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    Genetic enhancement of pearl millet (pennisetum glucum (L.) R. Br.) for resistance to striga bermonthica (Del.) benth and compatibility to fusarium oxysporum F. sp. strigae in Burkina Faso.
    (2024) Rouamba, Armel.; Shimelis, Hussein.
    Pearl millet (Pennisetum glaucum [L.] R. Br. 2n = 2x = 14) is one of the most important cereal crops cultivated in the semi-arid tropics of sub-Saharan Africa and India, serving millions of households, and local and regional markets. It is a staple food crop in Burkina Faso, widely grown in the Sahelian and Sudano-Sahelian zones, characterised by poor soil conditions and erratic rainfall, and high temperatures. However, the potential production and productivity of pearl millet in Africa, including Burkina Faso, is constrained by the parasitic weed [Striga hermonthica (Del.) Bentham], bird damage, downy mildew, head miner, and low-yielding landraces. Developing S. hermonthica-resistant pearl millet varieties adapted to semi-arid regions with the desirable farmer and market-preferred traits would enhance yield gains and sustainable production. Therefore, the overall objective of this study was to improve pearl millet production and productivity in Burkina Faso by developing pearl millet varieties with Striga-resistance, compatibility with a biocontrol agent, Fusarium oxysporum f.sp. Strigae (FOS) and adapted to local agroecologies. The specific objectives of this study were to: (i) investigate the constraints affecting pearl millet production and farmers’ approaches to S. hermonthica management in Burkina Faso to guide breeding and production, (ii) screen pearl millet genotypes for resistance to S. hermonthica and compatibility with a biocontrol agent, FOS, in the Sahel to select contrasting and promising parents for resistance breeding and production, (iii) determine the genome-wide association analyses of agronomic traits and S. hermonthica resistance in pearl millet to identify genetic markers for marker-assisted breeding and trait introgression, (iv) determine the generation mean analysis of S. hermonthica resistance in pearl millet to guide selection, genetic advancement and variety development, and (v) determine the combining ability effects and the response of pearl millet genotypes for agronomic traits and S. hermonthica resistance for selecting superior parents and hybrids. The first study employed a participatory rural appraisal (PRA) and was conducted in the Sahel and Sudano-Sahelian zones of Burkina Faso, involving 492 farmers to document farmers’ perceptions of the prevailing constraints affecting pearl millet production and related approaches to manage S. hermonthica. Recurrent drought, S. hermonthica infestation, shortage of labour, lack of fertilisers, lack of cash, and the use of low-yielding varieties were the main challenges hindering pearl millet production and productivity in the study areas. The study revealed a high population growth rate in rural areas, with 40% of respondents reporting families of up to 20 individuals per household. The majority of the respondents (40%) ranked S. hermonthica infestation as the primary constraint affecting pearl millet production, with yield losses of up to 80%. About 61.4% of the respondents in the study areas had achieved mean pearl millet yields of < 1.00 ton ha-1. Poor access, the high cost of improved seed, and a lack of farmers’ preferred traits in the existing improved pearl millet varieties were the main reasons for their low adoption, as 32% of respondents reported. S. hermonthica management options in pearl millet production fields included moisture conservation using terraces, manual hoeing, hand weeding, use of micro-plots locally referred to as ‘zaï’, crop rotation and mulching. These