ukuhlukahluka okukhulu kwe-PH, KPS, RB, SB, PB, ne-GY. Imiphumela yezakhi zofuzo ezengeziwe isimo se-PH, SB, PB ne-GY ngaphansi kwesomiso, okusikisela ifa lepolygenic lokubekezelela isomiso. Imiphumela enamandla yofuzo yezinzali kanye nokuxhumana yaqoshwa ku-RB kuzo zonke izindawo zokuhlola ngaphansi kwezimo ezicindezelekile zesomiso. Umugqa wezinzali i-LM75 wagcina imiphumela ye-GCA ngendlela enhle futhi efiselekayo ye-SB, PB ne-GY. Ukukhethwa kwesizukulwane sokuqala kusetshenziswa i-PH, SB, PB ne-GY kuzothuthukisa ukubekezelela isomiso ngokuxhaphaza isenzo sofuzo esingeziwe ngaphansi kwezimo zesomiso. Ukukhiqizwa okuphezulu kwe-RB kungagcinwa ngokukhethwa okuhle kwenzali yesilisa neyesifazane ukubamba imiphumela ebalulekile yenzali yesifazane nokubuyisela etholakala kulolu cwaningo.


Doctoral Degree. University of KwaZulu-Natal, Pietermaritzburg.