Genetic diversity in yield traits and kernel composition of selected Ethiopian sorghum landraces

Abstract

𝑬𝒏𝒈𝒍𝒊𝒔𝒉 Climate-resilient and high-yielding sorghum cultivars must be developed for sustainable food systems and improved livelihoods in sub-Saharan Africa. Low grain protein, Fe and Zn concentrations are a frequent problem in food crops and they affect the crop's nutritional value, particularly in cereals. In this study, a total of 361 Ethiopian sorghum landraces with four commercial checks were grown under well-watered, wet intermediate and natural drought conditions for two consecutive seasons. The purpose of this research was to assess the genetic diversity and drought tolerance of this Ethiopian sorghum landrace collection using agronomic and grain quality traits and to select promising lines for production and/or breeding. The specific objectives were to (i) assess the level and pattern of genetic variation and drought adaptation in a sorghum landrace collection using phenotypic traits, (ii) evaluate chemical composition, genotype by environment interaction, drought effects and environmental influence and determine performance and stability of sorghum landraces, (iii) identify genomic regions associated with grain quality to determine the genetic basis for starch, protein and mineral concentrations of Ethiopian sorghum landraces. In stress environments, yield and yield components as well as grain quality traits had low means, range, genetic variance (σ²g) and heritability values.

In terms of grain yield performance under different water regimes, Melkassa (irrigated) had a 54.5% higher mean grain yield than Miesso (drought stress) in 2020 and Melkassa (irrigated) had a 26.9% higher mean grain yield than Miesso (drought stress) in 2021. Therefor drought stress reduced mean grain yield by 44.6% and grain weight by 14%. In all environments, ten genotypes (G189, G210, G125, G324, G325, G353, G319, G219, G187 and G229) had the highest stress tolerance index (STI), geometric mean productivity (GMP), mean productivity (MP) and yield in non-stress conditions (Yp) and stress conditions (Ys). In stress environments, starch content decreased by 5%, while protein content increased by 21% when compared to wet intermediate conditions. The Zn content was 60% and 55% higher in wet intermediate environments than in irrigated and stress environments, respectively. The Fe content was 21% and 13% higher in wet intermediate environments than in irrigated and stress environments, respectively. A genome-wide association study (GWAS) on 365 diverse Ethiopian sorghum landraces identified 209,572 single nucleotide polymorphisms (SNPs) (HB 𝘱 ≤ 0.05). Several candidate genes were identified that were significantly associated with grain Zn, Fe, starch, protein and ash concentrations, such as LEA, CHI, bZIP, ARF12 and WOX6.

The Late Embryogenesis Abundant (LEA) and basic leucine zipper (bZIP) family of proteins are involved in various stress responses in plants. The ABC transporter and sugar carrier proteins, Auxin Response Factors 12 (ARF12), Alpha-glucan phosphorylase and Zinc finger CCHC gene, are known for starch synthesis and storage in growing seeds. The WUSCHEL-related homeobox 6 (WOX6) and TatD family of hydrolases genes, acts as a transcription factor and is known to regulate stem cell maintenance and differentiation. Chitinase (CHI), flavonoid glycosides, architecture1 (tga1) and Class III peroxidase 70 and 69 precursors are all engaged in biological processes including plant defence against pathogens. The Zinc finger proteins (ZNFs) family is involved in Zn and Fe ion uptake and transport. These genes are involved in various biological processes such as stress response, starch synthesis, plant development and defence. The identification of loci associated with grain quality provides new insight into the genetic control of the traits, while sorghum landraces with nutritious grains can serve as sources of genes for breeding for good nutritional value. ___________________________________________________________________