management techniques were ineffective because they do not suppress the below-ground S. hermonthica seed and are difficult to implement. Integrated management practices employing breeding for S. hermonthica-resistant varieties with the aforementioned control measures could offer a sustainable solution for Striga management and improved pearl millet productivity in Burkina Faso. The second study evaluated 150 pearl millet genotypes in S. hermonthica hotspot fields in rain-fed and greenhouse conditions using a 10 × 15 alpha lattice design in two replications in Burkina Faso. Significant differences were recorded among the tested pearl millet genotypes for the assessed agro-morphological and Striga resistance traits. Days to flowering were significantly delayed due to S. hermonthica infestation. Applying FOS on pearl millet seed significantly reduced the mean emerged Striga number in S. hermonthica-infested conditions. IP-3098, IP-6112, IP-9242, IP-10579, and IP-11358 were identified exhibiting S. hermonthica resistance and were compatible to FOS. The pearl millet genotypes supported few to none S. hermonthica emerged plants and had relatively low values under the Area under Striga Number Progress Curve (ASNPC). The selected genotypes are useful parents for breeding and integrated Striga management in Burkina Faso and related agro-ecologies. In the third chapter, 150 pearl millet genotypes were assayed in genome-wide association analyses study for agronomic and S. hermonthica resistance traits to identify genetic markers for marker-assisted breeding and trait introgression. 256 K single nucleotide polymorphisms (SNPs) were used in the study. Significant differences (P < 0.001) were detected among the assessed pearl millet genotypes for S. hermonthica parameters and agronomic traits. Further, there were significant genotype by S. hermonthica interaction for the number of S. hermonthica and ASNPC. Twenty-eight SNPs were significantly associated with a low number of emerged S. hermonthica located on chromosomes 1, 2, 3, 4, 6, and 7. Four SNPs were associated with days-to-50%-flowering on chromosomes 3, 5, 6, and 7, while five were associated with panicle length on chromosomes 2, 3, and 4. Seven SNPs were linked to thousand-grain weight on chromosomes 2, 3, and 6. The putative SNP markers associated with a low number of emerged S. hermonthica and agronomic traits in the assessed genotypes are valuable genomic resources for accelerated breeding and variety deployment of pearl millet with Striga resistance and farmer-and market-preferred agronomic traits. The fourth study determined the gene action and inheritance of S. hermonthica resistance in newly developed pearl millet populations to guide selection and genetic advancement. Bi-parental crosses were derived from contrasting pairs of Striga-resistant/Striga-susceptible of pearl millet lines. Two sets of parental lines and their subsequent F1s, F2s, and backcross generations were evaluated under greenhouse and S. hermonthica infested field conditions using a randomised complete block design with three replications. The analysis of variance showed significant (P < 0.001) differences among the generations across sets for Striga parameters. Striga resistance is quantitatively inherited and governed by multiple genes. Duplicate gene action controlled the inheritance of the number of emerged S. hermonthica. Unique F2 individuals with S. hermonthica resistance were selected from the two sets for genetic advancement through recurrent selection method for pearl millet variety development by integrating desirable agronomic and farmer-preferred traits. The last study assessed the combining ability effects of pearl millet genotypes for S. hermonthica resistance and agronomic traits. The analysis of