Developing new markers and QTL mapping for greenbug resistance in sorghum [Sorghum bicolor (L.) Moench]

Greenbug is a major damaging insect to sorghum production in the United States. Among various virulent greenbug biotypes, biotype I is the most predominant and severe for sorghum. To combat with the damaging pest, greenbug resistant sources were obtained from screening sorghum germplasm collection. This experiment was conducted to identify the genomic regions contributing resistance to greenbug biotype I in a sorghum accession, PI 607900. An F₂ mapping population consisting of 371 individuals developed from a cross of the resistant line with an elite cultivar, BTx623 (susceptible) were tested and scored for their response to greenbug feeding in the greenhouse. Significant differences in resistance were observed between the two parental lines and among their F₂ progeny in response to greenbug feeding at 7, 10, 14 and 21 days after infestation. A linkage map spanning a total length of 729.5 cM across the genome was constructed with 102 polymorphic SSR markers (69 genomic and 33 EST SSRs). Of those microsatellite markers, 48 were newly developed during this study, which are a useful addition for sorghum genotyping and genome mapping. Single marker analysis revealed 29 markers to be significantly associated with the plant response to greenbug feeding damage. The results from interval mapping, composite interval mapping and multiple interval mapping analyses identified four major QTLs for greenbug resistance on chromosome 9. These QTLs collectively accounted for 34–82 % of the phenotypic variance in greenbug resistance. Minor QTLs located on chromosome 3 explained 1 % of the phenotypic variance in greenbug resistance. The major allele for greenbug resistance was on chromosome 9 close to receptor-like kinase Xa21-binding protein 3. These markers are useful to screen more resistant genotypes. Furthermore, the markers tagged to QTL regions can be used to enhance the sorghum breeding program for greenbug resistance through marker-assisted selection and map-based cloning.     

Molecular mapping of the brace root traits in sorghum (Sorghum bicolor L. Moench)

The presence and morphology of plant brace roots are important root architecture traits. Brace roots contribute significantly to effective anchorage and water and nutrient uptake during late growth and development, and more importantly, have a substantial influence on grain yield under soil flooding or water limited conditions. However, little is known about the genetic mechanisms that underlie brace root traits. In this study, quantitative trait loci (QTLs) for presence of brace roots from the sorghum landrace “Sansui” were mapped and associated molecular markers were identified. A linkage map was constructed with 109 assigned simple sequence repeat markers using a F₂ mapping population derived from the cross Sansui/Jiliang 2. Two QTLs associated with presence of brace roots were localized on chromosomes 6 and 7. The major QTL on chromosome 7 between markers Dsenhsbm7 and Xcup 70 explained about 52.5% of the phenotypic variation, and the minor QTL on chromosome 6 was flanked by Xtxp127 and Xtxp6 and accounted for 7.0% of phenotypic variation. These results will provide information for the improvement of sorghum root architecture associated with brace roots.     

A major QTL for plant height is linked with bloom locus in sorghum [Sorghum bicolor (L.) Moench]

Plant height is one of the most important agronomic traits in sorghum with its relevance for biomass, grain yield, fodder and lodging. To understand its genetic basis, the quantitative trait loci (QTL) were identified using a recombinant inbred line (RIL) population consisting of 168 RILs derived from the cross between the two sorghum inbred lines 296B (dwarf) and IS18551 (tall) over six seasons. Two major QTL were identified one each on chromosomes SBI-06 and SBI-07 corresponding to the Dw2 and Dw3 gene loci together accounting 41 % plant height variation. In addition, a morphological bloom trait locus which remained unlinked in the linkage map was found to be significantly linked with plant height in single marker analysis explaining 22 % of the trait variation. By comparing the map positions of Dw1, Dw2 and Dw3, the new locus for plant height linked with bloom is proposed as Dw4 locus. Both SSR and the morphological bloom loci linked with height QTL of the present study can be employed as effective tools in marker-assisted breeding for rapid conversion of selected inbred parent lines either as dwarf seed (male sterile) parents or taller pollinators for hybrid seed industry, or for developing high biomass lines in sweet sorghum for exploitation as high bio-fuel crop.     