Klimaatbestande en hoë-opbrengs sorghumkultivars moet ontwikkel word vir volhoubare voedselstelsels en verbeterde lewensbestaan ​​in Afrika suid van die Sahara. Lae graanproteïen-, Fe- en Zn-konsentrasies is ’n gereelde probleem in voedselgewasse en dit beïnvloed die gewas se voedingswaarde, veral in graan. In hierdie studie is ’n totaal van 361 Ethiopiese sorghum landrasse met vier kommersiële ondersoeke gekweek onder goed natgemaakte, nat intermediêre en natuurlike droogtetoestande vir twee opeenvolgende seisoene. Die doel van hierdie navorsing was om die genetiese diversiteit en droogtetoleransie van hierdie Ethiopiese sorghum landrasversameling te bepaal deur gebruik te maak van agronomiese en graankwaliteit eienskappe en om belowende lyne vir produksie en/of plantteling te kies. Die spesifieke doelstellings was om (i) die vlak en patroon van genetiese variasie en droogte-aanpassing in ’n sorghumlandrasversameling te evalueer deur fenotipiese eienskappe te gebruik, (ii) chemiese samestelling, genotipe volgens omgewingsinteraksie, droogte-effekte en omgewingsinvloed te evalueer en prestasie en stabiliteit van sorghumlandrasse te bepaal, (iii) en genomiese streke te identifiseer wat met graankwaliteit geassosieer word om die genetiese basis vir stysel-, proteïen- en mineraalkonsentrasies van Ethiopiese sorghumlandrasse te bepaal. In stresomgewings het opbrengs- en opbrengskomponente sowel as graankwaliteit-eienskappe lae gemiddeldes, omvang, genetiese variansie (σ2g) en oorerflikheidswaardes gehad. Wat graanopbrengsprestasie onder verskillende waterregimes betref, het Melkassa (besproei) ’n 54,5% hoër gemiddelde graanopbrengs as Miesso (droogtestres) in 2020 gehad en Melkassa (besproei) het ’n 26,9% hoër gemiddelde graanopbrengs as Miesso (droogtestres) in 2021 gehad. Daarom het droogtestres die gemiddelde graanopbrengs met 44,6% en graangewig met 14% verminder. In alle omgewings het tien genotipes (G189, G210, G125, G324, G325, G353, G319, G219, G187 en G229) die hoogste strestoleransie-indeks (STI), geometriese gemiddelde produktiwiteit (GMP), gemiddelde produktiwiteit (MP) en opbrengs in nie-strestoestande (Yp) en strestoestande (Ys) gehad. In stresomgewings het styselinhoud met 5% afgeneem, terwyl proteïeninhoud met 21% toegeneem het in vergelyking met nat intermediêre toestande. Die Zn-inhoud was onderskeidelik 60% en 55% hoër in nat intermediêre omgewings as in besproeiings- en stres-omgewings. Die Fe-inhoud was onderskeidelik 21% en 13% hoër in nat intermediêre omgewings as in besproeiings- en stres-omgewings. ’n Genoomwye assosiasiestudie (GWAS) op 365 diverse Ethiopiese sorghum landrasse het 209 572 enkelnukleotied polimorfismes (SNPs) (HB p≤ 0,05) geïdentifiseer. Verskeie kandidaatgene is geïdentifiseer wat betekenisvol geassosieer is met graan Zn, Fe, stysel, proteïen en as konsentrasies, soos LEA, CHI, bZIP, ARF12 en WOX6. Die Late Embryogenesis Abundant (LEA) en basiese leucine zipper (bZIP) families van proteïene is betrokke by verskeie stresreaksies in plante. Die ABC-vervoerder en suikerdraerproteïene, Auxin Response Factors 12 (ARF12), Alfa-glukaanfosforilase en Sinkvinger CCHC-geen, is bekend vir styselsintese en berging in groeiende sade. Die WUSCHEL-verwante homeobox 6 (WOX6) en TatD familie van hidrolase gene, dien as ’n transkripsie faktor en is bekend om stamsel-instandhouding en -differensiasie te reguleer. Chitinase (CHI), flavonoïedglikosiede, argitektuur1 (tga1) en Klas III peroksidase 70 en 69 voorlopers is almal betrokke by biologiese prosesse, insluitend plantverdediging teen patogene. Die sinkvingerproteïene-familie (ZNF) is betrokke by Zn- en Fe-ioonopname en -vervoer. Hierdie gene is betrokke by verskeie biologiese prosesse soos stresreaksie, styselsintese, plantontwikkeling en verdediging. Die identifisering van lokusse wat met graankwaliteit geassosieer word, verskaf nuwe insig in die genetiese beheer van die eienskappe, terwyl sorghumlandrasse met voedsame grane as bronne van gene vir plantteling vir goeie voedingswaarde kan dien.