variance for combining ability effects showed significant (P < 0.01) differences among parents for days to flowering, panicle diameter, and grain yield. The difference between lines and testers were significant (P < 0.001) for panicle length and the number of emerged Striga. The genotype IP-11358 had high and positive general combining ability (GCA) effects (158.99) for grain yield. Negative GCA effects of -6.99, -6.40, and -134.08 were recorded for Striga count 60 days after planting, Striga count 80 days after planting, and ASNPC in that order for genotype IP-11358 in the greenhouse under S. hermonthica conditions. The hybrid IP-11358 × ICMB177111 displayed a higher specific combining ability (SCA) effect and standard heterosis for grain yield. The selected pearl millet genotypes are suitable for breeding high-yielding and Striga-resistant open-pollinated and hybrid varieties for Striga-prone areas in Burkina Faso and related agro-ecologies of sub-Saharan Africa. Overall, the study identified S. hermonthica as the most critical pearl millet production constraint in Burkina Faso. Also, the study highlighted significant genetic diversity among 150 genotypes for S. hermonthica resistance when assessed using economic traits and SNP markers under Striga hotspot areas. Best-performing genotypes such as IP-3098, IP-6112, IP-9242, IP-10579 and IP-11358 were selected as suitable parents for S. hermonthica resistance breeding. The family IP-11358 × ICMB177111 was identified as having high-yielding and Striga-resistance. The selected genotypes are recommended for production and as donor parents for new population improvement in pearl millet Striga resistance breeding. Iqoqa Amabele, iPearl millet (Pennisetum glaucum [L.] R. Br. 2n = 2x = 14) angolunye lohlobo lwamabele osanhlamvana atshalwa ezindaweni ezisalugwadule ezisemazansi ne-Afrika kanye nase-India, asetshenziswa izinkulungwane ngezinkulungwane zemindeni kanye nosomabhizinisi abaningi basezifundeni nezifundazwe ezahlukene. Amabele lawa yikhona kudla okujwayelekile okudliwayo eBurkina Faso, atshalwa kakhulu ezindaweni zaseSahelian naseSudano-Sahelian, ezaziwa ngokuba nomhlabathi ongemuhle kahle nezimvula ezingani njalo kanye nokushisa okukhulu. Nokho, ukutshalwa kwamabele, ipearl millet e-Afrika, kufaka neBurkina Faso, kuthikanyezwa ukhula oluyimpilangokunye iStriga hermonthica (Del.) [iBentham], nezinyoni ezilimaza amabele, amaqhuqhuva amila emacembeni, imiswenya, nokungajwayeli kahle indawo. Ukutshalwa kwamabele epearl millett akwazi ukubekezela, iS. Hermonthica, nasezindaweni ezisagwadule, kuye ngezimfuno zomlimi nabamabhizinisi, kungathuthukisa isivuno esihle nokugcineka okuhle kwemikhiqizo. Ngakho-ke, inhlosongqangi yalolu cwaningo bekuwukuthuthukisa ukukhiqizwa kwamabele, ipearl millet eBurkina Faso ngokukhiqiza izinhlobo ezahlukene zepearl millet ezikwazi ukubekezela ngokweStriga, zivumelane nokusetshenziswa kwezivikeli iFusarium oxysporum f.sp. Strigae (FOS) futhi ziphile ngaphansi kwesimo sezulu sendawo. Inhloso yocwaningo bekuyilena: (i) ukucubungula izinkinga ngokukhiqizwa kwamabele, ipearl millet kanye nezindlela ezisetshenziswa ngabalimi ukulawula iS. Hermonthica eBurkina Faso ukunikeza umhlahlandlela ngokutshalwa nokukhuliswa, (ii) ukucubungula izinhlobo zepearl millet nokubekezela kweS. hermonthica kanye nokuvumelana namakhemikhali, i-FOS, ekukhethweni kwemikhiqizo ekwazi ukubekezelela izimo ezahlukene, (iii) ukubheka ufuzo olujwayelekile kanye nokubekezelela izimo kwepearl millet yeS. hermonthica ukubheka izinto ezijwayelekile ekukhiqizweni nokukhula kwamabele, (iv) ukuhlonza izindlela zokukhiqiza nokukwazi ukubhekana nezimo kwepearl millet, iS. Hermonthica ukuze kube nomhlahlandlela wokukhetha, ukuthuthuka okujwayelekile kanye nokuthuthuka, futhi (v) ukubheka ukuhlangana kwamandla