Genetic analysis of threshability in grain sorghum [Sorghum bicolor (L.) Moench]

The ease with which seeds are detached from panicles is one of the early domestication traits. Genotypes with sticky panicles are hard to thresh, and whenever threshed, the grain tends to remain attached to the glume which reduces market value and processability. This study was conducted to determine the genetic mechanisms underlying the threshability trait in sorghum. Four seed parents and eleven pollinators differing for threshability were intercrossed in Design II mating scheme and the resulting hybrids and the parents were grown in four environments. Threshability was estimated as the ratio of seed yield to panicle weight (TW) and proportion of seeds without sticky glumes (TG). Variation was significant among the entries, inbreds and hybrids with GCA for TG and TW varying markedly. Mean TG for inbred and hybrids of low threshable genotypes was not markedly different indicating that threshability trait is under the control of additive genes with dominant or partially dominant effects. Segregation analysis indicates that the TG trait may be under the control of few major genes with approximately one to three loci affecting the trait.     

Mapping of QTLs underlying flowering time in sorghum [Sorghum bicolor (L.) Moench]

Due to its critical importance in crop yield, the photoperiodic regulation of flowering time is considered an important trait in sorghum breeding programs. In this study, quantitative trait loci for flowering time were detected using an F₂ population derived from a cross between Kikuchi Zairai, a late-flowering cultivar originating from Japan and SC112, an early-flowering cultivar originating from Ethiopia. F₂ plants were grown with their parents under a natural day length and a 12 h day length. Two linkage maps were constructed using 213 simple sequence repeats markers. Nine quantitative trait loci controlling flowering time were identified in F₂ plants grown under a natural day length, whereas 7 QTLs were identified under a 12 h day length. Five QTLs controlling flowering time were shared under both of the day length conditions.     

能源甜高粱遗传改良研究进展

甜高粱是最有应用前景的再生能源作物之一,它的能源转换效率取决于植株总生物量和茎秆汁液含糖量的高低。探明决定甜高粱总生物量和茎秆汁液含糖量积累相关过程的生物学机制并开发相应分子标记,是选育生物能专用甜高粱品种的有效途径。本文从甜高粱糖分积累、遗传多样性研究、遗传图谱的构建、含糖量相关性状的定位及遗传工程研究等方面介绍了近年来甜高粱遗传研究进展。     

Farmer and formal breeding of sorghum (Sorghum bicolor (L.) Moench) and the implications for integrated plant breeding

Sorghum (Sorghum bicolor (L.) Moench) is the fifth most important cereal crop worldwide and it is the fourth most important crop in Ethiopia. The national average yield amounts 1302 kg/ha. In order to assess the achievement in farmer breeding various types of research were undertaken. These include survey research to quantify the trend in productivity, the level of and reasons for adoption of improved varieties, yield performance and preference evaluation of farmers’ varieties (FVs) and improved varieties (IVs). As per the trend analysis over the last four decades, total production and yield per hectare has increased by 11.63 and 14.2%, respectively. However, area allocated to sorghum has decreased over years by −2.93%. The lack of consistent productivity is attributed to the fluctuation of environmental factors. Sorghum production in Ethiopia is predominantly based on varieties developed by farmers. The share of IVs is very low. FVs and IVs are adopted by 87.3 and 12.7% of the farmers, respectively. Besides, the adoption of IVs is limited to the lowland crop ecology. The comparative yield of FVs is higher than IVs by 132%. On top of yield, farmers do prefer their varieties for other multipurpose values namely feed, fuel wood and construction material. FVs under production are identified in each wereda. Farmer breeding has been successful compared to four decades of formal breeding. On the other hand, both farmer and formal breeding are not without weaknesses; a comparative balance sheet is outlined for both. Ideotypes for the three major crop ecologies are suggested and integrated plant breeding is anticipated to develop the proposed ideotypes thereby increase sorghum productivity in the region.     

Genetic divergence among a non-restorer collection of sorghum (Sorghum bicolor (L.) Moench) and its relationship with heterosis

Summary A genetic diversity analysis in a collection of 171 non-restorer lines of sorghum (Sorghum bicolor (L.) Moench) using D² technique and canonical variate analysis indicated that considerable variation in grain yield has been added to the collection by the addition of lines derived from random mating populations. The efficiency of D² and canonical variate techniques in distinguishing extremely diverse genotypes was confirmed. However, the two techniques showed weak correspondence in their clusters. The F₁ hybrids of 15 diverse lines exhibited no relationship between heterosis or per se performance of crosses and diversity in their parents. Therefore, traditional plant breeding methods are being advocated.Approved by ICRISAT as Journal Article no. 435.     