Izinhlobo zamabele ezimelana nesimo sezulu nezithela kakhulu kumele zithuthukiswe ukuze kube nezinhlelo zokudla ezisimeme kanye nempilo engcono e-sub-Saharan Africa. Amaprotheni okusanhlamvu aphansi, ukugxila kweFe kanye neZn kuyinkinga evamile ezitshalweni zokudla futhi kuthinta ukondleka kwezitshalo, ikakhulukazi okusanhlamvu. Kulolu cwaningo, isamba samabele angama-361 ase-Ethiopia anamasheke amane okuhweba atshalwe ngaphansi kwezimo eziniselwe kahle, ezimanzi ngokuphakathi nendawo nezimo zesomiso zemvelo izinkathi ezimbili ezilandelanayo. Inhloso yalolu cwaningo kwakuwukuhlola uhlukahlukanofuzo kanye nokubekezelela isomiso kwaleli qoqo lwamabele ase-Ethiopia kusetshenziswa izici zezingabunjalo lezolimo lokukhiqizwa kwezitshalo nokunakekelwa komhlabathi kanye nokusanhlamvu kanye nokukhetha imigqa ethembisayo yokukhiqiza kanye/noma ukuzalanisa. Izinjongo eziqondile kwakungu (i) ukuhlola izinga nephethini yohlukahlukanofuzo kanye nokujwayela kwesomiso eqoqweni lamabele kusetshenziswa izici ze-phenotypic, (ii) ukuhlola ukwakheka kwamakhemikhali, igenotype ngokusebenzisana kwemvelo, imiphumela yesomiso kanye nomthelela emvelweni nokunquma ukusebenza nokuzinza kwamabele endawo (iii) ukuhlonza izifunda zegenomic ezihlobene nezingabunjalo lokusanhlamvu ukuze kutholwe isisekelo sofuzo sesitashi, amaprotheni kanye nokugcwala kwamaminerali amabele ase-Ethiopia. Ezimweni zengcindezi, izingxenye zesivuno nesivuno kanye nezici zezingabunjalo lokusanhlamvu zibe nezindlela eziphansi, ububanzi, ukuhluka kofuzo (σ2g) namanani okuphila. Mayelana nokusebenza kokuvunwa okusanhlamvu ngaphansi kwamarijimu ahlukene amanzi, iMelkassa (eniseliwe) ibe nesivuno esiphezulu esingama-54.5% esinesilinganiso esiphezulu sokusanhlamvu kuneMiesso (ingcindezi yesomiso) ngo-2020 kanti iMelkassa (eniseliwe) yaba nesivuno esikhulu sokusanhlamvu esingu-26.9% kuneMiesso (ingcindezi yesomiso) ngo-2021. Ngakho-ke ingcindezi yesomiso inciphise isivuno sokusanhlamvu ngama-44.6% kanye nesisindo sokusanhlamvu ngama-14%. Kuzo zonke izindawo, izinhlobo eziyishumi zohlobo lofuzo (G189, G210, G125, G324, G325, G353, G319, G219, G187 kanye ne-G229) zinenkomba ephezulu yokubekezelela ukucindezeleka (STI), ukukhiqiza kwejiyomethri (GMP), ukukhiqiza okusho (MP) kanye isivuno ezimweni ezingenayo ingcindezi ( Yp ) nezimo zokucindezeleka (Ys). Ezimweni zokucindezeleka, isitashi sehle ngama-5%, kuyilapho okuqukethwe kwamaprotheni kukhuphuke ngama-21% uma kuqhathaniswa nezimo ezimanzi ngokuphakathi nendawo. Okwe-Zn kwakuphezulu ngama-60% kanye nama-55% ezindaweni ezimanzi ngokuphakathi nendawo kunasezindaweni eziniselwe nezinengcindezi, ngokulandelana. Okuqukethwe kweFe bekungama-21% kanye nama-13% ngaphezulu ezindaweni ezimanzi ngokuphakathi nendawo kunasezindaweni eziniselwe nezingcindezi, ngokulandelana. Ucwaningo lwegenome-wide association (GWAS) kumabele angama-365 ahlukahlukene ase-Ethiopia luhlonze ama-nucleotide polymorphisms (SNPs) ayizi-209,572 eyodwa (HB p ≤ 0.05). Kutholwe izakhi zofuzo eziningana ezihlotshaniswa kakhulu nokusanhlamvu