nokwamukela ukwakheka kofuzo lwepearl millet nokubekezela kweS. hermonthica ukukhetha indawo enamandla nohlobo oluqhamuka kokungafani. Ucwaningo lokuqala lwalusebenzisa indlela egxile kumbambiqhaza wasemakhaya, iparticipatory rural appraisal (PRA) ezindaweni zaseSahel naseSudano-Sahelian eBurkina Faso, kuhlanganisa abalimi abangama-492 ukuthola izimvo zabo mayelana nezinkinga eziqhubekayo ezimayelana nokukhiqizwa kwepearl millet nezindlela zokulawulwa neS. hermonthica. Ukuphindaphinda kwezikhawu zesomiso, ukuhlasela kweS. hermonthica, ukuntuleka kwezisebenzi, kukamanyolo, kwemali, nokusetshenziswa kwezinhlobo ezingekho ezingeni, yikhona okuba nomthelela ongemuhle ekukhiqizweni kwepearl millet kulolu cwaningo. Lolu cwaningo luveze ukwenyuka kwesibalo sabantu ezindaweni zasemakhaya, amaphesenti angama-40 ababambiqhaza bocwaningo baveza ukuthi umuzi ngamunye cishe unamalungu angama-20 ekhaya elilodwa. Iningi lababambiqhaza (40%) liveze ukuthi ukuhlasela kweS. hermonthica kuyimbangela enkulu ebhekene nokukhiqizwa kwepearl millet, okwenza kube nokulahleka kwenzuzo ngamaphesenti angama-80. Cishe amaphesenti angama-61.4 ababambiqhaza bocwaningo avune isivuno esincane sepearl millet esiyi < 1.00 ton ha-1. Ukutholakali kalula, ukubiza kakhulu kwembewu ethuthukisiwe, kanye nokungabi nolwazi olwanele lwabalimi ngokufunakalayo mayelana nezinhlobo ezithuthukisiwe zepearl millet ngezinye zezizathu ezinqala ezenza kungabi lula ukujwayela, njengoba kubike ababambiqhaza abangamaphesenti angama-32. Ezinye zezindlela zokulawula iS. hermonthica emasimini epearl millet kufaka ukugcinwa komswakama kusetshenziswa indlela yokwenza amasimu angahlali, ukulima ngezandla, ukuhlakula ngezandla, ukusebenzisa amaploti amancane, abizwa ngokuthi i‘zaï’, ukushintshashintsha izitshalo nokwemboza izitshalo zingashiswa yilanga. Lezi zindlela azikwazanga ukuza nemiphumela emihle ngoba zazingakwazi ukulwa nembewu yeS. hermonthica ngaphansi komhlabathi kanti futhi kwakuwumsebenzi ukuzenza. Indlela eyinhlanganisela yokulawula ukuzaleka kwezinhlobo ezahlukene zokubhekana neS. Hermonthica kanye nezindlela ezibalulwe ngenhla kungaletha isisombululo esingasebenza isikhathi eside ekulawulweni kweStriga nasekukhiqizweni kwepearl millet eBurkina Faso. Ucwaningo lwesibili luhlaziye izinhlobo eziyi-150 zepearl millet emasimini ehlaselwe kakhulu yiS. hermonthica esimweni sezimvula kanye nobuluhlaza kusetshenziswa indlela yokukala, i-alpha lattice design, wesikalo esiyi-10 × 15 kabili ngokufanayo eBurkina Faso. Kwatholakala umahluko omkhulu kakhulu ezinhlotsheni zepearl millet kulezo ezahlolwa ukubumbeka kokubekezela kweStriga. Izinsuku zokuqhakaza kwezimbali kwabambezeleka kakhulu ngenxa yokuhlasela kweS. hermonthica. Ukusebenzisa i-FOS embewini yepearl millet kwehlisa ngamandla amakhulu ukuvela kweStriga ezimbewini ezine-S. hermonthica. I-IP-3098, i-IP-6112, i-IP-9242, i-IP-10579, ne-IP-11358 kwabonakala kulwa neS. hermonthica futhi kuhambisana ne-FOS. Izinhlobo zepearl millet zakwazi ukubhekelela izitshalo ezimbalwa ezingenayo iS. hermonthica kanti akubanga nasizo olutheni ezindaweni ezineStriga Number Progress Curve (ASNPC). Izinhlobo ezikhethiwe zinikeza indawo enhle yokukhiqiza futhi indlela ehlangene yokulawula iStriga ingaba usizo eBurkina Faso kwezolimo. Esahlukweni sisithathu, izinhlobo eziyi-150 zepearl millet zahlolwa izinga lazo ocwaningweni oluhlola ufuzo olwakha izifo ezitshalweni kanye nokubekezela kweS. hermonthica ukubheka izinto eziveza ufuzo kulokho okwakhiwe ukuveza ufuzo kanye nokuqhubeka kwalo. Ama-256 K esingle nucleotide polymorphisms (SNPs) asetshenziswa kulolu cwaningo. Umehluko omkhulu (P < 0.001) wabonakala ezinhlobeni ezahlolwa zepearl millet maqondana nezikalo nofuzo kweS. hermonthica. Okunye, kwaba khona ukuhlangana phakathi kwezinhlobo ezahlukene zofuzo