A genetic study of popping quality in Sorghum (Sorghum bicolor (L.) Moench)

Summary Two crosses of sorghum, Sorghum bicolor (L.) Moench (IS 1054 × ICSV-1, and IS 5604 × IS 1054) were evaluated in parental, F1, F2, and backcross generations for the variation in their popping quality as measured by pop volume (ml). Dominance was in the direction of low pop volume. Dominance and additive gene effects, in that order, governed most of the variation, while significant dominance x dominance type of interaction effects could also be detected. There was no evidence for higher order gene interactions.Approved as Journal Article 630 by the International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, P.O. 502 324, Andhra Pradesh, India.     

In vitro screening and field evaluation of tissue-culture-regenerated sorghum (Sorghum bicolor (L.) Moench) for soil stress tolerance

Summary Sorghum bicolor (L.) Moench is generally quite sensitive to salt and acid (high aluminium) soil stresses, but quite tolerant of drought stress. As with any stress phenomenon, intra-specific variability exists within the genus. In vitro cell selection and somaclonal variation offer an alternative to traditional breeding methodology for generating improved breeding lines for hybrid development. A field selection protocol was developed for the three soil stresses and inter-stress evaluations were conducted in an effort to find multiple, stress-tolerant genotypes. The acid soil-drought stress, super-tolerant selections were located by the R₇ generation when exposed to a combined aluminium-drought stress field environment and when the regeneration population (number of regenerated lines from one callus source) was maintained at 15,000 plants or higher. A variant frequency of 0.1 to 0.2% for stress tolerance and acceptable agronomic traits among the surviving somaclones, provided an adequate number of phenotypes with desirable agronomic characteristics and a high level of soil stress tolerance. Subsequent research verified that the stress-tolerant regenerants had superior acid soil and drought stress tolerance to that of the donor parents, that their yield capabilities under stress were superior to their parents, and that their stress tolerance attributes were transferred in hybrid combinations. In vitro selection was not effective in increasing the number of field stress survivors. In fact, superior germplasms were developed from non-stressed callus or salt-stressed callus. In vitro selection reduced regeneration frequency and subsequent survival of plants under field stress. In vitro-stressed regenerants should be subjected only to non-stressed environments to maintain population numbers for field selection and thereafter should be subjected to stress environments during later (R₅₊) generations. The optimal strategy for the exploitation of somaclonal variation may be through short-term cell culture (< 12 months) with no attempt at in vitro selection.     

Identification and characterization of RAPD and SCAR markers linked to anthracnose resistance gene in sorghum [Sorghum bicolor (L.) Moench]

Anthracnose, one of the destructive foliar diseases of sorghum growing in warm humid regions, is incited by the fungus Colletotrichum graminicola.The inheritance of anthracnose resistance was studied using the parental cultivars of Sorghum bicolor (L.) Moench, HC 136 (susceptible to anthracnose) and G 73 (anthracnose resistant). The F₁ and F₂ plants were inoculated with the local isolates of C. graminicola cultures. The F₂ plants showed a segregation ratio of 3 (susceptible): 1(resistant) indicating that the locus for resistance to anthracnose in sorghum accession G 73 segregates as a recessive trait in a cross to susceptible cultivar HC 136. RAPD (random amplified polymorphic DNA) marker OPJ 01₁₄₃₇ was identified as marker closely linked to anthracnose resistance gene in sorghum by bulked segregant analysis of HC 136 × G73 derived recombinant inbred lines (RILs) of sorghum. A total of 84 random decamer primers were used to screen polymorphism among the parental genotypes. Among these, only 24 primers were polymorphic. On bulked segregant analysis, primer OPJ 01 amplified a 1437 bp fragment only in resistant parent G 73 and resistant bulk. The marker OPJ 01₁₄₃₇ was cloned and sequenced. The sequence of RAPD marker OPJ 01₁₄₃₇ was used to generate specific markers called sequence characterized amplified regions (SCARs). A pair of SCAR markers SCJ 01-1 and SCJ 01-2 was developed using Mac Vector program. SCAR amplification of resistant and susceptible parents along with their respective bulks and RILs confirmed that SCAR marker SCJ 01 is at the same loci as that of RAPD marker OPJ 01₁₄₃₇ and hence, is linked to anthracnose resistance gene. Resistant parent G 73 and resistant bulk amplified single specific band on PCR amplification using SCAR primer pairs. The RAPD marker OPJ 01₁₄₃₇ was mapped at a distance of 3.26 cM apart from the locus governing anthracnose resistance on the sorghum genetic map by the segregation analysis of the RILs. Using BLAST program, it was found that the marker showed 100 per cent alignment with the contig{_}3966 located on the longer arm of chromosome 8 of sorghum genome. Therefore, these identified RAPD and SCAR markers can be used in the resistance-breeding program of sorghum anthracnose by marker-assisted selection.An erratum to this article can be found at     