Zn, Fe, isitashi, amaprotheni kanye nokomlotha, njenge-LEA, CHI, ne-bZIP, ARF12 kanye ne-WOX6. ILate Embryogenesis Abundant (LEA) kanye nebasic leucine zipper ( bZIP ) umndeni wamaphrotheni abandakanyeka ekutheleleni kwengcindezi okuhlukahlukene ezitshalweni. Isidlulisi I-ABC kanye namaphrotheni aphethe ushukela, ama-Auxin Response Factors 12 (ARF12), i-Alpha-glucan phosphorylase kanye nofuzo lwe-Zinc finger CCHC, aziwa ngokuhlanganisa isitashi nokugcinwa kwembewu ekhulayo. Ihomeobox 6 ehlobene ne-WUSCHEL (WOX6) kanye nomndeni we-TatD wezakhi zofuzo zehydrolases, isebenza njengesici sokuloba futhi yaziwa ngokulawula ukugcinwa kwestem cell nokuhlukaniswa. IChitinase (CHI), iflavonoid glycosides, i-architecture1 (tga1) kanye neClass III peroxidase 70 kanye namaprecursors angama-69 konke kuhileleke ezinqubweni zesifundo ngokuphilayo okuhlanganisa ukuzivikela kwezitshalo ngokumelene namagciwane. Umndeni wamaZinc finger proteins (ZNFs) ubandakanyeka ekuthatheni nasekuthuthweni kweZn neFe ion. Lezi zakhi zofuzo zihileleke ezinqubweni ezihlukahlukene zesifundo ngokuphilayo njengokusabela kokucindezeleka, ukuhlanganiswa kwesitashi, ukuthuthukiswa kwezitshalo nokuzivikela. Ukuhlonzwa kwe-loci okuhlotshaniswa nezingabunjalo lokusanhlamvu kunikeza ukuqonda okusha ekulawuleni izakhi zofuzo, kuyilapho amabele anezinhlamvu ezinomsoco angasebenza njengemithombo yezakhi zofuzo zokuzalanisa ukuze kutholwe ukondleka okuhle.

Mefuta ya dijalo tsa mabele tse mamellang maemo a lehodimo le tse hlahisang tjhai e ngata di tlameha ho hlahiswa bakeng sa ditsamaiso tse tsitsitseng tsa dijo le ho ntlafatsa mokgwa wa ho iphedisa Afrika e ka Borwa ho Sahara. Diprotheine tse tlase tsa dijothollo, Fe le Zn ke bothata bo tlwaelehileng dijalong tsa dijo mme di ama boleng ba phepo ya dijalo, haholoholo dijothollo. Diphuputsong tsena, ho ile ha lengwa mefuta e 361 ya mabele a Ethiopia ka diteko tse nne tsa kgwebo tlasa maemo a ho nosetsoa ka nepo, a metsi a mahareng le a komello ya tlhaho ka dinako tse pedi tse latellanang. Morero wa diphuputso tsena e ne e le ho hlahloba mefuta ya diphatsa tsa lefutso le ho mamella komello ya pokello ena ya mabele a Ethiopia ho sebedisa ditshobotsi tsa boleng ba tlhokomelo ya dijothollo le mobu le ho kgetha mela e tshepisang bakeng sa tlhahiso le/kapa ho ikatisa. Dipheo tse tobileng e ne e le (i) ho lekola boemo le mokgwa wa ho fapana ha diphatsa tsa lefutso le ho ikamahanya le komello pokellong ya mefuta ya mobu wa mabele ka tshebediso ya ditshobotsi tsa phenotypic, (ii) ho lekola sebopeho sa dikhemikhale, mofuta wa diphatsa tsa lefutso ka tikoloho, ditlamorao tsa komello le tshusumetso ya tikoloho le ho tseba tshebetso le botsitso ba mefuta ya mobu wa mabele (iii) ho kgetholla dibaka tsa diphatsa tsa lefutso tsa diphedi tse amanang le boleng ba dijothollo ho tseba motheo wa diphatsa tsa lefutso bakeng sa setatjhe, protheine le diminerale tsa mefuta ya mobu wa mabele wa Ethiopia. Maemong a kgatello, dihlahiswa le dikarolo tsa dihlahiswa, hammoho le ditshobotsi tsa boleng ba dijothollo di ne di na le ditekanyetso tse