lweS. Hermonthica ne-ASNPC. Ama-SNP angamashumi amabili nesishiyagalolunye ayamaniswa nenombolo ephansi yokwakheka kweS. hermonthica kumakhromozomu 1, 2, 3, 4, 6, no-7. Ama-SNP amane ayamaniswa nezinsuku kuya kumaphesenti angama-50 okuthela izimbali namakhromozomu 3, 5, 6, no-7, kanti ayisihlanu wona ayamaniswa namakhromozomu 2, 3, no-4. Ayisikhombisa wona ayamaniswa namagatsha amakhromozomu ayi-2, 3, no-6. Okujwayelekile okukhombisa iSNP okuyamaniswa nobuncane beS. hermonthica kwavela kanye nokuphathelene nokulima ezinhlobeni ezahlukene zofuzo ekutshalweni nokukhiqizwa kwepearl millet ngokubekezela kweStriga nabalimi kanjalo nokufunwa ngabathengi kwezokutshala. Ucwaningo lwesine lwaveza ukusebenza kofuzo nobukhona bokuzabalaza kweS. hermonthica okolweni omusha wepearl millet ukulawula ukukhethwa kanye nokukhula kofuzo. Izinhlobo ezimbili ezakhiwe ezingafani zavela ekuzabalazeni kweStriga yepearl millet. Izinhlobo ezimbili ezakhiwe kanye nemixhantela ye-F1s, i-F2s, neminye eyakhiwe kuhlanganiswe nofuzo kwahlolwa ngaphansi kokukhula kohlaza namasimu afakwe iS. hermonthica kusetshenziswa indlela yokwenza engahleliwe kuzona zontathu izinhlobo. Ukuhlaziywa kwezinhlobo ezahlukene kwaveza umehluko omkhulu we-P < 0.001 kuzona zonke izinhlobo ezakhiwe zeStriga. Ukuzabalaza kweStriga kubonakala kuzenzakalela ngokwemvelo futhi kulawulwa izinhlobo eziningi ezahlukene zofuzo. Ukuphindaphinda ufuzo kabili kwalawula ukuvela ngokwemvelo kweS. hermonthica. Izinhlobo eziyikhethelo ze-F2 ezinokuzabalaza kweS. hermonthica zakhethwa ofuzweni olubili kusetshenziswa indlela yokubheka ukuphindeka kwento ukuhlola izinhlobo zepearl millet ngokuhlanganisa izindlela zokulima nezokufuna uhlobo oluthize lwesitshalo. Ucwaningo lokugcina beluhlola amandla ahlangisiwe ofuzo lwepearl millet lokulwa kweS. hermonthica kanye nobunjalo bezokutshala. Ukuhlaziya izinhlobo zamandla okukwazi okuhlangane kwaveza umehluko omkhulu ka-P < 0.01 kulezo zinhlobo ezikwazi ukuthwala ezinye ngezinsuku ezimbalwa ngaphambi kokuqhakaza kwezimbali, ukukala ukukhula ngobude, kanye nokuphuma kwezinhlamvu. Umehluko phakathi kwemigqa nezinto zokuhlola wawumkhulu (P < 0.001) ukubheka ukukhula ngobude kanye nesibalo seStriga. Ufuzo lwe-IP-11358 lwakhombisa ukuba namandla aphezulu okuhlangana (GCA) okunemiphumela (158.99) kokuphuma kwezinhlamvu. Imiphumela engemihle ye-GCA eyi-6.99, i-6.40, no-134.08 yatholakala yeStriga emuva kwezinsuku ezingama-60 kutshaliwe, neyeStriga emuva kwezinsuku ezingama-80 kutshaliwe, ne-ASNPC ngokulandelana kwezinhlobo zofuzo lwe-IP-11358 lohlaza ngaphansi kwezimo zeS. hermonthica. Ingxubevange ye-IP-11358 × ICMB177111 yaveza amandla amakhulu okudibanisa (SCA) kanye nokuhluma kwezinhlamvu okuxubile. Izinhlobo zofuzo ezikhethiwe zepearl millet zikulungele ukukhiqiza ngendlela esezingeni eliphezulu kanye nokuzabalaza kweStriga esilekelelwa izinyosi ukuze kuqhakaze kanye nengxubevange yeStriga ngokwezindawo ezahlukene eBurkina Faso nezindawo ezitshala amabele emazweni asemazansi ne-Afrika. Sekukonke, lolu cwaningo lukwazile ukuveza ukuthi iS. hermonthica iyona enamandla amakhulu okudicilela phansi ukutshalwa kwepearl millet eBurkina Faso. Kanti futhi lolu cwaningo lukwazile ukuveza izinhlobo ezahlukene zofuzo oluyi-150 lokuzabalaza kweS. hermonthica uma kuhlolwa kusetshenziswa ukunyakaza komnotho ne-SNP ngaphansi kwezindawo ezigcwele iStriga. Izinhlobo ezenza kangcono zofuzo ezifana ne-IP-3098, i-IP-6112, i-IP-9242, i-IP-10579 ne-IP-11358 kwakhethwa njengesizinda esihle sokuzabalaza kweS. hermonthica uma yakhiwa. Uhlobo lwe-IP-11358 × ICMB177111 lwahlonzwa njengolunamandla amakhulu okukhula kanye nokulwa kweStriga. Izinhlobo ezikhethiwe zofuzo zinconywa njengezifanelekile emkhiqizweni futhi njengesizinda esihle sokufukamela umkhiqizo omusha wokuzabalaza kwepearl millet Striga.