Quantitative-genetic parameters of sorghum [Sorghum bicolor (L.) Moench] grown in semi-arid areas of Kenya

Low and erratic rainfall constitutes a major constraint to sorghum production, and impedes sorghum improvement in semi-arid tropics. To estimate quantitative-genetic parameters for sorghum under variable stress conditions, three sets of factorial crosses between four by four lines each were grown with parents and a local cultivar in eight macro-environments in semi-arid areas of Kenya. Fourteen traits were recorded including grain yield, above-ground drymatter, harvest index, days to anthesis, leaf rolling score, and stay-green. Environmental means for grain yield ranged from 167 to 595 g m-2. Mean hybrid superiority over mid-parent values was 47, 31, and 9% for grain yield, above-ground drymatter, and harvest index, respectively. Differences among both lines and hybrids were highly significant for all traits. Genotype × environment interaction variances were larger than genotypic variances for grain yield, above-ground drymatter, and harvest index. Corresponding heritabilities ranged between 0.72 and 0.84. Variation among hybrids was determined by GCA and SCA effects for most characters. Predominance of additive-genetic effects was found for grain yield components, plant height, and leaf rolling score. Lack of variation in GCA was noted among female lines for major performance traits. While low leaf rolling score was correlated with high grain yield, there was no such association for stay-green. Hybrid breeding could contribute to sorghum improvement for semi-arid areas of Kenya. To increase selection progress for major performance traits, genetic variation among female lines should be enhanced. Importance of genotype × environment interaction underlines the necessity of evaluating breeding materials under a broad range of dryland conditions.     

Genetic and Phenotypic Association between Yield Components in Hybrid Sorghum (Sorghum bicolor (L.) Moench) populations

Summary The magnitude of genetic expression and associations among traits are important for the prediction of response to selection in diverse environments and provide the basis for planning and evaluating breeding programs. In this regard, a cross classification mating design was used to produce hybrid sorghum populations, which were evaluated in a randomized completed block design with three replications at four environments in Northern Cameroon. Data on grain yield, days to anthesis, plant height, inflorescence length, threshing percentage and seed mass were collected and subjected to statistical genetic analyses. Significant genotype × environment interaction effects were observed for all traits. Genetic variance was essentially attributed to additive gene effects, with dominance variance for grain yield being negligible. However, the reverse was observed for threshability. Genetic variance components were much higher for plant height and grain yield than for days to anthesis, seed mass and threshability. Heritability estimates for plant height and inflorescence length were high (77 and 54 percent respectively) while the estimates for grain yield and threshability were low (14 and 5 percent respectively). Grain yield had positive genotypic correlation with most of the traits. Days to anthesis were negatively correlated with vegetative and reproductive traits. These results suggest that improvement of days to anthesis, plant height, and inflorescence length should be faster because of higher heritabilities and greater phenotypic variation. However, selection for earliness and reduced plant height would not be possible without hampering grain yield. Selecting for yield primary components namely inflorescence length and seed weight would be effective for increasing production. In addition, optimizing agronomic practices and improved experimental design would increase the selection efficiencies.     