tlase, mefuta, mefutafuta ya diphatsa tsa lefutso (σ2g) le boleng ba ho futseha. Mabapi le tlhahiso ya dijothollo tlasa mekgwa e fapaneng ya metsi, Melkassa (e nosetswang) e bile le tlhahiso e phahameng ya dijothollo ka 54.5% ho feta Miesso (kgatello ya komello) ka 2020 mme Melkassa (e nosetswang) e bile le tlhahiso e phahameng ya dijothollo ka 26.9% ho feta Miesso (kgatello ya komello) ka 2021. Ka lebaka leo, kgatello e bakwang ke komello e ile ya fokotsa tjhai e tlwaelehileng ya dijoothollo ka 44,6% le boima ba dijothollo ka 14%. Dibakeng tsohle, mefuta ya diphatsa tsa lefutso e leshome (G189, G210, G125, G324, G325, G353, G319, G219, G187 le G229) e ne e na le palo e phahameng ka ho fetisisa ya ho mamella kgatello (STI), tlhahiso e tlwaelehileng ya mela (GMP), tlhahiso e tlwaelehileng (MP) le tjhai maemong a se nang kgatello (Yp) le maemo a kgatello (Ys). Ha ho bapiswa le maemo a mongobo a mahareng, ha ho bapiswa le maemo a kgatello, setotswana se fokotseha ka 5%, mme ha ho bapiswa le maemo a metsi, protheine e eketseha ka 21%. Boitsebiso ba Zn bo ne bo phahame ka 60% le 55% dibakeng tse metsi tse mahareng ho feta dibakeng tse nosetswang le tse nang le kgatello. Dikateng tsa Fe e ne e le 21% le 13% dibakeng tse metsi tse mahareng ho feta dibakeng tse nosetswang le tse nang le kgatello. Diphuputso tse entsweng ka kamano ya diphatsakakaretso (GWAS) ya mefuta e 365 e fapaneng ya mabele a Ethiopia e fumane polymorphism tsa nucleotide tse 209,572 (SNPs) (HB p ≤ 0.05). Ho ile ha fumanwa diphatsa tse mmalwa tsa lefutso tse neng di amahanywa haholo le dijothollo tse nang le Zn, Fe, setatjhe, protheine le molora, tse kang LEA, CHI, bZIP, ARF12 le WOX6. Lelapa la diprotheine tsa Late Embryogenesis Abundant (LEA) le tsa basic leucine zipper (bZIP) di ameha dikarabong tse fapaneng tsa kgatello dimeleng. Diprotheine tse tsamaisang ABC le tse tsamaisang tswekere, Auxin Response Factors 12 (ARF12), Alpha-glucan phosphorylase le phatsa ya lefutso ya Zinc finger CCHC, di tsejwa ka ho etsa setatjhe le ho se boloka ka hara peo e ntseng e hola. WUSCHEL-related homeobox 6 (WOX6) le TatD lelapa la diphatsa tsa lefutso tsa hydrolases, e sebetsa e le moralo mme e tseba ho laola tlhokomelo le phapano ya disele tsa motso. Chitinase (CHI), flavonoid glycosides, architecture1 (tga1) le Class III peroxidase 70 le 69 tse tlang pele kaofela di kenella ditshebetsong tsa dikokwanahloko ho kenyelletsa le ho itshireletsa ha semela kgahlanong le dikokwanahloko. Lelapa la Zinc finger proteins (ZNFs) le ameha ho nkeng le ho tsamaiseng Zn le Fe ion. Diphatsa tsena tsa lefutso di ameha ditshebetsong tse sa tshwaneng tsa dikokwanahloko tse kang ho itshwara ha kgatello ya kelello, ho qatjwa ha setatjhe, ho hola ha dimela le ho itshireletsa. Ho kgetholla loci tse amanang le boleng ba dijothollo ho fana ka lesedi le letjha mabapi le taolo ya diphatsa tsa lefutso ya ditshobotsi, ha masala a mabele mobung a nang le dijothollo tse nang le phepo e ntle a ka sebetsa e le mehlodi ya diphatsa tsa lefutso ho ka ikatisa bakeng sa boleng bo botle ba phepo.