Isolation and characterization of resistance gene analogs (RGAs) from sorghum (Sorghum bicolor L. Moench)

Degenerate primers designed based on known resistant genes (R-genes) and resistance gene analogs (RGAs) were used in combinations to elucidate RGAs from Sorghum bicolor, cultivar M 35-1. Most of the previously tried primer combinations resulted in amplicons of expected 500–600 bp sizes in sorghum along with few novel combinations. Restriction analysis of PCR amplicons of expected size revealed a group of fragments present in a single band indicating the heterogeneous nature of the amplicon. Many of these were cloned and some were considered for analysis. The nucleotide sequence of different cloned fragments was done and their predicted amino acid sequences compared to each other and to the amino acid sequences of known R-genes revealed significant sequence similarity. A cluster analysis based on neighbor-joining (N-J) method was carried out using sorghum RGAs (SRGAs) together with several analogous known R-genes resulting in two major groups; cluster-I comprising only SRGAs and cluster-II comprised of known R-gene sequences along with three SRGAs. Further analysis clearly indicated similarity of SRGAs in overall sense with already known ones from other crop plants. These sequences can be used as guidelines to detect, map and eventually isolate numerous R-genes in sorghum.     

Genotype-by-trait association of sorghum (Sorghum bicolor (L.) Moench) advanced lines grown under arid and semi-arid regions of Zimbabwe

Journal of Crop Science and Biotechnology - Inadequate information is available on trait relations and profiles of sorghum genotypes, yet this information is vital for precise decisions to be...     

Combining ability and heterosis as influenced by male-sterility inducing cytoplasms in sorghum [Sorghum bicolor (L.) Moench]

An investigation was carried out to assess the efficiency of A₂ cytoplasmic-nuclear male-sterility (CMS) system in comparison to the widely used A₁ cytoplasm in terms of general combining ability (gca) effects of male-sterile (A-) lines and mean performance, specific combining ability (sca) effects and mid-parent heterosis of hybrids for days to 50% flowering, plant height and grain yield at International Crops Research Institute for the Semi-Arid Tropics, Patancheru, Andhra Pradesh, India in 2001 and 2002 rainy seasons. The material for the study consisted of six pairs of iso-nuclear, allo-plasmic (A₁ and A₂) A-lines and 36 iso-nuclear hybrids produced by crossing these A-lines with three dual restorer (R-) lines. The results revealed that cytoplasm and its first-order interaction with year, R- and A-lines did not appear to contribute to variation in iso-nuclear hybrids for plant height and grain yield. Cytoplasm had limited effect on gca effects of A-lines and on sca effects and mid-parent heterosis of iso-nuclear hybrids for days to 50% flowering, plant height and grain yield. The mean days to 50% flowering, plant height and grain yield of A₂ cytoplasm-based hybrids were comparable with those of widely used A₁ cytoplasm-based hybrids. The relative frequency of the occurrence of the A₁- and A₂-based hybrids with significant sca effects and mid-parent heterosis indicated that A₂ CMS system is as efficient as A₁ with a slight edge over A₁ for commercial exploitation. The implications of these results are discussed in relation to opportunities for broadening not only cytoplasm base but also nuclear genetic base of both the hybrid parents.     

Geographical patterns of morphological variation in sorghum (Sorghum bicolor (L.) Moench) germplasm from Ethiopia and Eritrea: Quantitative characters

A total of 415 sorghum (Sorghum bicolor (L.) Moench) accessions representing different regions of Ethiopia, Eritrea and a group of introduced lines were evaluated for 15 quantitative characters to determine the extent and geographical pattern of morphological variation. The extent of variation was highly pronounced for agronomically important characters for sorghum. These characters included plant height, days for 50% flowering, peduncle exsertion, panicle length and width, number and length of primary branches per panicle and thousand seed weight. Significant regional variation was also observed for most of the characters. The results implied that environmental factors such as altitude, rainfall, temperature and growing period are important in regional variation. Mean for plant height and for days for 50% flowering showed clinal variation along the gradients of rainfall pattern and growing period in Ethiopia. Moreover, there were significant positive correlation coefficients between most of the characters. This included the correlation between agronomic characters of primary interest in sorghum breeding such as plant height and days for 50% flowering and also between various characters and the altitude of the collection sites. The implications of the results in plant breeding, germplasm collection and conservation as well as the probable sources of the wide range of variation are discussed. This revised version was published online in July 2006 with corrections to the Cover Date.